null Mon 24 Dec 07:34:55 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 2p8j-2.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p8j-2.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p8j-2.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-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/2p8j-2.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-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 07:35:00 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/2p8j-2.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-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 546 and 0 Target number of residues in the AU: 546 Target solvent content: 0.5429 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.65 Input MTZ file: 2p8j-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: 152 Cell parameters: 83.860 83.860 159.200 90.000 90.000 120.000 Input sequence file: 2p8j-2.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 3344 target number of atoms Had to go as low as 0.85 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: 72.625 2.001 Wilson plot Bfac: 33.59 44382 reflections ( 99.74 % complete ) and 0 restraints for refining 3749 atoms. Observations/parameters ratio is 2.96 ------------------------------------------------------ Starting model: R = 0.3303 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2784 (Rfree = 0.000) for 3749 atoms. Found 128 (128 requested) and removed 44 (64 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.27 1.85 NCS extension: 0 residues added, 3833 seeds are put forward Round 1: 333 peptides, 29 chains. Longest chain 35 peptides. Score 0.687 Round 2: 359 peptides, 20 chains. Longest chain 69 peptides. Score 0.783 Round 3: 383 peptides, 16 chains. Longest chain 54 peptides. Score 0.830 Round 4: 394 peptides, 10 chains. Longest chain 72 peptides. Score 0.868 Round 5: 395 peptides, 11 chains. Longest chain 114 peptides. Score 0.864 Taking the results from Round 4 Chains 11, Residues 384, Estimated correctness of the model 98.3 % 9 chains (375 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 86 A and 90 A Built loop between residues 149 A and 156 A Built loop between residues 169 A and 172 A Built loop between residues 65 B and 68 B Built loop between residues 111 B and 116 B Built loop between residues 186 B and 190 B 4 chains (403 residues) following loop building 3 chains (395 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3900 restraints for refining 3906 atoms. 570 conditional restraints added. Observations/parameters ratio is 2.84 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2785 (Rfree = 0.000) for 3906 atoms. Found 133 (133 requested) and removed 74 (66 requested) atoms. Cycle 2: After refmac, R = 0.2491 (Rfree = 0.000) for 3937 atoms. Found 132 (132 requested) and removed 65 (67 requested) atoms. Cycle 3: After refmac, R = 0.2346 (Rfree = 0.000) for 3984 atoms. Found 128 (133 requested) and removed 42 (68 requested) atoms. Cycle 4: After refmac, R = 0.2279 (Rfree = 0.000) for 4050 atoms. Found 118 (136 requested) and removed 45 (69 requested) atoms. Cycle 5: After refmac, R = 0.2218 (Rfree = 0.000) for 4110 atoms. Found 124 (138 requested) and removed 48 (70 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.22 1.81 NCS extension: 54 residues added (223 deleted due to clashes), 4247 seeds are put forward Round 1: 397 peptides, 6 chains. Longest chain 204 peptides. Score 0.887 Round 2: 398 peptides, 8 chains. Longest chain 131 peptides. Score 0.879 Round 3: 402 peptides, 6 chains. Longest chain 205 peptides. Score 0.890 Round 4: 391 peptides, 11 chains. Longest chain 131 peptides. Score 0.861 Round 5: 401 peptides, 7 chains. Longest chain 145 peptides. Score 0.886 Taking the results from Round 3 Chains 7, Residues 396, Estimated correctness of the model 98.8 % 5 chains (387 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 55 A and 58 A Built loop between residues 169 A and 173 A 4 chains (399 residues) following loop building 3 chains (392 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3843 restraints for refining 3924 atoms. 557 conditional restraints added. Observations/parameters ratio is 2.83 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2353 (Rfree = 0.000) for 3924 atoms. Found 131 (131 requested) and removed 68 (67 requested) atoms. Cycle 7: After refmac, R = 0.2225 (Rfree = 0.000) for 3977 atoms. Found 123 (131 requested) and removed 56 (68 requested) atoms. Cycle 8: After refmac, R = 0.2145 (Rfree = 0.000) for 4034 atoms. Found 102 (132 requested) and removed 54 (69 requested) atoms. Cycle 9: After refmac, R = 0.2083 (Rfree = 0.000) for 4077 atoms. Found 89 (131 requested) and removed 61 (69 requested) atoms. Cycle 10: After refmac, R = 0.2042 (Rfree = 0.000) for 4102 atoms. Found 101 (129 requested) and removed 55 (70 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.22 1.81 NCS extension: 102 residues added (117 deleted due to clashes), 4253 seeds are put forward Round 1: 402 peptides, 6 chains. Longest chain 178 peptides. Score 0.890 Round 2: 402 peptides, 5 chains. Longest chain 131 peptides. Score 0.894 Round 3: 401 peptides, 7 chains. Longest chain 144 peptides. Score 0.886 Round 4: 401 peptides, 7 chains. Longest chain 86 peptides. Score 0.886 Round 5: 396 peptides, 9 chains. Longest chain 144 peptides. Score 0.873 Taking the results from Round 2 Chains 5, Residues 397, Estimated correctness of the model 98.8 % 5 chains (397 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 55 A and 58 A Built loop between residues 149 A and 156 A Built loop between residues 76 B and 79 B 2 chains (407 residues) following loop building 2 chains (407 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3821 restraints for refining 4012 atoms. 439 conditional restraints added. Observations/parameters ratio is 2.77 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2318 (Rfree = 0.000) for 4012 atoms. Found 123 (123 requested) and removed 71 (68 requested) atoms. Cycle 12: After refmac, R = 0.2169 (Rfree = 0.000) for 4056 atoms. Found 115 (122 requested) and removed 52 (69 requested) atoms. Cycle 13: After refmac, R = 0.2083 (Rfree = 0.000) for 4117 atoms. Found 92 (123 requested) and removed 51 (70 requested) atoms. Cycle 14: After refmac, R = 0.2038 (Rfree = 0.000) for 4153 atoms. Found 96 (122 requested) and removed 60 (71 requested) atoms. Cycle 15: After refmac, R = 0.2020 (Rfree = 0.000) for 4185 atoms. Found 89 (120 requested) and removed 63 (71 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.22 1.81 NCS extension: 0 residues added, 4213 seeds are put forward Round 1: 400 peptides, 6 chains. Longest chain 155 peptides. Score 0.889 Round 2: 401 peptides, 8 chains. Longest chain 140 peptides. Score 0.881 Round 3: 396 peptides, 8 chains. Longest chain 144 peptides. Score 0.878 Round 4: 402 peptides, 6 chains. Longest chain 135 peptides. Score 0.890 Round 5: 401 peptides, 9 chains. Longest chain 123 peptides. Score 0.877 Taking the results from Round 4 Chains 6, Residues 396, Estimated correctness of the model 98.8 % 6 chains (396 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 A and 32 A Built loop between residues 114 A and 117 A Built loop between residues 149 A and 155 A Built loop between residues 138 B and 141 B 2 chains (407 residues) following loop building 2 chains (407 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3812 restraints for refining 4029 atoms. 430 conditional restraints added. Observations/parameters ratio is 2.75 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2317 (Rfree = 0.000) for 4029 atoms. Found 112 (112 requested) and removed 70 (68 requested) atoms. Cycle 17: After refmac, R = 0.2155 (Rfree = 0.000) for 4064 atoms. Found 98 (111 requested) and removed 44 (69 requested) atoms. Cycle 18: After refmac, R = 0.2077 (Rfree = 0.000) for 4112 atoms. Found 95 (112 requested) and removed 45 (70 requested) atoms. Cycle 19: After refmac, R = 0.2029 (Rfree = 0.000) for 4154 atoms. Found 87 (114 requested) and removed 44 (71 requested) atoms. Cycle 20: After refmac, R = 0.1980 (Rfree = 0.000) for 4192 atoms. Found 91 (112 requested) and removed 46 (71 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.23 1.81 NCS extension: 90 residues added (115 deleted due to clashes), 4327 seeds are put forward Round 1: 403 peptides, 4 chains. Longest chain 176 peptides. Score 0.899 Round 2: 400 peptides, 10 chains. Longest chain 107 peptides. Score 0.872 Round 3: 397 peptides, 10 chains. Longest chain 70 peptides. Score 0.870 Round 4: 401 peptides, 8 chains. Longest chain 144 peptides. Score 0.881 Round 5: 399 peptides, 8 chains. Longest chain 93 peptides. Score 0.880 Taking the results from Round 1 Chains 5, Residues 399, Estimated correctness of the model 98.9 % 4 chains (398 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 149 A and 155 A Built loop between residues 30 B and 34 B 3 chains (407 residues) following loop building 2 chains (406 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3849 restraints for refining 4062 atoms. 472 conditional restraints added. Observations/parameters ratio is 2.73 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2267 (Rfree = 0.000) for 4062 atoms. Found 105 (105 requested) and removed 70 (69 requested) atoms. Cycle 22: After refmac, R = 0.2119 (Rfree = 0.000) for 4086 atoms. Found 104 (104 requested) and removed 41 (70 requested) atoms. Cycle 23: After refmac, R = 0.2048 (Rfree = 0.000) for 4145 atoms. Found 89 (104 requested) and removed 54 (70 requested) atoms. Cycle 24: After refmac, R = 0.1995 (Rfree = 0.000) for 4174 atoms. Found 82 (102 requested) and removed 49 (71 requested) atoms. Cycle 25: After refmac, R = 0.1977 (Rfree = 0.000) for 4202 atoms. Found 94 (100 requested) and removed 50 (71 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.22 1.81 NCS extension: 0 residues added, 4247 seeds are put forward Round 1: 403 peptides, 5 chains. Longest chain 178 peptides. Score 0.895 Round 2: 403 peptides, 7 chains. Longest chain 131 peptides. Score 0.887 Round 3: 404 peptides, 6 chains. Longest chain 144 peptides. Score 0.892 Round 4: 395 peptides, 8 chains. Longest chain 131 peptides. Score 0.877 Round 5: 400 peptides, 7 chains. Longest chain 144 peptides. Score 0.885 Taking the results from Round 1 Chains 5, Residues 398, Estimated correctness of the model 98.9 % 5 chains (398 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 30 A and 33 A Built loop between residues 149 A and 155 A Built loop between residues 29 B and 32 B 2 chains (407 residues) following loop building 2 chains (407 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3821 restraints for refining 4055 atoms. 440 conditional restraints added. Observations/parameters ratio is 2.74 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2252 (Rfree = 0.000) for 4055 atoms. Found 94 (94 requested) and removed 69 (69 requested) atoms. Cycle 27: After refmac, R = 0.2119 (Rfree = 0.000) for 4070 atoms. Found 92 (92 requested) and removed 22 (69 requested) atoms. Cycle 28: After refmac, R = 0.2043 (Rfree = 0.000) for 4133 atoms. Found 89 (93 requested) and removed 38 (70 requested) atoms. Cycle 29: After refmac, R = 0.1998 (Rfree = 0.000) for 4178 atoms. Found 87 (94 requested) and removed 51 (71 requested) atoms. Cycle 30: After refmac, R = 0.1977 (Rfree = 0.000) for 4209 atoms. Found 85 (92 requested) and removed 58 (72 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.23 1.81 NCS extension: 97 residues added (107 deleted due to clashes), 4335 seeds are put forward Round 1: 401 peptides, 6 chains. Longest chain 178 peptides. Score 0.890 Round 2: 402 peptides, 8 chains. Longest chain 131 peptides. Score 0.882 Round 3: 404 peptides, 5 chains. Longest chain 144 peptides. Score 0.896 Round 4: 403 peptides, 7 chains. Longest chain 131 peptides. Score 0.887 Round 5: 404 peptides, 6 chains. Longest chain 144 peptides. Score 0.892 Taking the results from Round 3 Chains 5, Residues 399, Estimated correctness of the model 98.9 % 5 chains (399 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 117 A and 120 A Built loop between residues 150 A and 155 A Built loop between residues 63 B and 66 B 2 chains (407 residues) following loop building 2 chains (407 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3836 restraints for refining 4042 atoms. 454 conditional restraints added. Observations/parameters ratio is 2.75 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2293 (Rfree = 0.000) for 4042 atoms. Found 86 (86 requested) and removed 70 (69 requested) atoms. Cycle 32: After refmac, R = 0.2153 (Rfree = 0.000) for 4052 atoms. Found 83 (83 requested) and removed 36 (69 requested) atoms. Cycle 33: After refmac, R = 0.2098 (Rfree = 0.000) for 4093 atoms. Found 84 (84 requested) and removed 40 (70 requested) atoms. Cycle 34: After refmac, R = 0.2048 (Rfree = 0.000) for 4132 atoms. Found 79 (85 requested) and removed 45 (70 requested) atoms. Cycle 35: After refmac, R = 0.2024 (Rfree = 0.000) for 4164 atoms. Found 82 (82 requested) and removed 42 (71 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.23 1.81 NCS extension: 0 residues added, 4204 seeds are put forward Round 1: 404 peptides, 6 chains. Longest chain 144 peptides. Score 0.892 Round 2: 408 peptides, 4 chains. Longest chain 206 peptides. Score 0.902 Round 3: 403 peptides, 9 chains. Longest chain 131 peptides. Score 0.878 Round 4: 407 peptides, 5 chains. Longest chain 206 peptides. Score 0.898 Round 5: 404 peptides, 8 chains. Longest chain 206 peptides. Score 0.883 Taking the results from Round 2 Chains 4, Residues 404, Estimated correctness of the model 99.0 % 4 chains (404 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 77 A and 80 A Built loop between residues 150 A and 155 A 2 chains (410 residues) following loop building 2 chains (410 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3845 restraints for refining 4068 atoms. 441 conditional restraints added. Observations/parameters ratio is 2.73 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2279 (Rfree = 0.000) for 4068 atoms. Found 78 (78 requested) and removed 71 (69 requested) atoms. Cycle 37: After refmac, R = 0.2133 (Rfree = 0.000) for 4071 atoms. Found 75 (75 requested) and removed 36 (69 requested) atoms. Cycle 38: After refmac, R = 0.2063 (Rfree = 0.000) for 4105 atoms. Found 76 (76 requested) and removed 34 (70 requested) atoms. Cycle 39: After refmac, R = 0.2039 (Rfree = 0.000) for 4140 atoms. Found 76 (76 requested) and removed 48 (70 requested) atoms. Cycle 40: After refmac, R = 0.2004 (Rfree = 0.000) for 4168 atoms. Found 74 (74 requested) and removed 49 (71 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.22 1.81 NCS extension: 0 residues added, 4194 seeds are put forward Round 1: 404 peptides, 7 chains. Longest chain 154 peptides. Score 0.888 Round 2: 403 peptides, 8 chains. Longest chain 75 peptides. Score 0.883 Round 3: 399 peptides, 11 chains. Longest chain 79 peptides. Score 0.867 Round 4: 406 peptides, 4 chains. Longest chain 204 peptides. Score 0.901 Round 5: 402 peptides, 7 chains. Longest chain 176 peptides. Score 0.886 Taking the results from Round 4 Chains 4, Residues 402, Estimated correctness of the model 99.0 % 4 chains (402 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 112 A and 115 A Built loop between residues 150 A and 155 A 2 chains (408 residues) following loop building 2 chains (408 residues) in sequence following loop building ------------------------------------------------------ 44382 reflections ( 99.74 % complete ) and 3808 restraints for refining 4018 atoms. 419 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2270 (Rfree = 0.000) for 4018 atoms. Found 68 (68 requested) and removed 69 (68 requested) atoms. Cycle 42: After refmac, R = 0.2134 (Rfree = 0.000) for 4009 atoms. Found 68 (68 requested) and removed 20 (68 requested) atoms. Cycle 43: After refmac, R = 0.2061 (Rfree = 0.000) for 4050 atoms. Found 69 (69 requested) and removed 14 (69 requested) atoms. Cycle 44: After refmac, R = 0.2024 (Rfree = 0.000) for 4095 atoms. Found 65 (70 requested) and removed 27 (70 requested) atoms. Cycle 45: After refmac, R = 0.1999 (Rfree = 0.000) for 4129 atoms. Found 70 (70 requested) and removed 35 (70 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.22 1.81 NCS extension: 0 residues added, 4164 seeds are put forward Round 1: 404 peptides, 6 chains. Longest chain 178 peptides. Score 0.892 Round 2: 404 peptides, 8 chains. Longest chain 75 peptides. Score 0.883 Round 3: 400 peptides, 9 chains. Longest chain 136 peptides. Score 0.876 Round 4: 403 peptides, 7 chains. Longest chain 176 peptides. Score 0.887 Round 5: 402 peptides, 7 chains. Longest chain 144 peptides. Score 0.886 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 398, Estimated correctness of the model 98.8 % 6 chains (398 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 30 A and 33 A Built loop between residues 87 A and 90 A Built loop between residues 151 A and 156 A Built loop between residues 29 B and 32 B 2 chains (408 residues) following loop building 2 chains (408 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 44382 reflections ( 99.74 % complete ) and 3389 restraints for refining 3331 atoms. Observations/parameters ratio is 3.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2694 (Rfree = 0.000) for 3331 atoms. Found 56 (56 requested) and removed 0 (56 requested) atoms. Cycle 47: After refmac, R = 0.2450 (Rfree = 0.000) for 3331 atoms. Found 36 (57 requested) and removed 2 (57 requested) atoms. Cycle 48: After refmac, R = 0.2312 (Rfree = 0.000) for 3331 atoms. Found 24 (58 requested) and removed 3 (58 requested) atoms. Cycle 49: After refmac, R = 0.2241 (Rfree = 0.000) for 3331 atoms. Found 16 (58 requested) and removed 6 (58 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:39:15 GMT 2018 Job finished. TimeTaking 64.33 Used memory is bytes: 6845984