Mon 24 Dec 00:21:22 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ajr-2.5-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ajr-2.5-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ajr-2.5-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-2.5-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-2.5-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-2.5-parrot-mrncs ############### 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 00:21:28 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-2.5-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ajr-2.5-parrot-mrncs/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 684 and 0 Target number of residues in the AU: 684 Target solvent content: 0.5571 Checking the provided sequence file Detected sequence length: 331 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 662 Adjusted target solvent content: 0.57 Input MTZ file: 2ajr-2.5-parrot-mrncs.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: 92 Cell parameters: 115.754 115.754 124.745 90.000 90.000 90.000 Input sequence file: 2ajr-2.5-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5296 target number of atoms Had to go as low as 0.60 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 3 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: 29.168 2.457 Wilson plot Bfac: 37.46 31336 reflections ( 99.47 % complete ) and 0 restraints for refining 5880 atoms. Observations/parameters ratio is 1.33 ------------------------------------------------------ Starting model: R = 0.3639 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3451 (Rfree = 0.000) for 5880 atoms. Found 112 (112 requested) and removed 110 (56 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.70 2.46 NCS extension: 0 residues added, 5882 seeds are put forward Round 1: 356 peptides, 69 chains. Longest chain 13 peptides. Score 0.340 Round 2: 395 peptides, 63 chains. Longest chain 15 peptides. Score 0.462 Round 3: 419 peptides, 62 chains. Longest chain 17 peptides. Score 0.511 Round 4: 428 peptides, 60 chains. Longest chain 21 peptides. Score 0.539 Round 5: 441 peptides, 55 chains. Longest chain 19 peptides. Score 0.593 Taking the results from Round 5 Chains 58, Residues 386, Estimated correctness of the model 73.6 % 9 chains (74 residues) have been docked in sequence ------------------------------------------------------ 31336 reflections ( 99.47 % complete ) and 9791 restraints for refining 4971 atoms. 8069 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3461 (Rfree = 0.000) for 4971 atoms. Found 73 (94 requested) and removed 64 (47 requested) atoms. Cycle 2: After refmac, R = 0.3316 (Rfree = 0.000) for 4942 atoms. Found 64 (94 requested) and removed 56 (47 requested) atoms. Cycle 3: After refmac, R = 0.3144 (Rfree = 0.000) for 4923 atoms. Found 49 (94 requested) and removed 55 (47 requested) atoms. Cycle 4: After refmac, R = 0.3005 (Rfree = 0.000) for 4901 atoms. Found 45 (93 requested) and removed 51 (46 requested) atoms. Cycle 5: After refmac, R = 0.2942 (Rfree = 0.000) for 4882 atoms. Found 24 (93 requested) and removed 48 (46 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.63 2.39 NCS extension: 2 residues added (4 deleted due to clashes), 4885 seeds are put forward Round 1: 411 peptides, 57 chains. Longest chain 20 peptides. Score 0.534 Round 2: 461 peptides, 51 chains. Longest chain 31 peptides. Score 0.646 Round 3: 461 peptides, 48 chains. Longest chain 29 peptides. Score 0.664 Round 4: 476 peptides, 44 chains. Longest chain 54 peptides. Score 0.704 Round 5: 478 peptides, 44 chains. Longest chain 36 peptides. Score 0.706 Taking the results from Round 5 Chains 47, Residues 434, Estimated correctness of the model 85.5 % 9 chains (169 residues) have been docked in sequence Building loops using Loopy2018 47 chains (434 residues) following loop building 9 chains (169 residues) in sequence following loop building ------------------------------------------------------ 31336 reflections ( 99.47 % complete ) and 8509 restraints for refining 4974 atoms. 6243 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3323 (Rfree = 0.000) for 4974 atoms. Found 94 (94 requested) and removed 66 (47 requested) atoms. Cycle 7: After refmac, R = 0.3150 (Rfree = 0.000) for 4971 atoms. Found 89 (93 requested) and removed 63 (47 requested) atoms. Cycle 8: After refmac, R = 0.3020 (Rfree = 0.000) for 4971 atoms. Found 82 (91 requested) and removed 50 (47 requested) atoms. Cycle 9: After refmac, R = 0.2993 (Rfree = 0.000) for 4986 atoms. Found 89 (89 requested) and removed 49 (47 requested) atoms. Cycle 10: After refmac, R = 0.2863 (Rfree = 0.000) for 5017 atoms. Found 68 (87 requested) and removed 48 (47 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.56 2.33 NCS extension: 51 residues added (8 deleted due to clashes), 5109 seeds are put forward Round 1: 439 peptides, 49 chains. Longest chain 34 peptides. Score 0.629 Round 2: 471 peptides, 43 chains. Longest chain 39 peptides. Score 0.704 Round 3: 489 peptides, 41 chains. Longest chain 39 peptides. Score 0.733 Round 4: 505 peptides, 40 chains. Longest chain 57 peptides. Score 0.754 Round 5: 500 peptides, 43 chains. Longest chain 32 peptides. Score 0.735 Taking the results from Round 4 Chains 45, Residues 465, Estimated correctness of the model 89.5 % 10 chains (234 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 30 A and 36 A Built loop between residues 52 A and 58 A 42 chains (470 residues) following loop building 8 chains (244 residues) in sequence following loop building ------------------------------------------------------ 31336 reflections ( 99.47 % complete ) and 7596 restraints for refining 4974 atoms. 4829 conditional restraints added. Observations/parameters ratio is 1.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2966 (Rfree = 0.000) for 4974 atoms. Found 85 (85 requested) and removed 65 (47 requested) atoms. Cycle 12: After refmac, R = 0.2793 (Rfree = 0.000) for 4971 atoms. Found 78 (84 requested) and removed 51 (47 requested) atoms. Cycle 13: After refmac, R = 0.2685 (Rfree = 0.000) for 4985 atoms. Found 50 (82 requested) and removed 48 (47 requested) atoms. Cycle 14: After refmac, R = 0.2548 (Rfree = 0.000) for 4981 atoms. Found 44 (80 requested) and removed 48 (47 requested) atoms. Cycle 15: After refmac, R = 0.2558 (Rfree = 0.000) for 4972 atoms. Found 46 (77 requested) and removed 47 (47 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.55 2.32 NCS extension: 162 residues added (38 deleted due to clashes), 5165 seeds are put forward Round 1: 490 peptides, 41 chains. Longest chain 44 peptides. Score 0.734 Round 2: 511 peptides, 36 chains. Longest chain 57 peptides. Score 0.778 Round 3: 507 peptides, 37 chains. Longest chain 44 peptides. Score 0.770 Round 4: 518 peptides, 30 chains. Longest chain 57 peptides. Score 0.809 Round 5: 507 peptides, 37 chains. Longest chain 58 peptides. Score 0.770 Taking the results from Round 4 Chains 36, Residues 488, Estimated correctness of the model 93.4 % 10 chains (297 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 79 B and 83 B 33 chains (489 residues) following loop building 9 chains (300 residues) in sequence following loop building ------------------------------------------------------ 31336 reflections ( 99.47 % complete ) and 7039 restraints for refining 4973 atoms. 4001 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2818 (Rfree = 0.000) for 4973 atoms. Found 75 (75 requested) and removed 65 (47 requested) atoms. Cycle 17: After refmac, R = 0.2672 (Rfree = 0.000) for 4970 atoms. Found 73 (73 requested) and removed 51 (47 requested) atoms. Cycle 18: After refmac, R = 0.2592 (Rfree = 0.000) for 4985 atoms. Found 34 (72 requested) and removed 49 (47 requested) atoms. Cycle 19: After refmac, R = 0.2591 (Rfree = 0.000) for 4964 atoms. Found 57 (70 requested) and removed 47 (47 requested) atoms. Cycle 20: After refmac, R = 0.2494 (Rfree = 0.000) for 4969 atoms. Found 40 (68 requested) and removed 47 (47 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.56 2.33 NCS extension: 48 residues added (21 deleted due to clashes), 5036 seeds are put forward Round 1: 490 peptides, 33 chains. Longest chain 64 peptides. Score 0.773 Round 2: 504 peptides, 28 chains. Longest chain 70 peptides. Score 0.807 Round 3: 502 peptides, 33 chains. Longest chain 43 peptides. Score 0.783 Round 4: 512 peptides, 28 chains. Longest chain 48 peptides. Score 0.813 Round 5: 507 peptides, 29 chains. Longest chain 75 peptides. Score 0.805 Taking the results from Round 4 Chains 32, Residues 484, Estimated correctness of the model 93.6 % 12 chains (319 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 75 A and 78 A Built loop between residues 250 A and 253 A Built loop between residues 41 B and 48 B Built loop between residues 63 B and 66 B 27 chains (490 residues) following loop building 8 chains (331 residues) in sequence following loop building ------------------------------------------------------ 31336 reflections ( 99.47 % complete ) and 6825 restraints for refining 4973 atoms. 3641 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2741 (Rfree = 0.000) for 4973 atoms. Found 66 (66 requested) and removed 55 (47 requested) atoms. Cycle 22: After refmac, R = 0.2533 (Rfree = 0.000) for 4978 atoms. Found 59 (64 requested) and removed 50 (47 requested) atoms. Cycle 23: After refmac, R = 0.2434 (Rfree = 0.000) for 4982 atoms. Found 34 (63 requested) and removed 47 (47 requested) atoms. Cycle 24: After refmac, R = 0.2419 (Rfree = 0.000) for 4962 atoms. Found 34 (60 requested) and removed 47 (47 requested) atoms. Cycle 25: After refmac, R = 0.2419 (Rfree = 0.000) for 4944 atoms. Found 52 (58 requested) and removed 47 (47 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.55 2.32 NCS extension: 56 residues added (25 deleted due to clashes), 5022 seeds are put forward Round 1: 490 peptides, 33 chains. Longest chain 48 peptides. Score 0.773 Round 2: 512 peptides, 30 chains. Longest chain 61 peptides. Score 0.805 Round 3: 528 peptides, 29 chains. Longest chain 71 peptides. Score 0.821 Round 4: 530 peptides, 24 chains. Longest chain 67 peptides. Score 0.841 Round 5: 524 peptides, 29 chains. Longest chain 62 peptides. Score 0.818 Taking the results from Round 4 Chains 28, Residues 506, Estimated correctness of the model 95.3 % 11 chains (363 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 55 A Built loop between residues 80 A and 83 A Built loop between residues 135 B and 146 B Built loop between residues 250 B and 253 B 23 chains (515 residues) following loop building 7 chains (379 residues) in sequence following loop building ------------------------------------------------------ 31336 reflections ( 99.47 % complete ) and 6428 restraints for refining 5044 atoms. 2930 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2623 (Rfree = 0.000) for 5044 atoms. Found 58 (58 requested) and removed 58 (48 requested) atoms. Cycle 27: After refmac, R = 0.2447 (Rfree = 0.000) for 5025 atoms. Found 56 (56 requested) and removed 48 (48 requested) atoms. Cycle 28: After refmac, R = 0.2420 (Rfree = 0.000) for 5028 atoms. Found 48 (53 requested) and removed 48 (47 requested) atoms. Cycle 29: After refmac, R = 0.2315 (Rfree = 0.000) for 5025 atoms. Found 46 (51 requested) and removed 47 (47 requested) atoms. Cycle 30: After refmac, R = 0.2316 (Rfree = 0.000) for 5019 atoms. Found 37 (49 requested) and removed 48 (47 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.54 2.31 NCS extension: 133 residues added (134 deleted due to clashes), 5153 seeds are put forward Round 1: 544 peptides, 27 chains. Longest chain 80 peptides. Score 0.839 Round 2: 564 peptides, 22 chains. Longest chain 100 peptides. Score 0.868 Round 3: 561 peptides, 24 chains. Longest chain 65 peptides. Score 0.860 Round 4: 565 peptides, 28 chains. Longest chain 61 peptides. Score 0.849 Round 5: 557 peptides, 28 chains. Longest chain 59 peptides. Score 0.844 Taking the results from Round 2 Chains 26, Residues 542, Estimated correctness of the model 96.6 % 14 chains (454 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 A and 33 A Built loop between residues 80 A and 83 A Built loop between residues 144 B and 147 B Built loop between residues 168 B and 176 B Built loop between residues 208 B and 211 B 20 chains (554 residues) following loop building 9 chains (470 residues) in sequence following loop building ------------------------------------------------------ 31336 reflections ( 99.47 % complete ) and 5901 restraints for refining 5147 atoms. 1870 conditional restraints added. Observations/parameters ratio is 1.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2501 (Rfree = 0.000) for 5147 atoms. Found 49 (49 requested) and removed 70 (49 requested) atoms. Cycle 32: After refmac, R = 0.2348 (Rfree = 0.000) for 5118 atoms. Found 48 (48 requested) and removed 49 (48 requested) atoms. Cycle 33: After refmac, R = 0.2260 (Rfree = 0.000) for 5116 atoms. Found 48 (48 requested) and removed 48 (48 requested) atoms. Cycle 34: After refmac, R = 0.2221 (Rfree = 0.000) for 5112 atoms. Found 48 (48 requested) and removed 48 (48 requested) atoms. Cycle 35: After refmac, R = 0.2206 (Rfree = 0.000) for 5107 atoms. Found 48 (48 requested) and removed 48 (48 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.53 2.30 NCS extension: 8 residues added (10 deleted due to clashes), 5133 seeds are put forward Round 1: 552 peptides, 25 chains. Longest chain 66 peptides. Score 0.851 Round 2: 576 peptides, 22 chains. Longest chain 98 peptides. Score 0.875 Round 3: 575 peptides, 20 chains. Longest chain 93 peptides. Score 0.880 Round 4: 569 peptides, 23 chains. Longest chain 70 peptides. Score 0.868 Round 5: 570 peptides, 21 chains. Longest chain 93 peptides. Score 0.874 Taking the results from Round 3 Chains 28, Residues 555, Estimated correctness of the model 97.2 % 15 chains (498 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 49 A and 54 A Built loop between residues 111 A and 115 A Built loop between residues 309 A and 313 A Built loop between residues 63 B and 66 B Built loop between residues 160 B and 164 B Built loop between residues 185 B and 196 B Built loop between residues 308 B and 311 B 17 chains (572 residues) following loop building 8 chains (525 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 31336 reflections ( 99.47 % complete ) and 5855 restraints for refining 5233 atoms. 1475 conditional restraints added. Observations/parameters ratio is 1.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2414 (Rfree = 0.000) for 5233 atoms. Found 49 (49 requested) and removed 60 (49 requested) atoms. Cycle 37: After refmac, R = 0.2268 (Rfree = 0.000) for 5209 atoms. Found 49 (49 requested) and removed 51 (49 requested) atoms. Cycle 38: After refmac, R = 0.2169 (Rfree = 0.000) for 5203 atoms. Found 49 (49 requested) and removed 52 (49 requested) atoms. Cycle 39: After refmac, R = 0.2122 (Rfree = 0.000) for 5197 atoms. Found 49 (49 requested) and removed 53 (49 requested) atoms. Cycle 40: After refmac, R = 0.2088 (Rfree = 0.000) for 5186 atoms. Found 49 (49 requested) and removed 53 (49 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.52 2.29 NCS extension: 32 residues added (139 deleted due to clashes), 5226 seeds are put forward Round 1: 580 peptides, 19 chains. Longest chain 117 peptides. Score 0.885 Round 2: 582 peptides, 18 chains. Longest chain 158 peptides. Score 0.889 Round 3: 590 peptides, 12 chains. Longest chain 116 peptides. Score 0.909 Round 4: 581 peptides, 19 chains. Longest chain 101 peptides. Score 0.886 Round 5: 586 peptides, 22 chains. Longest chain 84 peptides. Score 0.880 Taking the results from Round 3 Chains 13, Residues 578, Estimated correctness of the model 98.3 % 9 chains (500 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 80 A and 83 A Built loop between residues 129 A and 132 A 11 chains (582 residues) following loop building 7 chains (504 residues) in sequence following loop building ------------------------------------------------------ 31336 reflections ( 99.47 % complete ) and 5833 restraints for refining 5146 atoms. 1482 conditional restraints added. Observations/parameters ratio is 1.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2301 (Rfree = 0.000) for 5146 atoms. Found 49 (49 requested) and removed 63 (49 requested) atoms. Cycle 42: After refmac, R = 0.2139 (Rfree = 0.000) for 5127 atoms. Found 48 (48 requested) and removed 51 (48 requested) atoms. Cycle 43: After refmac, R = 0.2045 (Rfree = 0.000) for 5114 atoms. Found 48 (48 requested) and removed 51 (48 requested) atoms. Cycle 44: After refmac, R = 0.2001 (Rfree = 0.000) for 5107 atoms. Found 48 (48 requested) and removed 51 (48 requested) atoms. Cycle 45: After refmac, R = 0.1955 (Rfree = 0.000) for 5102 atoms. Found 48 (48 requested) and removed 50 (48 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.52 2.29 NCS extension: 218 residues added (222 deleted due to clashes), 5321 seeds are put forward Round 1: 581 peptides, 23 chains. Longest chain 89 peptides. Score 0.874 Round 2: 593 peptides, 16 chains. Longest chain 194 peptides. Score 0.900 Round 3: 598 peptides, 15 chains. Longest chain 163 peptides. Score 0.905 Round 4: 599 peptides, 19 chains. Longest chain 93 peptides. Score 0.894 Round 5: 591 peptides, 20 chains. Longest chain 90 peptides. Score 0.888 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 583, Estimated correctness of the model 98.2 % 13 chains (574 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 132 A and 144 A Built loop between residues 160 A and 169 A Built loop between residues 206 A and 219 A Built loop between residues 272 A and 275 A Built loop between residues 296 A and 299 A Built loop between residues 174 B and 178 B Built loop between residues 192 B and 196 B Built loop between residues 250 B and 256 B Built loop between residues 285 B and 298 B Built loop between residues 307 B and 311 B 3 chains (635 residues) following loop building 3 chains (635 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 31336 reflections ( 99.47 % complete ) and 5121 restraints for refining 5031 atoms. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2454 (Rfree = 0.000) for 5031 atoms. Found 38 (47 requested) and removed 0 (47 requested) atoms. Cycle 47: After refmac, R = 0.2213 (Rfree = 0.000) for 5031 atoms. Found 21 (48 requested) and removed 2 (48 requested) atoms. Cycle 48: After refmac, R = 0.2129 (Rfree = 0.000) for 5031 atoms. Found 12 (48 requested) and removed 4 (48 requested) atoms. Cycle 49: After refmac, R = 0.2087 (Rfree = 0.000) for 5031 atoms. TimeTaking 82.3