null Mon 24 Dec 07:39:26 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1z82-2.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1z82-2.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1z82-2.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-2.0-parrot-noncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-2.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-2.0-parrot-noncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 07:39:30 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-2.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1z82-2.0-parrot-noncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 575 and 0 Target number of residues in the AU: 575 Target solvent content: 0.4891 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.40 Input MTZ file: 1z82-2.0-parrot-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 4 Cell parameters: 65.170 67.461 75.617 90.000 113.643 90.000 Input sequence file: 1z82-2.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 5360 target number of atoms Had to go as low as 0.40 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 29.850 2.000 Wilson plot Bfac: 21.30 40537 reflections ( 99.47 % complete ) and 0 restraints for refining 5966 atoms. Observations/parameters ratio is 1.70 ------------------------------------------------------ Starting model: R = 0.3184 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2699 (Rfree = 0.000) for 5966 atoms. Found 75 (204 requested) and removed 110 (102 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.09 2.39 NCS extension: 0 residues added, 5931 seeds are put forward Round 1: 422 peptides, 63 chains. Longest chain 22 peptides. Score 0.592 Round 2: 487 peptides, 41 chains. Longest chain 54 peptides. Score 0.820 Round 3: 534 peptides, 33 chains. Longest chain 66 peptides. Score 0.885 Round 4: 557 peptides, 21 chains. Longest chain 101 peptides. Score 0.929 Round 5: 558 peptides, 21 chains. Longest chain 66 peptides. Score 0.930 Taking the results from Round 5 Chains 25, Residues 537, Estimated correctness of the model 99.5 % 14 chains (455 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 168 A and 178 A Built loop between residues 63 B and 71 B Built loop between residues 138 B and 141 B Built loop between residues 205 B and 209 B Built loop between residues 227 B and 237 B Built loop between residues 272 B and 279 B 16 chains (564 residues) following loop building 8 chains (491 residues) in sequence following loop building ------------------------------------------------------ 40537 reflections ( 99.47 % complete ) and 6447 restraints for refining 5393 atoms. 2303 conditional restraints added. Observations/parameters ratio is 1.88 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3141 (Rfree = 0.000) for 5393 atoms. Found 124 (184 requested) and removed 109 (92 requested) atoms. Cycle 2: After refmac, R = 0.2862 (Rfree = 0.000) for 5375 atoms. Found 103 (181 requested) and removed 94 (92 requested) atoms. Cycle 3: After refmac, R = 0.2701 (Rfree = 0.000) for 5347 atoms. Found 91 (177 requested) and removed 93 (92 requested) atoms. Cycle 4: After refmac, R = 0.2561 (Rfree = 0.000) for 5306 atoms. Found 91 (172 requested) and removed 41 (91 requested) atoms. Cycle 5: After refmac, R = 0.2489 (Rfree = 0.000) for 5332 atoms. Found 88 (172 requested) and removed 40 (91 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.04 2.33 NCS extension: 14 residues added (39 deleted due to clashes), 5408 seeds are put forward Round 1: 570 peptides, 23 chains. Longest chain 104 peptides. Score 0.929 Round 2: 590 peptides, 16 chains. Longest chain 114 peptides. Score 0.950 Round 3: 585 peptides, 16 chains. Longest chain 173 peptides. Score 0.949 Round 4: 588 peptides, 19 chains. Longest chain 128 peptides. Score 0.944 Round 5: 594 peptides, 16 chains. Longest chain 135 peptides. Score 0.951 Taking the results from Round 5 Chains 16, Residues 578, Estimated correctness of the model 99.7 % 13 chains (543 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 100 A and 104 A Built loop between residues 121 A and 124 A Built loop between residues 257 A and 260 A Built loop between residues 271 A and 275 A Built loop between residues 300 A and 303 A Built loop between residues 63 B and 66 B Built loop between residues 131 B and 134 B Built loop between residues 240 B and 243 B 8 chains (596 residues) following loop building 5 chains (561 residues) in sequence following loop building ------------------------------------------------------ 40537 reflections ( 99.47 % complete ) and 5885 restraints for refining 5411 atoms. 1323 conditional restraints added. Observations/parameters ratio is 1.87 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2533 (Rfree = 0.000) for 5411 atoms. Found 138 (174 requested) and removed 98 (92 requested) atoms. Cycle 7: After refmac, R = 0.2370 (Rfree = 0.000) for 5440 atoms. Found 96 (171 requested) and removed 84 (93 requested) atoms. Cycle 8: After refmac, R = 0.2280 (Rfree = 0.000) for 5440 atoms. Found 96 (167 requested) and removed 45 (93 requested) atoms. Cycle 9: After refmac, R = 0.2223 (Rfree = 0.000) for 5480 atoms. Found 96 (169 requested) and removed 44 (94 requested) atoms. Cycle 10: After refmac, R = 0.2167 (Rfree = 0.000) for 5519 atoms. Found 94 (170 requested) and removed 41 (94 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.05 2.35 NCS extension: 15 residues added (262 deleted due to clashes), 5588 seeds are put forward Round 1: 603 peptides, 10 chains. Longest chain 187 peptides. Score 0.964 Round 2: 605 peptides, 7 chains. Longest chain 243 peptides. Score 0.970 Round 3: 601 peptides, 9 chains. Longest chain 240 peptides. Score 0.966 Round 4: 601 peptides, 10 chains. Longest chain 244 peptides. Score 0.964 Round 5: 604 peptides, 9 chains. Longest chain 160 peptides. Score 0.966 Taking the results from Round 2 Chains 10, Residues 598, Estimated correctness of the model 99.9 % 6 chains (582 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 100 B and 104 B Built loop between residues 117 B and 120 B Built loop between residues 253 B and 256 B 6 chains (604 residues) following loop building 3 chains (589 residues) in sequence following loop building ------------------------------------------------------ 40537 reflections ( 99.47 % complete ) and 5693 restraints for refining 5497 atoms. 979 conditional restraints added. Observations/parameters ratio is 1.84 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2278 (Rfree = 0.000) for 5497 atoms. Found 141 (169 requested) and removed 95 (94 requested) atoms. Cycle 12: After refmac, R = 0.2170 (Rfree = 0.000) for 5529 atoms. Found 97 (166 requested) and removed 65 (94 requested) atoms. Cycle 13: After refmac, R = 0.2096 (Rfree = 0.000) for 5555 atoms. Found 83 (163 requested) and removed 46 (95 requested) atoms. Cycle 14: After refmac, R = 0.2044 (Rfree = 0.000) for 5585 atoms. Found 79 (160 requested) and removed 42 (95 requested) atoms. Cycle 15: After refmac, R = 0.2015 (Rfree = 0.000) for 5611 atoms. Found 95 (157 requested) and removed 37 (96 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.04 2.33 NCS extension: 134 residues added (201 deleted due to clashes), 5805 seeds are put forward Round 1: 597 peptides, 12 chains. Longest chain 144 peptides. Score 0.960 Round 2: 608 peptides, 7 chains. Longest chain 238 peptides. Score 0.971 Round 3: 594 peptides, 15 chains. Longest chain 119 peptides. Score 0.953 Round 4: 597 peptides, 11 chains. Longest chain 138 peptides. Score 0.961 Round 5: 597 peptides, 16 chains. Longest chain 119 peptides. Score 0.952 Taking the results from Round 2 Chains 7, Residues 601, Estimated correctness of the model 99.9 % 5 chains (583 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 27 A and 30 A Built loop between residues 253 B and 256 B 5 chains (605 residues) following loop building 3 chains (587 residues) in sequence following loop building ------------------------------------------------------ 40537 reflections ( 99.47 % complete ) and 5710 restraints for refining 5512 atoms. 996 conditional restraints added. Observations/parameters ratio is 1.84 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2165 (Rfree = 0.000) for 5512 atoms. Found 138 (154 requested) and removed 96 (94 requested) atoms. Cycle 17: After refmac, R = 0.2059 (Rfree = 0.000) for 5547 atoms. Found 76 (152 requested) and removed 47 (95 requested) atoms. Cycle 18: After refmac, R = 0.2009 (Rfree = 0.000) for 5572 atoms. Found 71 (149 requested) and removed 29 (95 requested) atoms. Cycle 19: After refmac, R = 0.1962 (Rfree = 0.000) for 5607 atoms. Found 87 (150 requested) and removed 36 (96 requested) atoms. Cycle 20: After refmac, R = 0.1962 (Rfree = 0.000) for 5651 atoms. Found 89 (151 requested) and removed 49 (96 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.05 2.35 NCS extension: 126 residues added (211 deleted due to clashes), 5817 seeds are put forward Round 1: 598 peptides, 11 chains. Longest chain 145 peptides. Score 0.962 Round 2: 602 peptides, 7 chains. Longest chain 244 peptides. Score 0.970 Round 3: 597 peptides, 9 chains. Longest chain 206 peptides. Score 0.965 Round 4: 605 peptides, 7 chains. Longest chain 244 peptides. Score 0.970 Round 5: 599 peptides, 12 chains. Longest chain 125 peptides. Score 0.960 Taking the results from Round 4 Chains 8, Residues 598, Estimated correctness of the model 99.9 % 6 chains (588 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 62 B and 65 B Built loop between residues 83 B and 86 B Built loop between residues 103 B and 106 B 5 chains (604 residues) following loop building 3 chains (594 residues) in sequence following loop building ------------------------------------------------------ 40537 reflections ( 99.47 % complete ) and 5719 restraints for refining 5559 atoms. 974 conditional restraints added. Observations/parameters ratio is 1.82 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2141 (Rfree = 0.000) for 5559 atoms. Found 143 (144 requested) and removed 97 (95 requested) atoms. Cycle 22: After refmac, R = 0.2057 (Rfree = 0.000) for 5595 atoms. Found 108 (142 requested) and removed 49 (96 requested) atoms. Cycle 23: After refmac, R = 0.1994 (Rfree = 0.000) for 5644 atoms. Found 80 (143 requested) and removed 42 (96 requested) atoms. Cycle 24: After refmac, R = 0.1950 (Rfree = 0.000) for 5675 atoms. Found 77 (140 requested) and removed 50 (97 requested) atoms. Cycle 25: After refmac, R = 0.1929 (Rfree = 0.000) for 5689 atoms. Found 74 (136 requested) and removed 48 (97 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.05 2.35 NCS extension: 118 residues added (214 deleted due to clashes), 5834 seeds are put forward Round 1: 601 peptides, 13 chains. Longest chain 108 peptides. Score 0.959 Round 2: 606 peptides, 8 chains. Longest chain 136 peptides. Score 0.969 Round 3: 596 peptides, 13 chains. Longest chain 129 peptides. Score 0.958 Round 4: 587 peptides, 8 chains. Longest chain 140 peptides. Score 0.965 Round 5: 585 peptides, 12 chains. Longest chain 86 peptides. Score 0.957 Taking the results from Round 2 Chains 8, Residues 598, Estimated correctness of the model 99.9 % 7 chains (586 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 216 A and 219 A Built loop between residues 100 B and 103 B Built loop between residues 139 B and 142 B Built loop between residues 242 B and 245 B 4 chains (606 residues) following loop building 3 chains (594 residues) in sequence following loop building ------------------------------------------------------ 40537 reflections ( 99.47 % complete ) and 5685 restraints for refining 5562 atoms. 936 conditional restraints added. Observations/parameters ratio is 1.82 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2109 (Rfree = 0.000) for 5562 atoms. Found 129 (129 requested) and removed 96 (95 requested) atoms. Cycle 27: After refmac, R = 0.2019 (Rfree = 0.000) for 5584 atoms. Found 102 (126 requested) and removed 59 (95 requested) atoms. Cycle 28: After refmac, R = 0.1976 (Rfree = 0.000) for 5622 atoms. Found 83 (123 requested) and removed 38 (96 requested) atoms. Cycle 29: After refmac, R = 0.1944 (Rfree = 0.000) for 5657 atoms. Found 75 (124 requested) and removed 42 (97 requested) atoms. Cycle 30: After refmac, R = 0.1926 (Rfree = 0.000) for 5681 atoms. Found 79 (120 requested) and removed 43 (97 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.03 2.32 NCS extension: 106 residues added (224 deleted due to clashes), 5824 seeds are put forward Round 1: 596 peptides, 13 chains. Longest chain 105 peptides. Score 0.958 Round 2: 600 peptides, 6 chains. Longest chain 244 peptides. Score 0.971 Round 3: 591 peptides, 9 chains. Longest chain 156 peptides. Score 0.964 Round 4: 591 peptides, 8 chains. Longest chain 237 peptides. Score 0.966 Round 5: 596 peptides, 11 chains. Longest chain 144 peptides. Score 0.961 Taking the results from Round 2 Chains 6, Residues 594, Estimated correctness of the model 99.9 % 5 chains (587 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 242 B and 245 B Built loop between residues 292 B and 295 B 4 chains (598 residues) following loop building 3 chains (591 residues) in sequence following loop building ------------------------------------------------------ 40537 reflections ( 99.47 % complete ) and 5792 restraints for refining 5580 atoms. 1094 conditional restraints added. Observations/parameters ratio is 1.82 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2089 (Rfree = 0.000) for 5580 atoms. Found 115 (115 requested) and removed 98 (95 requested) atoms. Cycle 32: After refmac, R = 0.1996 (Rfree = 0.000) for 5588 atoms. Found 110 (111 requested) and removed 41 (95 requested) atoms. Cycle 33: After refmac, R = 0.1952 (Rfree = 0.000) for 5652 atoms. Found 72 (112 requested) and removed 49 (96 requested) atoms. Cycle 34: After refmac, R = 0.1921 (Rfree = 0.000) for 5663 atoms. Found 81 (109 requested) and removed 28 (97 requested) atoms. Cycle 35: After refmac, R = 0.1888 (Rfree = 0.000) for 5706 atoms. Found 74 (109 requested) and removed 41 (97 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.03 2.32 NCS extension: 126 residues added (207 deleted due to clashes), 5867 seeds are put forward Round 1: 596 peptides, 12 chains. Longest chain 112 peptides. Score 0.959 Round 2: 599 peptides, 8 chains. Longest chain 126 peptides. Score 0.967 Round 3: 594 peptides, 13 chains. Longest chain 126 peptides. Score 0.957 Round 4: 589 peptides, 11 chains. Longest chain 156 peptides. Score 0.960 Round 5: 601 peptides, 9 chains. Longest chain 154 peptides. Score 0.966 Taking the results from Round 2 Chains 9, Residues 591, Estimated correctness of the model 99.9 % 7 chains (581 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 205 A and 208 A Built loop between residues 261 A and 264 A Built loop between residues 140 B and 143 B Built loop between residues 242 B and 245 B 5 chains (599 residues) following loop building 3 chains (589 residues) in sequence following loop building ------------------------------------------------------ 40537 reflections ( 99.47 % complete ) and 5814 restraints for refining 5580 atoms. 1115 conditional restraints added. Observations/parameters ratio is 1.82 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2090 (Rfree = 0.000) for 5580 atoms. Found 103 (103 requested) and removed 95 (95 requested) atoms. Cycle 37: After refmac, R = 0.1991 (Rfree = 0.000) for 5581 atoms. Found 99 (99 requested) and removed 38 (95 requested) atoms. Cycle 38: After refmac, R = 0.1943 (Rfree = 0.000) for 5638 atoms. Found 86 (100 requested) and removed 47 (96 requested) atoms. Cycle 39: After refmac, R = 0.1915 (Rfree = 0.000) for 5667 atoms. Found 81 (97 requested) and removed 38 (97 requested) atoms. Cycle 40: After refmac, R = 0.1896 (Rfree = 0.000) for 5702 atoms. Found 79 (97 requested) and removed 46 (97 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.04 2.33 NCS extension: 137 residues added (201 deleted due to clashes), 5872 seeds are put forward Round 1: 593 peptides, 14 chains. Longest chain 148 peptides. Score 0.955 Round 2: 604 peptides, 9 chains. Longest chain 246 peptides. Score 0.966 Round 3: 593 peptides, 13 chains. Longest chain 125 peptides. Score 0.957 Round 4: 596 peptides, 7 chains. Longest chain 202 peptides. Score 0.969 Round 5: 584 peptides, 12 chains. Longest chain 126 peptides. Score 0.957 Taking the results from Round 4 Chains 8, Residues 589, Estimated correctness of the model 99.9 % 7 chains (588 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 A and 64 A Built loop between residues 140 A and 143 A Built loop between residues 194 A and 197 A Built loop between residues 121 B and 124 B 3 chains (596 residues) following loop building 3 chains (596 residues) in sequence following loop building ------------------------------------------------------ 40537 reflections ( 99.47 % complete ) and 5748 restraints for refining 5582 atoms. 1024 conditional restraints added. Observations/parameters ratio is 1.82 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2070 (Rfree = 0.000) for 5582 atoms. Found 95 (95 requested) and removed 95 (95 requested) atoms. Cycle 42: After refmac, R = 0.1993 (Rfree = 0.000) for 5573 atoms. Found 95 (95 requested) and removed 42 (95 requested) atoms. Cycle 43: After refmac, R = 0.1942 (Rfree = 0.000) for 5620 atoms. Found 94 (96 requested) and removed 45 (96 requested) atoms. Cycle 44: After refmac, R = 0.1926 (Rfree = 0.000) for 5660 atoms. Found 84 (97 requested) and removed 40 (97 requested) atoms. Cycle 45: After refmac, R = 0.1917 (Rfree = 0.000) for 5694 atoms. Found 79 (97 requested) and removed 51 (97 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.04 2.33 NCS extension: 9 residues added (56 deleted due to clashes), 5732 seeds are put forward Round 1: 597 peptides, 11 chains. Longest chain 236 peptides. Score 0.961 Round 2: 596 peptides, 10 chains. Longest chain 138 peptides. Score 0.963 Round 3: 595 peptides, 11 chains. Longest chain 89 peptides. Score 0.961 Round 4: 598 peptides, 10 chains. Longest chain 145 peptides. Score 0.964 Round 5: 591 peptides, 16 chains. Longest chain 80 peptides. Score 0.951 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 588, Estimated correctness of the model 99.8 % 8 chains (582 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 25 A and 28 A Built loop between residues 58 A and 61 A Built loop between residues 140 A and 143 A Built loop between residues 194 A and 197 A Built loop between residues 178 B and 181 B 5 chains (598 residues) following loop building 3 chains (592 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 40537 reflections ( 99.47 % complete ) and 4708 restraints for refining 4633 atoms. Observations/parameters ratio is 2.19 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2801 (Rfree = 0.000) for 4633 atoms. Found 66 (79 requested) and removed 0 (79 requested) atoms. Cycle 47: After refmac, R = 0.2628 (Rfree = 0.000) for 4633 atoms. Found 40 (80 requested) and removed 1 (80 requested) atoms. Cycle 48: After refmac, R = 0.2503 (Rfree = 0.000) for 4633 atoms. Found 23 (81 requested) and removed 2 (81 requested) atoms. Cycle 49: After refmac, R = 0.2418 (Rfree = 0.000) for 4633 atoms. Found 13 (81 requested) and removed 9 (81 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:47:10 GMT 2018 Job finished. TimeTaking 67.75 Used memory is bytes: 3838472