Mon 24 Dec 07:26:50 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 1vmf-1.7-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vmf-1.7-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vmf-1.7-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-1.7-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/1vmf-1.7-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-1.7-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 07:26:55 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/1vmf-1.7-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vmf-1.7-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 470 and 0 Target number of residues in the AU: 470 Target solvent content: 0.4405 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 435 Adjusted target solvent content: 0.48 Input MTZ file: 1vmf-1.7-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: 19 Cell parameters: 57.443 58.601 135.061 90.000 90.000 90.000 Input sequence file: 1vmf-1.7-parrot-noncs.fasta_lf Building free atoms model in initial map for 3480 target number of atoms Had to go as low as 0.25 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: 67.531 1.730 Wilson plot Bfac: 13.04 48424 reflections ( 99.96 % complete ) and 0 restraints for refining 3861 atoms. Observations/parameters ratio is 3.14 ------------------------------------------------------ Starting model: R = 0.3025 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2558 (Rfree = 0.000) for 3861 atoms. Found 199 (199 requested) and removed 102 (99 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.68 1.73 NCS extension: 0 residues added, 3958 seeds are put forward Round 1: 357 peptides, 24 chains. Longest chain 54 peptides. Score 0.851 Round 2: 385 peptides, 14 chains. Longest chain 65 peptides. Score 0.919 Round 3: 388 peptides, 9 chains. Longest chain 100 peptides. Score 0.938 Round 4: 395 peptides, 11 chains. Longest chain 122 peptides. Score 0.935 Round 5: 396 peptides, 8 chains. Longest chain 123 peptides. Score 0.945 Taking the results from Round 5 Chains 8, Residues 388, Estimated correctness of the model 99.8 % 4 chains (346 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 111 C and 115 C 7 chains (391 residues) following loop building 3 chains (349 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4096 restraints for refining 3651 atoms. 1117 conditional restraints added. Observations/parameters ratio is 3.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2660 (Rfree = 0.000) for 3651 atoms. Found 165 (189 requested) and removed 77 (94 requested) atoms. Cycle 2: After refmac, R = 0.2450 (Rfree = 0.000) for 3729 atoms. Found 115 (193 requested) and removed 21 (96 requested) atoms. Cycle 3: After refmac, R = 0.2184 (Rfree = 0.000) for 3819 atoms. Found 120 (198 requested) and removed 24 (99 requested) atoms. Cycle 4: After refmac, R = 0.2051 (Rfree = 0.000) for 3904 atoms. Found 102 (202 requested) and removed 34 (101 requested) atoms. Cycle 5: After refmac, R = 0.1964 (Rfree = 0.000) for 3955 atoms. Found 103 (205 requested) and removed 36 (102 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.66 1.70 NCS extension: 4 residues added (13 deleted due to clashes), 4027 seeds are put forward Round 1: 399 peptides, 6 chains. Longest chain 121 peptides. Score 0.953 Round 2: 399 peptides, 8 chains. Longest chain 120 peptides. Score 0.946 Round 3: 399 peptides, 8 chains. Longest chain 121 peptides. Score 0.946 Round 4: 399 peptides, 8 chains. Longest chain 120 peptides. Score 0.946 Round 5: 395 peptides, 11 chains. Longest chain 120 peptides. Score 0.935 Taking the results from Round 1 Chains 6, Residues 393, Estimated correctness of the model 99.8 % 4 chains (371 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 129 B and 133 B 5 chains (396 residues) following loop building 3 chains (374 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4053 restraints for refining 3842 atoms. 934 conditional restraints added. Observations/parameters ratio is 3.15 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2035 (Rfree = 0.000) for 3842 atoms. Found 160 (198 requested) and removed 55 (99 requested) atoms. Cycle 7: After refmac, R = 0.1915 (Rfree = 0.000) for 3938 atoms. Found 119 (204 requested) and removed 54 (102 requested) atoms. Cycle 8: After refmac, R = 0.1848 (Rfree = 0.000) for 3995 atoms. Found 113 (207 requested) and removed 53 (103 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1805 (Rfree = 0.000) for 4043 atoms. Found 112 (210 requested) and removed 56 (105 requested) atoms. Cycle 10: After refmac, R = 0.1770 (Rfree = 0.000) for 4088 atoms. Found 115 (212 requested) and removed 65 (106 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.66 1.70 NCS extension: 9 residues added (19 deleted due to clashes), 4148 seeds are put forward Round 1: 395 peptides, 8 chains. Longest chain 121 peptides. Score 0.945 Round 2: 394 peptides, 7 chains. Longest chain 121 peptides. Score 0.948 Round 3: 393 peptides, 10 chains. Longest chain 121 peptides. Score 0.937 Round 4: 392 peptides, 8 chains. Longest chain 121 peptides. Score 0.944 Round 5: 396 peptides, 8 chains. Longest chain 121 peptides. Score 0.945 Taking the results from Round 2 Chains 7, Residues 387, Estimated correctness of the model 99.8 % 4 chains (356 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 111 C and 115 C 6 chains (390 residues) following loop building 3 chains (359 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4261 restraints for refining 3882 atoms. 1231 conditional restraints added. Observations/parameters ratio is 3.12 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1928 (Rfree = 0.000) for 3882 atoms. Found 173 (197 requested) and removed 55 (100 requested) atoms. Cycle 12: After refmac, R = 0.1867 (Rfree = 0.000) for 3986 atoms. Found 109 (203 requested) and removed 59 (103 requested) atoms. Cycle 13: After refmac, R = 0.1800 (Rfree = 0.000) for 4030 atoms. Found 108 (201 requested) and removed 46 (104 requested) atoms. Cycle 14: After refmac, R = 0.1759 (Rfree = 0.000) for 4083 atoms. Found 107 (203 requested) and removed 49 (105 requested) atoms. Cycle 15: After refmac, R = 0.1734 (Rfree = 0.000) for 4130 atoms. Found 104 (205 requested) and removed 54 (107 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.65 1.69 NCS extension: 2 residues added (1 deleted due to clashes), 4182 seeds are put forward Round 1: 392 peptides, 8 chains. Longest chain 119 peptides. Score 0.944 Round 2: 392 peptides, 11 chains. Longest chain 121 peptides. Score 0.933 Round 3: 393 peptides, 8 chains. Longest chain 120 peptides. Score 0.944 Round 4: 389 peptides, 10 chains. Longest chain 121 peptides. Score 0.935 Round 5: 394 peptides, 9 chains. Longest chain 121 peptides. Score 0.941 Taking the results from Round 3 Chains 8, Residues 385, Estimated correctness of the model 99.8 % 5 chains (351 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 59 A and 62 A Built loop between residues 111 C and 115 C 6 chains (390 residues) following loop building 3 chains (356 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4310 restraints for refining 3903 atoms. 1294 conditional restraints added. Observations/parameters ratio is 3.10 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1877 (Rfree = 0.000) for 3903 atoms. Found 176 (190 requested) and removed 41 (101 requested) atoms. Cycle 17: After refmac, R = 0.1832 (Rfree = 0.000) for 4030 atoms. Found 110 (196 requested) and removed 53 (104 requested) atoms. Cycle 18: After refmac, R = 0.1770 (Rfree = 0.000) for 4077 atoms. Found 107 (198 requested) and removed 45 (105 requested) atoms. Cycle 19: After refmac, R = 0.1745 (Rfree = 0.000) for 4132 atoms. Found 107 (201 requested) and removed 67 (107 requested) atoms. Cycle 20: After refmac, R = 0.1736 (Rfree = 0.000) for 4163 atoms. Found 111 (199 requested) and removed 71 (108 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.65 1.69 NCS extension: 0 residues added, 4203 seeds are put forward Round 1: 395 peptides, 9 chains. Longest chain 121 peptides. Score 0.942 Round 2: 392 peptides, 8 chains. Longest chain 119 peptides. Score 0.944 Round 3: 390 peptides, 11 chains. Longest chain 123 peptides. Score 0.932 Round 4: 396 peptides, 7 chains. Longest chain 122 peptides. Score 0.948 Round 5: 398 peptides, 6 chains. Longest chain 122 peptides. Score 0.952 Taking the results from Round 5 Chains 6, Residues 392, Estimated correctness of the model 99.8 % 3 chains (358 residues) have been docked in sequence Building loops using Loopy2018 6 chains (392 residues) following loop building 3 chains (358 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4243 restraints for refining 3917 atoms. 1208 conditional restraints added. Observations/parameters ratio is 3.09 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1892 (Rfree = 0.000) for 3917 atoms. Found 182 (182 requested) and removed 47 (101 requested) atoms. Cycle 22: After refmac, R = 0.1833 (Rfree = 0.000) for 4035 atoms. Found 117 (188 requested) and removed 61 (104 requested) atoms. Cycle 23: After refmac, R = 0.1770 (Rfree = 0.000) for 4087 atoms. Found 109 (186 requested) and removed 55 (105 requested) atoms. Cycle 24: After refmac, R = 0.1742 (Rfree = 0.000) for 4131 atoms. Found 100 (184 requested) and removed 62 (107 requested) atoms. Cycle 25: After refmac, R = 0.1723 (Rfree = 0.000) for 4159 atoms. Found 105 (181 requested) and removed 67 (107 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.66 1.70 NCS extension: 0 residues added, 4197 seeds are put forward Round 1: 396 peptides, 7 chains. Longest chain 121 peptides. Score 0.948 Round 2: 390 peptides, 11 chains. Longest chain 101 peptides. Score 0.932 Round 3: 392 peptides, 8 chains. Longest chain 122 peptides. Score 0.944 Round 4: 395 peptides, 9 chains. Longest chain 122 peptides. Score 0.942 Round 5: 393 peptides, 11 chains. Longest chain 100 peptides. Score 0.934 Taking the results from Round 1 Chains 7, Residues 389, Estimated correctness of the model 99.8 % 5 chains (367 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 111 C and 115 C Built loop between residues 129 B and 133 B 5 chains (395 residues) following loop building 3 chains (373 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4080 restraints for refining 3922 atoms. 972 conditional restraints added. Observations/parameters ratio is 3.09 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1870 (Rfree = 0.000) for 3922 atoms. Found 166 (166 requested) and removed 47 (101 requested) atoms. Cycle 27: After refmac, R = 0.1814 (Rfree = 0.000) for 4025 atoms. Found 121 (171 requested) and removed 61 (104 requested) atoms. Cycle 28: After refmac, R = 0.1771 (Rfree = 0.000) for 4075 atoms. Found 114 (169 requested) and removed 67 (105 requested) atoms. Cycle 29: After refmac, R = 0.1736 (Rfree = 0.000) for 4114 atoms. Found 103 (166 requested) and removed 69 (106 requested) atoms. Cycle 30: After refmac, R = 0.1732 (Rfree = 0.000) for 4140 atoms. Found 113 (163 requested) and removed 75 (107 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.65 1.69 NCS extension: 7 residues added (21 deleted due to clashes), 4185 seeds are put forward Round 1: 396 peptides, 8 chains. Longest chain 119 peptides. Score 0.945 Round 2: 393 peptides, 8 chains. Longest chain 120 peptides. Score 0.944 Round 3: 393 peptides, 7 chains. Longest chain 120 peptides. Score 0.947 Round 4: 396 peptides, 8 chains. Longest chain 123 peptides. Score 0.945 Round 5: 395 peptides, 8 chains. Longest chain 123 peptides. Score 0.945 Taking the results from Round 3 Chains 7, Residues 386, Estimated correctness of the model 99.8 % 4 chains (357 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 88 A and 91 A 6 chains (388 residues) following loop building 3 chains (359 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4231 restraints for refining 3881 atoms. 1212 conditional restraints added. Observations/parameters ratio is 3.12 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1907 (Rfree = 0.000) for 3881 atoms. Found 149 (149 requested) and removed 63 (100 requested) atoms. Cycle 32: After refmac, R = 0.1823 (Rfree = 0.000) for 3952 atoms. Found 125 (152 requested) and removed 35 (102 requested) atoms. Cycle 33: After refmac, R = 0.1762 (Rfree = 0.000) for 4036 atoms. Found 106 (155 requested) and removed 46 (104 requested) atoms. Cycle 34: After refmac, R = 0.1739 (Rfree = 0.000) for 4091 atoms. Found 85 (157 requested) and removed 67 (106 requested) atoms. Cycle 35: After refmac, R = 0.1716 (Rfree = 0.000) for 4099 atoms. Found 107 (153 requested) and removed 62 (106 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.65 1.69 NCS extension: 1 residues added (2 deleted due to clashes), 4145 seeds are put forward Round 1: 394 peptides, 7 chains. Longest chain 120 peptides. Score 0.948 Round 2: 393 peptides, 8 chains. Longest chain 122 peptides. Score 0.944 Round 3: 394 peptides, 9 chains. Longest chain 122 peptides. Score 0.941 Round 4: 394 peptides, 8 chains. Longest chain 122 peptides. Score 0.944 Round 5: 397 peptides, 7 chains. Longest chain 133 peptides. Score 0.949 Taking the results from Round 5 Chains 7, Residues 390, Estimated correctness of the model 99.8 % 5 chains (367 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 55 C and 58 C Built loop between residues 111 C and 115 C 5 chains (395 residues) following loop building 3 chains (372 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 48424 reflections ( 99.96 % complete ) and 4094 restraints for refining 3886 atoms. 986 conditional restraints added. Observations/parameters ratio is 3.12 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1896 (Rfree = 0.000) for 3886 atoms. Found 141 (141 requested) and removed 50 (100 requested) atoms. Cycle 37: After refmac, R = 0.1813 (Rfree = 0.000) for 3961 atoms. Found 119 (143 requested) and removed 42 (102 requested) atoms. Cycle 38: After refmac, R = 0.1778 (Rfree = 0.000) for 4034 atoms. Found 117 (146 requested) and removed 53 (104 requested) atoms. Cycle 39: After refmac, R = 0.1747 (Rfree = 0.000) for 4095 atoms. Found 113 (148 requested) and removed 70 (106 requested) atoms. Cycle 40: After refmac, R = 0.1745 (Rfree = 0.000) for 4123 atoms. Found 121 (146 requested) and removed 75 (107 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.65 1.69 NCS extension: 6 residues added (23 deleted due to clashes), 4175 seeds are put forward Round 1: 396 peptides, 7 chains. Longest chain 121 peptides. Score 0.948 Round 2: 397 peptides, 8 chains. Longest chain 122 peptides. Score 0.946 Round 3: 395 peptides, 9 chains. Longest chain 119 peptides. Score 0.942 Round 4: 397 peptides, 8 chains. Longest chain 122 peptides. Score 0.946 Round 5: 394 peptides, 10 chains. Longest chain 122 peptides. Score 0.938 Taking the results from Round 1 Chains 7, Residues 389, Estimated correctness of the model 99.8 % 5 chains (366 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 111 C and 115 C Built loop between residues 130 B and 133 B 5 chains (394 residues) following loop building 3 chains (371 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4146 restraints for refining 3929 atoms. 1046 conditional restraints added. Observations/parameters ratio is 3.08 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1888 (Rfree = 0.000) for 3929 atoms. Found 134 (134 requested) and removed 51 (101 requested) atoms. Cycle 42: After refmac, R = 0.1812 (Rfree = 0.000) for 3990 atoms. Found 125 (137 requested) and removed 35 (103 requested) atoms. Cycle 43: After refmac, R = 0.1763 (Rfree = 0.000) for 4077 atoms. Found 109 (139 requested) and removed 46 (105 requested) atoms. Cycle 44: After refmac, R = 0.1730 (Rfree = 0.000) for 4133 atoms. Found 89 (141 requested) and removed 72 (107 requested) atoms. Cycle 45: After refmac, R = 0.1704 (Rfree = 0.000) for 4137 atoms. Found 127 (137 requested) and removed 73 (107 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.65 1.69 NCS extension: 4 residues added (26 deleted due to clashes), 4195 seeds are put forward Round 1: 397 peptides, 7 chains. Longest chain 122 peptides. Score 0.949 Round 2: 392 peptides, 11 chains. Longest chain 86 peptides. Score 0.933 Round 3: 394 peptides, 8 chains. Longest chain 122 peptides. Score 0.944 Round 4: 395 peptides, 9 chains. Longest chain 122 peptides. Score 0.942 Round 5: 397 peptides, 7 chains. Longest chain 122 peptides. Score 0.949 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 390, Estimated correctness of the model 99.8 % 5 chains (367 residues) have been docked in sequence Sequence coverage is 93 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 111 C and 115 C Built loop between residues 130 B and 133 B 5 chains (395 residues) following loop building 3 chains (372 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 48424 reflections ( 99.96 % complete ) and 3108 restraints for refining 3048 atoms. Observations/parameters ratio is 3.97 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2686 (Rfree = 0.000) for 3048 atoms. Found 97 (97 requested) and removed 0 (97 requested) atoms. Cycle 47: After refmac, R = 0.2452 (Rfree = 0.000) for 3048 atoms. Found 92 (100 requested) and removed 1 (81 requested) atoms. Cycle 48: After refmac, R = 0.2289 (Rfree = 0.000) for 3048 atoms. Found 48 (104 requested) and removed 3 (83 requested) atoms. Cycle 49: After refmac, R = 0.2178 (Rfree = 0.000) for 3048 atoms. TimeTaking 60.52