Mon 24 Dec 07:30:23 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 2otm-1.9-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2otm-1.9-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2otm-1.9-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2otm-1.9-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/2otm-1.9-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2otm-1.9-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 07:30:28 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/noncs/ArpWArp/wArpResults/WorkingDir/2otm-1.9-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2otm-1.9-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 538 and 0 Target number of residues in the AU: 538 Target solvent content: 0.4738 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 462 Adjusted target solvent content: 0.55 Input MTZ file: 2otm-1.9-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: 5 Cell parameters: 112.035 62.893 78.663 90.000 93.262 90.000 Input sequence file: 2otm-1.9-parrot-noncs.fasta_lf Building free atoms model in initial map for 3696 target number of atoms Had to go as low as 0.45 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: 78.536 1.850 Wilson plot Bfac: 18.47 46757 reflections ( 99.95 % complete ) and 0 restraints for refining 4126 atoms. Observations/parameters ratio is 2.83 ------------------------------------------------------ Starting model: R = 0.3050 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2561 (Rfree = 0.000) for 4126 atoms. Found 176 (176 requested) and removed 88 (88 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.86 1.74 NCS extension: 0 residues added, 4214 seeds are put forward Round 1: 375 peptides, 33 chains. Longest chain 40 peptides. Score 0.766 Round 2: 406 peptides, 18 chains. Longest chain 65 peptides. Score 0.878 Round 3: 413 peptides, 15 chains. Longest chain 73 peptides. Score 0.895 Round 4: 422 peptides, 14 chains. Longest chain 106 peptides. Score 0.904 Round 5: 435 peptides, 8 chains. Longest chain 112 peptides. Score 0.932 Taking the results from Round 5 Chains 11, Residues 427, Estimated correctness of the model 99.6 % 7 chains (418 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 23 A and 30 A Built loop between residues 80 A and 83 A Built loop between residues 84 C and 91 C Built loop between residues 115 B and 120 B 6 chains (443 residues) following loop building 3 chains (436 residues) in sequence following loop building ------------------------------------------------------ 46757 reflections ( 99.95 % complete ) and 4018 restraints for refining 3980 atoms. 595 conditional restraints added. Observations/parameters ratio is 2.94 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2445 (Rfree = 0.000) for 3980 atoms. Found 149 (170 requested) and removed 83 (85 requested) atoms. Cycle 2: After refmac, R = 0.2066 (Rfree = 0.000) for 4035 atoms. Found 145 (170 requested) and removed 35 (86 requested) atoms. Cycle 3: After refmac, R = 0.1932 (Rfree = 0.000) for 4132 atoms. Found 119 (173 requested) and removed 56 (88 requested) atoms. Cycle 4: After refmac, R = 0.1846 (Rfree = 0.000) for 4180 atoms. Found 108 (175 requested) and removed 53 (89 requested) atoms. Cycle 5: After refmac, R = 0.1787 (Rfree = 0.000) for 4225 atoms. Found 107 (177 requested) and removed 70 (90 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.82 1.70 NCS extension: 1 residues added (11 deleted due to clashes), 4265 seeds are put forward Round 1: 448 peptides, 7 chains. Longest chain 90 peptides. Score 0.940 Round 2: 438 peptides, 8 chains. Longest chain 99 peptides. Score 0.933 Round 3: 450 peptides, 6 chains. Longest chain 148 peptides. Score 0.944 Round 4: 450 peptides, 5 chains. Longest chain 153 peptides. Score 0.947 Round 5: 448 peptides, 6 chains. Longest chain 99 peptides. Score 0.943 Taking the results from Round 4 Chains 7, Residues 445, Estimated correctness of the model 99.7 % 5 chains (440 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 86 C and 89 C Built loop between residues 84 B and 87 B 5 chains (449 residues) following loop building 3 chains (444 residues) in sequence following loop building ------------------------------------------------------ 46757 reflections ( 99.95 % complete ) and 4003 restraints for refining 4054 atoms. 523 conditional restraints added. Observations/parameters ratio is 2.88 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1885 (Rfree = 0.000) for 4054 atoms. Found 166 (166 requested) and removed 69 (86 requested) atoms. Cycle 7: After refmac, R = 0.1792 (Rfree = 0.000) for 4142 atoms. Found 120 (170 requested) and removed 78 (88 requested) atoms. Cycle 8: After refmac, R = 0.1720 (Rfree = 0.000) for 4181 atoms. Found 143 (167 requested) and removed 51 (89 requested) atoms. Cycle 9: After refmac, R = 0.1695 (Rfree = 0.000) for 4265 atoms. Found 102 (171 requested) and removed 88 (91 requested) atoms. Cycle 10: After refmac, R = 0.1657 (Rfree = 0.000) for 4273 atoms. Found 140 (168 requested) and removed 70 (91 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.82 1.70 NCS extension: 0 residues added (6 deleted due to clashes), 4344 seeds are put forward Round 1: 451 peptides, 5 chains. Longest chain 152 peptides. Score 0.947 Round 2: 450 peptides, 7 chains. Longest chain 150 peptides. Score 0.941 Round 3: 449 peptides, 7 chains. Longest chain 152 peptides. Score 0.941 Round 4: 448 peptides, 7 chains. Longest chain 142 peptides. Score 0.940 Round 5: 447 peptides, 6 chains. Longest chain 83 peptides. Score 0.943 Taking the results from Round 1 Chains 5, Residues 446, Estimated correctness of the model 99.7 % 5 chains (446 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 91 A and 94 A Built loop between residues 92 C and 95 C 3 chains (450 residues) following loop building 3 chains (450 residues) in sequence following loop building ------------------------------------------------------ 46757 reflections ( 99.95 % complete ) and 3991 restraints for refining 4071 atoms. 484 conditional restraints added. Observations/parameters ratio is 2.87 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1788 (Rfree = 0.000) for 4071 atoms. Found 160 (160 requested) and removed 64 (87 requested) atoms. Cycle 12: After refmac, R = 0.1714 (Rfree = 0.000) for 4156 atoms. Found 118 (164 requested) and removed 67 (89 requested) atoms. Cycle 13: After refmac, R = 0.1678 (Rfree = 0.000) for 4201 atoms. Found 114 (161 requested) and removed 60 (89 requested) atoms. Cycle 14: After refmac, R = 0.1646 (Rfree = 0.000) for 4247 atoms. Found 93 (160 requested) and removed 85 (91 requested) atoms. Cycle 15: After refmac, R = 0.1626 (Rfree = 0.000) for 4250 atoms. Found 115 (157 requested) and removed 73 (91 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.82 1.70 NCS extension: 0 residues added, 4292 seeds are put forward Round 1: 451 peptides, 5 chains. Longest chain 152 peptides. Score 0.947 Round 2: 453 peptides, 4 chains. Longest chain 152 peptides. Score 0.951 Round 3: 448 peptides, 7 chains. Longest chain 152 peptides. Score 0.940 Round 4: 450 peptides, 6 chains. Longest chain 150 peptides. Score 0.944 Round 5: 447 peptides, 9 chains. Longest chain 84 peptides. Score 0.934 Taking the results from Round 2 Chains 4, Residues 449, Estimated correctness of the model 99.8 % 4 chains (449 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 B and 51 B 3 chains (451 residues) following loop building 3 chains (451 residues) in sequence following loop building ------------------------------------------------------ 46757 reflections ( 99.95 % complete ) and 3987 restraints for refining 4077 atoms. 471 conditional restraints added. Observations/parameters ratio is 2.87 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1787 (Rfree = 0.000) for 4077 atoms. Found 146 (146 requested) and removed 54 (87 requested) atoms. Cycle 17: After refmac, R = 0.1701 (Rfree = 0.000) for 4160 atoms. Found 104 (150 requested) and removed 69 (89 requested) atoms. Cycle 18: After refmac, R = 0.1650 (Rfree = 0.000) for 4193 atoms. Found 112 (147 requested) and removed 51 (89 requested) atoms. Cycle 19: After refmac, R = 0.1634 (Rfree = 0.000) for 4247 atoms. Found 85 (148 requested) and removed 65 (90 requested) atoms. Cycle 20: After refmac, R = 0.1615 (Rfree = 0.000) for 4265 atoms. Found 102 (146 requested) and removed 62 (91 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.83 1.71 NCS extension: 1 residues added (2 deleted due to clashes), 4306 seeds are put forward Round 1: 449 peptides, 5 chains. Longest chain 151 peptides. Score 0.947 Round 2: 448 peptides, 6 chains. Longest chain 150 peptides. Score 0.943 Round 3: 451 peptides, 6 chains. Longest chain 151 peptides. Score 0.944 Round 4: 447 peptides, 7 chains. Longest chain 99 peptides. Score 0.940 Round 5: 452 peptides, 6 chains. Longest chain 151 peptides. Score 0.945 Taking the results from Round 1 Chains 5, Residues 444, Estimated correctness of the model 99.7 % 5 chains (444 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 93 C and 97 C Built loop between residues 113 C and 116 C 3 chains (449 residues) following loop building 3 chains (449 residues) in sequence following loop building ------------------------------------------------------ 46757 reflections ( 99.95 % complete ) and 4007 restraints for refining 4062 atoms. 509 conditional restraints added. Observations/parameters ratio is 2.88 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1781 (Rfree = 0.000) for 4062 atoms. Found 135 (135 requested) and removed 65 (86 requested) atoms. Cycle 22: After refmac, R = 0.1714 (Rfree = 0.000) for 4125 atoms. Found 113 (137 requested) and removed 64 (88 requested) atoms. Cycle 23: After refmac, R = 0.1665 (Rfree = 0.000) for 4169 atoms. Found 123 (135 requested) and removed 50 (89 requested) atoms. Cycle 24: After refmac, R = 0.1661 (Rfree = 0.000) for 4235 atoms. Found 102 (138 requested) and removed 80 (90 requested) atoms. Cycle 25: After refmac, R = 0.1639 (Rfree = 0.000) for 4254 atoms. Found 125 (135 requested) and removed 54 (91 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.83 1.71 NCS extension: 0 residues added, 4325 seeds are put forward Round 1: 450 peptides, 5 chains. Longest chain 151 peptides. Score 0.947 Round 2: 449 peptides, 5 chains. Longest chain 150 peptides. Score 0.947 Round 3: 452 peptides, 5 chains. Longest chain 152 peptides. Score 0.948 Round 4: 450 peptides, 5 chains. Longest chain 152 peptides. Score 0.947 Round 5: 445 peptides, 8 chains. Longest chain 83 peptides. Score 0.936 Taking the results from Round 3 Chains 5, Residues 447, Estimated correctness of the model 99.8 % 5 chains (447 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 84 A and 87 A Built loop between residues 86 C and 89 C 3 chains (451 residues) following loop building 3 chains (451 residues) in sequence following loop building ------------------------------------------------------ 46757 reflections ( 99.95 % complete ) and 3970 restraints for refining 4097 atoms. 455 conditional restraints added. Observations/parameters ratio is 2.85 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1778 (Rfree = 0.000) for 4097 atoms. Found 129 (129 requested) and removed 58 (87 requested) atoms. Cycle 27: After refmac, R = 0.1708 (Rfree = 0.000) for 4158 atoms. Found 97 (132 requested) and removed 63 (89 requested) atoms. Cycle 28: After refmac, R = 0.1653 (Rfree = 0.000) for 4181 atoms. Found 116 (129 requested) and removed 45 (89 requested) atoms. Cycle 29: After refmac, R = 0.1635 (Rfree = 0.000) for 4248 atoms. Found 83 (130 requested) and removed 79 (90 requested) atoms. Cycle 30: After refmac, R = 0.1619 (Rfree = 0.000) for 4248 atoms. Found 104 (127 requested) and removed 56 (90 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.83 1.71 NCS extension: 0 residues added, 4296 seeds are put forward Round 1: 449 peptides, 6 chains. Longest chain 152 peptides. Score 0.944 Round 2: 450 peptides, 6 chains. Longest chain 149 peptides. Score 0.944 Round 3: 451 peptides, 5 chains. Longest chain 150 peptides. Score 0.947 Round 4: 448 peptides, 6 chains. Longest chain 149 peptides. Score 0.943 Round 5: 444 peptides, 8 chains. Longest chain 79 peptides. Score 0.936 Taking the results from Round 3 Chains 5, Residues 446, Estimated correctness of the model 99.7 % 5 chains (446 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 C and 84 C Built loop between residues 84 B and 87 B 3 chains (450 residues) following loop building 3 chains (450 residues) in sequence following loop building ------------------------------------------------------ 46757 reflections ( 99.95 % complete ) and 3993 restraints for refining 4069 atoms. 486 conditional restraints added. Observations/parameters ratio is 2.87 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1768 (Rfree = 0.000) for 4069 atoms. Found 118 (118 requested) and removed 55 (87 requested) atoms. Cycle 32: After refmac, R = 0.1696 (Rfree = 0.000) for 4126 atoms. Found 113 (120 requested) and removed 49 (88 requested) atoms. Cycle 33: After refmac, R = 0.1658 (Rfree = 0.000) for 4185 atoms. Found 106 (122 requested) and removed 63 (89 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1629 (Rfree = 0.000) for 4221 atoms. Found 107 (119 requested) and removed 69 (90 requested) atoms. Cycle 35: After refmac, R = 0.1610 (Rfree = 0.000) for 4255 atoms. Found 105 (116 requested) and removed 66 (91 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.83 1.71 NCS extension: 0 residues added, 4294 seeds are put forward Round 1: 445 peptides, 7 chains. Longest chain 151 peptides. Score 0.939 Round 2: 450 peptides, 6 chains. Longest chain 150 peptides. Score 0.944 Round 3: 448 peptides, 6 chains. Longest chain 151 peptides. Score 0.943 Round 4: 446 peptides, 5 chains. Longest chain 146 peptides. Score 0.946 Round 5: 442 peptides, 7 chains. Longest chain 126 peptides. Score 0.938 Taking the results from Round 4 Chains 5, Residues 441, Estimated correctness of the model 99.7 % 5 chains (441 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 A and 86 A Built loop between residues 84 B and 87 B 3 chains (446 residues) following loop building 3 chains (446 residues) in sequence following loop building ------------------------------------------------------ 46757 reflections ( 99.95 % complete ) and 4040 restraints for refining 4080 atoms. 563 conditional restraints added. Observations/parameters ratio is 2.87 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1764 (Rfree = 0.000) for 4080 atoms. Found 108 (108 requested) and removed 48 (87 requested) atoms. Cycle 37: After refmac, R = 0.1694 (Rfree = 0.000) for 4126 atoms. Found 110 (110 requested) and removed 38 (88 requested) atoms. Cycle 38: After refmac, R = 0.1643 (Rfree = 0.000) for 4191 atoms. Found 111 (111 requested) and removed 46 (89 requested) atoms. Cycle 39: After refmac, R = 0.1610 (Rfree = 0.000) for 4251 atoms. Found 94 (113 requested) and removed 62 (91 requested) atoms. Cycle 40: After refmac, R = 0.1592 (Rfree = 0.000) for 4276 atoms. Found 105 (110 requested) and removed 61 (91 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.82 1.70 NCS extension: 1 residues added (5 deleted due to clashes), 4321 seeds are put forward Round 1: 449 peptides, 6 chains. Longest chain 151 peptides. Score 0.944 Round 2: 450 peptides, 5 chains. Longest chain 151 peptides. Score 0.947 Round 3: 450 peptides, 6 chains. Longest chain 83 peptides. Score 0.944 Round 4: 450 peptides, 6 chains. Longest chain 126 peptides. Score 0.944 Round 5: 444 peptides, 7 chains. Longest chain 83 peptides. Score 0.939 Taking the results from Round 2 Chains 5, Residues 445, Estimated correctness of the model 99.7 % 4 chains (441 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 77 C and 86 C 3 chains (449 residues) following loop building 3 chains (449 residues) in sequence following loop building ------------------------------------------------------ 46757 reflections ( 99.95 % complete ) and 4024 restraints for refining 4080 atoms. 525 conditional restraints added. Observations/parameters ratio is 2.87 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1762 (Rfree = 0.000) for 4080 atoms. Found 101 (101 requested) and removed 60 (87 requested) atoms. Cycle 42: After refmac, R = 0.1678 (Rfree = 0.000) for 4113 atoms. Found 99 (99 requested) and removed 30 (88 requested) atoms. Cycle 43: After refmac, R = 0.1638 (Rfree = 0.000) for 4175 atoms. Found 100 (100 requested) and removed 44 (89 requested) atoms. Cycle 44: After refmac, R = 0.1605 (Rfree = 0.000) for 4224 atoms. Found 100 (101 requested) and removed 60 (90 requested) atoms. Cycle 45: After refmac, R = 0.1589 (Rfree = 0.000) for 4259 atoms. Found 98 (98 requested) and removed 66 (91 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.82 1.70 NCS extension: 0 residues added, 4291 seeds are put forward Round 1: 449 peptides, 5 chains. Longest chain 151 peptides. Score 0.947 Round 2: 444 peptides, 6 chains. Longest chain 105 peptides. Score 0.942 Round 3: 448 peptides, 5 chains. Longest chain 147 peptides. Score 0.946 Round 4: 447 peptides, 6 chains. Longest chain 151 peptides. Score 0.943 Round 5: 449 peptides, 7 chains. Longest chain 152 peptides. Score 0.941 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 444, Estimated correctness of the model 99.7 % 5 chains (444 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 92 C and 95 C Built loop between residues 91 B and 94 B 3 chains (448 residues) following loop building 3 chains (448 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 46757 reflections ( 99.95 % complete ) and 3492 restraints for refining 3426 atoms. Observations/parameters ratio is 3.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2319 (Rfree = 0.000) for 3426 atoms. Found 76 (76 requested) and removed 0 (76 requested) atoms. Cycle 47: After refmac, R = 0.2142 (Rfree = 0.000) for 3426 atoms. Found 77 (77 requested) and removed 1 (74 requested) atoms. Cycle 48: After refmac, R = 0.1982 (Rfree = 0.000) for 3426 atoms. Found 54 (80 requested) and removed 2 (76 requested) atoms. Cycle 49: After refmac, R = 0.1875 (Rfree = 0.000) for 3426 atoms. TimeTaking 58.88