Sun 23 Dec 23:47:01 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 1vpm-1.7-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vpm-1.7-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vpm-1.7-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpm-1.7-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/1vpm-1.7-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpm-1.7-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 ============================================================ Sun 23 Dec 23:47:06 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/1vpm-1.7-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpm-1.7-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 487 and 0 Target number of residues in the AU: 487 Target solvent content: 0.5034 Checking the provided sequence file Detected sequence length: 169 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 507 Adjusted target solvent content: 0.48 Input MTZ file: 1vpm-1.7-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: 24 Cell parameters: 82.941 106.484 120.177 90.000 90.000 90.000 Input sequence file: 1vpm-1.7-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4056 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: 79.699 1.660 Wilson plot Bfac: 24.05 62685 reflections ( 99.49 % complete ) and 0 restraints for refining 4515 atoms. Observations/parameters ratio is 3.47 ------------------------------------------------------ Starting model: R = 0.3186 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2591 (Rfree = 0.000) for 4515 atoms. Found 197 (262 requested) and removed 142 (131 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.95 2.00 NCS extension: 0 residues added, 4570 seeds are put forward Round 1: 389 peptides, 24 chains. Longest chain 50 peptides. Score 0.845 Round 2: 407 peptides, 11 chains. Longest chain 120 peptides. Score 0.915 Round 3: 421 peptides, 8 chains. Longest chain 111 peptides. Score 0.933 Round 4: 428 peptides, 9 chains. Longest chain 150 peptides. Score 0.932 Round 5: 435 peptides, 6 chains. Longest chain 151 peptides. Score 0.945 Taking the results from Round 5 Chains 7, Residues 429, Estimated correctness of the model 99.8 % 5 chains (413 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 A and 41 A Built loop between residues 59 A and 63 A 4 chains (435 residues) following loop building 3 chains (422 residues) in sequence following loop building ------------------------------------------------------ 62685 reflections ( 99.49 % complete ) and 4265 restraints for refining 4060 atoms. 910 conditional restraints added. Observations/parameters ratio is 3.86 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2663 (Rfree = 0.000) for 4060 atoms. Found 160 (236 requested) and removed 99 (118 requested) atoms. Cycle 2: After refmac, R = 0.2456 (Rfree = 0.000) for 4117 atoms. Found 130 (235 requested) and removed 39 (120 requested) atoms. Cycle 3: After refmac, R = 0.2235 (Rfree = 0.000) for 4199 atoms. Found 121 (239 requested) and removed 36 (122 requested) atoms. Cycle 4: After refmac, R = 0.2129 (Rfree = 0.000) for 4268 atoms. Found 91 (244 requested) and removed 49 (124 requested) atoms. Cycle 5: After refmac, R = 0.2056 (Rfree = 0.000) for 4294 atoms. Found 109 (240 requested) and removed 39 (125 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.92 1.97 NCS extension: 23 residues added (35 deleted due to clashes), 4391 seeds are put forward Round 1: 439 peptides, 7 chains. Longest chain 152 peptides. Score 0.943 Round 2: 440 peptides, 5 chains. Longest chain 152 peptides. Score 0.949 Round 3: 439 peptides, 5 chains. Longest chain 152 peptides. Score 0.949 Round 4: 439 peptides, 5 chains. Longest chain 152 peptides. Score 0.949 Round 5: 436 peptides, 6 chains. Longest chain 125 peptides. Score 0.945 Taking the results from Round 4 Chains 7, Residues 434, Estimated correctness of the model 99.8 % 6 chains (432 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 93 A and 98 A Built loop between residues 31 C and 40 C 4 chains (444 residues) following loop building 4 chains (444 residues) in sequence following loop building ------------------------------------------------------ 62685 reflections ( 99.49 % complete ) and 4192 restraints for refining 4189 atoms. 706 conditional restraints added. Observations/parameters ratio is 3.74 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2239 (Rfree = 0.000) for 4189 atoms. Found 167 (234 requested) and removed 94 (122 requested) atoms. Cycle 7: After refmac, R = 0.2115 (Rfree = 0.000) for 4256 atoms. Found 115 (232 requested) and removed 51 (123 requested) atoms. Cycle 8: After refmac, R = 0.2041 (Rfree = 0.000) for 4317 atoms. Found 121 (236 requested) and removed 43 (125 requested) atoms. Cycle 9: After refmac, R = 0.1998 (Rfree = 0.000) for 4386 atoms. Found 98 (240 requested) and removed 55 (127 requested) atoms. Cycle 10: After refmac, R = 0.1943 (Rfree = 0.000) for 4423 atoms. Found 97 (236 requested) and removed 63 (128 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.91 1.96 NCS extension: 14 residues added (25 deleted due to clashes), 4475 seeds are put forward Round 1: 444 peptides, 6 chains. Longest chain 152 peptides. Score 0.948 Round 2: 448 peptides, 4 chains. Longest chain 238 peptides. Score 0.955 Round 3: 447 peptides, 5 chains. Longest chain 152 peptides. Score 0.952 Round 4: 449 peptides, 3 chains. Longest chain 301 peptides. Score 0.958 Round 5: 446 peptides, 7 chains. Longest chain 125 peptides. Score 0.946 Taking the results from Round 4 Chains 8, Residues 446, Estimated correctness of the model 99.9 % 5 chains (439 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 31 C and 35 C 7 chains (449 residues) following loop building 4 chains (442 residues) in sequence following loop building ------------------------------------------------------ 62685 reflections ( 99.49 % complete ) and 4184 restraints for refining 4230 atoms. 693 conditional restraints added. Observations/parameters ratio is 3.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2160 (Rfree = 0.000) for 4230 atoms. Found 188 (221 requested) and removed 92 (123 requested) atoms. Cycle 12: After refmac, R = 0.2083 (Rfree = 0.000) for 4317 atoms. Found 120 (226 requested) and removed 63 (125 requested) atoms. Cycle 13: After refmac, R = 0.2004 (Rfree = 0.000) for 4368 atoms. Found 109 (224 requested) and removed 41 (127 requested) atoms. Cycle 14: After refmac, R = 0.1962 (Rfree = 0.000) for 4427 atoms. Found 115 (227 requested) and removed 68 (129 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1950 (Rfree = 0.000) for 4459 atoms. Found 110 (224 requested) and removed 64 (130 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.92 1.97 NCS extension: 13 residues added (20 deleted due to clashes), 4520 seeds are put forward Round 1: 443 peptides, 7 chains. Longest chain 152 peptides. Score 0.945 Round 2: 446 peptides, 5 chains. Longest chain 152 peptides. Score 0.951 Round 3: 445 peptides, 6 chains. Longest chain 152 peptides. Score 0.948 Round 4: 448 peptides, 6 chains. Longest chain 152 peptides. Score 0.949 Round 5: 445 peptides, 6 chains. Longest chain 152 peptides. Score 0.948 Taking the results from Round 2 Chains 5, Residues 441, Estimated correctness of the model 99.8 % 5 chains (441 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 100 A Built loop between residues 31 C and 35 C 3 chains (446 residues) following loop building 3 chains (446 residues) in sequence following loop building ------------------------------------------------------ 62685 reflections ( 99.49 % complete ) and 4201 restraints for refining 4256 atoms. 698 conditional restraints added. Observations/parameters ratio is 3.68 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2137 (Rfree = 0.000) for 4256 atoms. Found 195 (207 requested) and removed 83 (123 requested) atoms. Cycle 17: After refmac, R = 0.2071 (Rfree = 0.000) for 4359 atoms. Found 125 (213 requested) and removed 76 (127 requested) atoms. Cycle 18: After refmac, R = 0.2008 (Rfree = 0.000) for 4397 atoms. Found 103 (210 requested) and removed 49 (128 requested) atoms. Cycle 19: After refmac, R = 0.1953 (Rfree = 0.000) for 4438 atoms. Found 114 (212 requested) and removed 50 (129 requested) atoms. Cycle 20: After refmac, R = 0.1929 (Rfree = 0.000) for 4493 atoms. Found 104 (215 requested) and removed 60 (131 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.92 1.97 NCS extension: 7 residues added (34 deleted due to clashes), 4547 seeds are put forward Round 1: 445 peptides, 7 chains. Longest chain 152 peptides. Score 0.945 Round 2: 448 peptides, 5 chains. Longest chain 152 peptides. Score 0.952 Round 3: 448 peptides, 5 chains. Longest chain 152 peptides. Score 0.952 Round 4: 447 peptides, 5 chains. Longest chain 152 peptides. Score 0.952 Round 5: 449 peptides, 5 chains. Longest chain 152 peptides. Score 0.953 Taking the results from Round 5 Chains 5, Residues 444, Estimated correctness of the model 99.9 % 5 chains (444 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 A and 46 A Built loop between residues 94 A and 97 A 3 chains (448 residues) following loop building 3 chains (448 residues) in sequence following loop building ------------------------------------------------------ 62685 reflections ( 99.49 % complete ) and 4212 restraints for refining 4263 atoms. 694 conditional restraints added. Observations/parameters ratio is 3.68 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2115 (Rfree = 0.000) for 4263 atoms. Found 198 (198 requested) and removed 86 (124 requested) atoms. Cycle 22: After refmac, R = 0.2039 (Rfree = 0.000) for 4366 atoms. Found 126 (203 requested) and removed 71 (127 requested) atoms. Cycle 23: After refmac, R = 0.1970 (Rfree = 0.000) for 4417 atoms. Found 133 (200 requested) and removed 52 (128 requested) atoms. Cycle 24: After refmac, R = 0.1945 (Rfree = 0.000) for 4490 atoms. Found 100 (204 requested) and removed 86 (130 requested) atoms. Cycle 25: After refmac, R = 0.1926 (Rfree = 0.000) for 4495 atoms. Found 130 (199 requested) and removed 76 (131 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.92 1.97 NCS extension: 16 residues added (39 deleted due to clashes), 4566 seeds are put forward Round 1: 445 peptides, 6 chains. Longest chain 152 peptides. Score 0.948 Round 2: 449 peptides, 5 chains. Longest chain 152 peptides. Score 0.953 Round 3: 446 peptides, 6 chains. Longest chain 152 peptides. Score 0.949 Round 4: 447 peptides, 6 chains. Longest chain 152 peptides. Score 0.949 Round 5: 448 peptides, 6 chains. Longest chain 152 peptides. Score 0.949 Taking the results from Round 2 Chains 6, Residues 444, Estimated correctness of the model 99.9 % 5 chains (443 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 94 A and 97 A Built loop between residues 35 C and 40 C 4 chains (450 residues) following loop building 3 chains (449 residues) in sequence following loop building ------------------------------------------------------ 62685 reflections ( 99.49 % complete ) and 4179 restraints for refining 4272 atoms. 647 conditional restraints added. Observations/parameters ratio is 3.67 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2105 (Rfree = 0.000) for 4272 atoms. Found 179 (184 requested) and removed 79 (124 requested) atoms. Cycle 27: After refmac, R = 0.2037 (Rfree = 0.000) for 4358 atoms. Found 135 (188 requested) and removed 66 (127 requested) atoms. Cycle 28: After refmac, R = 0.1977 (Rfree = 0.000) for 4424 atoms. Found 109 (190 requested) and removed 73 (128 requested) atoms. Cycle 29: After refmac, R = 0.1940 (Rfree = 0.000) for 4452 atoms. Found 125 (186 requested) and removed 65 (129 requested) atoms. Cycle 30: After refmac, R = 0.1926 (Rfree = 0.000) for 4500 atoms. Found 110 (183 requested) and removed 74 (131 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.92 1.97 NCS extension: 11 residues added (2 deleted due to clashes), 4549 seeds are put forward Round 1: 446 peptides, 6 chains. Longest chain 152 peptides. Score 0.949 Round 2: 450 peptides, 5 chains. Longest chain 152 peptides. Score 0.953 Round 3: 448 peptides, 5 chains. Longest chain 152 peptides. Score 0.952 Round 4: 450 peptides, 5 chains. Longest chain 152 peptides. Score 0.953 Round 5: 444 peptides, 8 chains. Longest chain 152 peptides. Score 0.942 Taking the results from Round 4 Chains 6, Residues 445, Estimated correctness of the model 99.9 % 5 chains (444 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 94 A and 97 A Built loop between residues 31 C and 35 C 4 chains (450 residues) following loop building 3 chains (449 residues) in sequence following loop building ------------------------------------------------------ 62685 reflections ( 99.49 % complete ) and 4183 restraints for refining 4265 atoms. 651 conditional restraints added. Observations/parameters ratio is 3.67 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2118 (Rfree = 0.000) for 4265 atoms. Found 169 (169 requested) and removed 78 (124 requested) atoms. Cycle 32: After refmac, R = 0.2027 (Rfree = 0.000) for 4349 atoms. Found 133 (172 requested) and removed 62 (126 requested) atoms. Cycle 33: After refmac, R = 0.1982 (Rfree = 0.000) for 4416 atoms. Found 109 (175 requested) and removed 57 (128 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1946 (Rfree = 0.000) for 4459 atoms. Found 91 (172 requested) and removed 48 (130 requested) atoms. Cycle 35: After refmac, R = 0.1917 (Rfree = 0.000) for 4490 atoms. Found 104 (168 requested) and removed 57 (131 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.92 1.97 NCS extension: 11 residues added (1 deleted due to clashes), 4549 seeds are put forward Round 1: 445 peptides, 5 chains. Longest chain 152 peptides. Score 0.951 Round 2: 446 peptides, 5 chains. Longest chain 152 peptides. Score 0.951 Round 3: 448 peptides, 5 chains. Longest chain 152 peptides. Score 0.952 Round 4: 447 peptides, 5 chains. Longest chain 152 peptides. Score 0.952 Round 5: 448 peptides, 6 chains. Longest chain 152 peptides. Score 0.949 Taking the results from Round 4 Chains 6, Residues 442, Estimated correctness of the model 99.9 % 5 chains (441 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 85 A Built loop between residues 31 C and 35 C 4 chains (448 residues) following loop building 4 chains (448 residues) in sequence following loop building ------------------------------------------------------ 62685 reflections ( 99.49 % complete ) and 4194 restraints for refining 4261 atoms. 682 conditional restraints added. Observations/parameters ratio is 3.68 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2105 (Rfree = 0.000) for 4261 atoms. Found 154 (154 requested) and removed 70 (124 requested) atoms. Cycle 37: After refmac, R = 0.2030 (Rfree = 0.000) for 4339 atoms. Found 124 (156 requested) and removed 38 (126 requested) atoms. Cycle 38: After refmac, R = 0.1977 (Rfree = 0.000) for 4417 atoms. Found 108 (159 requested) and removed 58 (128 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1940 (Rfree = 0.000) for 4453 atoms. Found 113 (155 requested) and removed 60 (129 requested) atoms. Cycle 40: After refmac, R = 0.1914 (Rfree = 0.000) for 4495 atoms. Found 112 (152 requested) and removed 54 (131 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.92 1.97 NCS extension: 8 residues added (30 deleted due to clashes), 4565 seeds are put forward Round 1: 441 peptides, 8 chains. Longest chain 124 peptides. Score 0.941 Round 2: 448 peptides, 5 chains. Longest chain 152 peptides. Score 0.952 Round 3: 449 peptides, 4 chains. Longest chain 152 peptides. Score 0.955 Round 4: 450 peptides, 4 chains. Longest chain 152 peptides. Score 0.956 Round 5: 444 peptides, 8 chains. Longest chain 130 peptides. Score 0.942 Taking the results from Round 4 Chains 4, Residues 446, Estimated correctness of the model 99.9 % 4 chains (446 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 94 A and 97 A 3 chains (448 residues) following loop building 3 chains (448 residues) in sequence following loop building ------------------------------------------------------ 62685 reflections ( 99.49 % complete ) and 4185 restraints for refining 4295 atoms. 665 conditional restraints added. Observations/parameters ratio is 3.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2104 (Rfree = 0.000) for 4295 atoms. Found 145 (145 requested) and removed 70 (125 requested) atoms. Cycle 42: After refmac, R = 0.2021 (Rfree = 0.000) for 4359 atoms. Found 132 (147 requested) and removed 40 (127 requested) atoms. Cycle 43: After refmac, R = 0.1970 (Rfree = 0.000) for 4440 atoms. Found 118 (150 requested) and removed 61 (129 requested) atoms. Cycle 44: After refmac, R = 0.1932 (Rfree = 0.000) for 4488 atoms. Found 114 (146 requested) and removed 60 (130 requested) atoms. Cycle 45: After refmac, R = 0.1916 (Rfree = 0.000) for 4531 atoms. Found 97 (143 requested) and removed 69 (132 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.92 1.97 NCS extension: 15 residues added (41 deleted due to clashes), 4575 seeds are put forward Round 1: 443 peptides, 6 chains. Longest chain 152 peptides. Score 0.948 Round 2: 444 peptides, 6 chains. Longest chain 152 peptides. Score 0.948 Round 3: 445 peptides, 5 chains. Longest chain 152 peptides. Score 0.951 Round 4: 444 peptides, 6 chains. Longest chain 152 peptides. Score 0.948 Round 5: 439 peptides, 6 chains. Longest chain 152 peptides. Score 0.946 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 440, Estimated correctness of the model 99.8 % 5 chains (439 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 81 A and 85 A Built loop between residues 30 C and 35 C 4 chains (447 residues) following loop building 4 chains (447 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 62685 reflections ( 99.49 % complete ) and 3503 restraints for refining 3446 atoms. Observations/parameters ratio is 4.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2628 (Rfree = 0.000) for 3446 atoms. Found 94 (104 requested) and removed 0 (104 requested) atoms. Cycle 47: After refmac, R = 0.2493 (Rfree = 0.000) for 3446 atoms. Found 36 (107 requested) and removed 1 (103 requested) atoms. Cycle 48: After refmac, R = 0.2311 (Rfree = 0.000) for 3446 atoms. Found 33 (108 requested) and removed 1 (104 requested) atoms. Cycle 49: After refmac, R = 0.2226 (Rfree = 0.000) for 3446 atoms. Found 16 (109 requested) and removed 10 (105 requested) atoms. Writing output files ... TimeTaking 78.32