Sun 23 Dec 22:22:41 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vmf-1.7-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vmf-1.7-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vmf-1.7-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-1.7-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-1.7-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-1.7-parrot-hancs ############### 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 22:22:50 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/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-1.7-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmf-1.7-parrot-hancs/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-hancs.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-hancs.fasta_lf Building free atoms model in initial map for 3480 target number of atoms Had to go as low as 0.30 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 3858 atoms. Observations/parameters ratio is 3.14 ------------------------------------------------------ Starting model: R = 0.3040 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2563 (Rfree = 0.000) for 3858 atoms. Found 199 (199 requested) and removed 101 (99 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.68 1.73 NCS extension: 0 residues added, 3956 seeds are put forward Round 1: 375 peptides, 21 chains. Longest chain 51 peptides. Score 0.883 Round 2: 380 peptides, 10 chains. Longest chain 100 peptides. Score 0.931 Round 3: 396 peptides, 7 chains. Longest chain 120 peptides. Score 0.948 Round 4: 389 peptides, 11 chains. Longest chain 87 peptides. Score 0.932 Round 5: 392 peptides, 8 chains. Longest chain 120 peptides. Score 0.944 Taking the results from Round 3 Chains 7, Residues 389, Estimated correctness of the model 99.8 % 3 chains (357 residues) have been docked in sequence Building loops using Loopy2018 7 chains (389 residues) following loop building 3 chains (357 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4026 restraints for refining 3656 atoms. 1015 conditional restraints added. Observations/parameters ratio is 3.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2595 (Rfree = 0.000) for 3656 atoms. Found 148 (189 requested) and removed 60 (94 requested) atoms. Cycle 2: After refmac, R = 0.2353 (Rfree = 0.000) for 3736 atoms. Found 121 (193 requested) and removed 31 (96 requested) atoms. Cycle 3: After refmac, R = 0.2087 (Rfree = 0.000) for 3814 atoms. Found 114 (198 requested) and removed 24 (99 requested) atoms. Cycle 4: After refmac, R = 0.1972 (Rfree = 0.000) for 3896 atoms. Found 95 (202 requested) and removed 27 (101 requested) atoms. Cycle 5: After refmac, R = 0.1891 (Rfree = 0.000) for 3955 atoms. Found 105 (205 requested) and removed 47 (102 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.66 1.70 NCS extension: 0 residues added, 4014 seeds are put forward Round 1: 397 peptides, 7 chains. Longest chain 120 peptides. Score 0.949 Round 2: 397 peptides, 8 chains. Longest chain 121 peptides. Score 0.946 Round 3: 399 peptides, 7 chains. Longest chain 121 peptides. Score 0.950 Round 4: 401 peptides, 6 chains. Longest chain 123 peptides. Score 0.953 Round 5: 401 peptides, 7 chains. Longest chain 121 peptides. Score 0.950 Taking the results from Round 4 Chains 6, Residues 395, Estimated correctness of the model 99.8 % 3 chains (361 residues) have been docked in sequence Building loops using Loopy2018 6 chains (395 residues) following loop building 3 chains (361 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4104 restraints for refining 3817 atoms. 1050 conditional restraints added. Observations/parameters ratio is 3.17 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2006 (Rfree = 0.000) for 3817 atoms. Found 163 (197 requested) and removed 48 (98 requested) atoms. Cycle 7: After refmac, R = 0.1891 (Rfree = 0.000) for 3924 atoms. Found 95 (203 requested) and removed 40 (101 requested) atoms. Cycle 8: After refmac, R = 0.1825 (Rfree = 0.000) for 3973 atoms. Found 87 (206 requested) and removed 32 (103 requested) atoms. Cycle 9: After refmac, R = 0.1786 (Rfree = 0.000) for 4015 atoms. Found 98 (208 requested) and removed 40 (104 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1769 (Rfree = 0.000) for 4064 atoms. Found 84 (210 requested) and removed 53 (105 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.66 1.70 NCS extension: 2 residues added (1 deleted due to clashes), 4097 seeds are put forward Round 1: 400 peptides, 6 chains. Longest chain 122 peptides. Score 0.953 Round 2: 399 peptides, 7 chains. Longest chain 121 peptides. Score 0.950 Round 3: 398 peptides, 8 chains. Longest chain 123 peptides. Score 0.946 Round 4: 398 peptides, 8 chains. Longest chain 123 peptides. Score 0.946 Round 5: 399 peptides, 7 chains. Longest chain 121 peptides. Score 0.950 Taking the results from Round 1 Chains 6, Residues 394, Estimated correctness of the model 99.8 % 4 chains (371 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 B and 134 B 5 chains (396 residues) following loop building 3 chains (373 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4077 restraints for refining 3882 atoms. 958 conditional restraints added. Observations/parameters ratio is 3.12 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1930 (Rfree = 0.000) for 3882 atoms. Found 174 (197 requested) and removed 49 (100 requested) atoms. Cycle 12: After refmac, R = 0.1844 (Rfree = 0.000) for 4002 atoms. Found 117 (203 requested) and removed 65 (103 requested) atoms. Cycle 13: After refmac, R = 0.1808 (Rfree = 0.000) for 4050 atoms. Found 114 (201 requested) and removed 55 (104 requested) atoms. Cycle 14: After refmac, R = 0.1795 (Rfree = 0.000) for 4099 atoms. Found 106 (204 requested) and removed 72 (106 requested) atoms. Cycle 15: After refmac, R = 0.1764 (Rfree = 0.000) for 4124 atoms. Found 119 (201 requested) and removed 61 (107 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.66 1.70 NCS extension: 6 residues added (24 deleted due to clashes), 4189 seeds are put forward Round 1: 399 peptides, 6 chains. Longest chain 122 peptides. Score 0.953 Round 2: 397 peptides, 8 chains. Longest chain 122 peptides. Score 0.946 Round 3: 397 peptides, 6 chains. Longest chain 122 peptides. Score 0.952 Round 4: 398 peptides, 7 chains. Longest chain 121 peptides. Score 0.949 Round 5: 397 peptides, 9 chains. Longest chain 123 peptides. Score 0.942 Taking the results from Round 1 Chains 6, Residues 393, Estimated correctness of the model 99.8 % 4 chains (370 residues) have been docked in sequence Building loops using Loopy2018 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 ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4107 restraints for refining 3909 atoms. 999 conditional restraints added. Observations/parameters ratio is 3.10 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1905 (Rfree = 0.000) for 3909 atoms. Found 169 (186 requested) and removed 57 (101 requested) atoms. Cycle 17: After refmac, R = 0.1848 (Rfree = 0.000) for 4004 atoms. Found 99 (191 requested) and removed 59 (104 requested) atoms. Cycle 18: After refmac, R = 0.1785 (Rfree = 0.000) for 4038 atoms. Found 112 (188 requested) and removed 42 (104 requested) atoms. Cycle 19: After refmac, R = 0.1775 (Rfree = 0.000) for 4100 atoms. Found 85 (191 requested) and removed 74 (106 requested) atoms. Cycle 20: After refmac, R = 0.1747 (Rfree = 0.000) for 4106 atoms. Found 107 (187 requested) and removed 50 (106 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.66 1.70 NCS extension: 3 residues added (13 deleted due to clashes), 4167 seeds are put forward Round 1: 399 peptides, 7 chains. Longest chain 122 peptides. Score 0.950 Round 2: 398 peptides, 7 chains. Longest chain 121 peptides. Score 0.949 Round 3: 395 peptides, 8 chains. Longest chain 121 peptides. Score 0.945 Round 4: 397 peptides, 8 chains. Longest chain 122 peptides. Score 0.946 Round 5: 398 peptides, 7 chains. Longest chain 122 peptides. Score 0.949 Taking the results from Round 1 Chains 7, Residues 392, Estimated correctness of the model 99.8 % 4 chains (358 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 A and 46 A 6 chains (394 residues) following loop building 3 chains (360 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4247 restraints for refining 3905 atoms. 1197 conditional restraints added. Observations/parameters ratio is 3.10 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1908 (Rfree = 0.000) for 3905 atoms. Found 164 (178 requested) and removed 50 (101 requested) atoms. Cycle 22: After refmac, R = 0.1837 (Rfree = 0.000) for 4006 atoms. Found 96 (183 requested) and removed 46 (104 requested) atoms. Cycle 23: After refmac, R = 0.1774 (Rfree = 0.000) for 4048 atoms. Found 80 (185 requested) and removed 48 (105 requested) atoms. Cycle 24: After refmac, R = 0.1749 (Rfree = 0.000) for 4066 atoms. Found 88 (181 requested) and removed 41 (105 requested) atoms. Cycle 25: After refmac, R = 0.1734 (Rfree = 0.000) for 4107 atoms. Found 76 (183 requested) and removed 57 (106 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.66 1.70 NCS extension: 1 residues added (2 deleted due to clashes), 4128 seeds are put forward Round 1: 396 peptides, 8 chains. Longest chain 121 peptides. Score 0.945 Round 2: 396 peptides, 7 chains. Longest chain 122 peptides. Score 0.948 Round 3: 398 peptides, 6 chains. Longest chain 122 peptides. Score 0.952 Round 4: 397 peptides, 8 chains. Longest chain 122 peptides. Score 0.946 Round 5: 397 peptides, 7 chains. Longest chain 122 peptides. Score 0.949 Taking the results from Round 3 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 4281 restraints for refining 3886 atoms. 1246 conditional restraints added. Observations/parameters ratio is 3.12 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1905 (Rfree = 0.000) for 3886 atoms. Found 169 (169 requested) and removed 54 (100 requested) atoms. Cycle 27: After refmac, R = 0.1833 (Rfree = 0.000) for 3993 atoms. Found 107 (174 requested) and removed 58 (103 requested) atoms. Cycle 28: After refmac, R = 0.1771 (Rfree = 0.000) for 4038 atoms. Found 118 (171 requested) and removed 36 (104 requested) atoms. Cycle 29: After refmac, R = 0.1769 (Rfree = 0.000) for 4111 atoms. Found 87 (175 requested) and removed 68 (106 requested) atoms. Cycle 30: After refmac, R = 0.1730 (Rfree = 0.000) for 4120 atoms. Found 100 (170 requested) and removed 46 (106 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.66 1.70 NCS extension: 3 residues added (119 deleted due to clashes), 4179 seeds are put forward Round 1: 394 peptides, 9 chains. Longest chain 121 peptides. Score 0.941 Round 2: 396 peptides, 8 chains. Longest chain 122 peptides. Score 0.945 Round 3: 391 peptides, 9 chains. Longest chain 122 peptides. Score 0.940 Round 4: 397 peptides, 8 chains. Longest chain 122 peptides. Score 0.946 Round 5: 394 peptides, 10 chains. Longest chain 80 peptides. Score 0.938 Taking the results from Round 4 Chains 8, Residues 389, Estimated correctness of the model 99.8 % 5 chains (355 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 C and 32 C Built loop between residues 59 C and 62 C 6 chains (393 residues) following loop building 3 chains (359 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4265 restraints for refining 3925 atoms. 1226 conditional restraints added. Observations/parameters ratio is 3.08 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1906 (Rfree = 0.000) for 3925 atoms. Found 157 (162 requested) and removed 63 (101 requested) atoms. Cycle 32: After refmac, R = 0.1830 (Rfree = 0.000) for 4004 atoms. Found 108 (166 requested) and removed 42 (104 requested) atoms. Cycle 33: After refmac, R = 0.1773 (Rfree = 0.000) for 4063 atoms. Found 97 (168 requested) and removed 46 (105 requested) atoms. Cycle 34: After refmac, R = 0.1754 (Rfree = 0.000) for 4107 atoms. Found 83 (170 requested) and removed 51 (106 requested) atoms. Cycle 35: After refmac, R = 0.1733 (Rfree = 0.000) for 4132 atoms. Found 99 (167 requested) and removed 61 (107 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.65 1.69 NCS extension: 1 residues added (122 deleted due to clashes), 4173 seeds are put forward Round 1: 397 peptides, 7 chains. Longest chain 122 peptides. Score 0.949 Round 2: 396 peptides, 7 chains. Longest chain 122 peptides. Score 0.948 Round 3: 395 peptides, 7 chains. Longest chain 122 peptides. Score 0.948 Round 4: 396 peptides, 7 chains. Longest chain 122 peptides. Score 0.948 Round 5: 397 peptides, 7 chains. Longest chain 122 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 43 C and 46 C Built loop between residues 35 B and 38 B 5 chains (394 residues) following loop building 3 chains (371 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4121 restraints for refining 3897 atoms. 1017 conditional restraints added. Observations/parameters ratio is 3.11 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1901 (Rfree = 0.000) for 3897 atoms. Found 153 (153 requested) and removed 64 (100 requested) atoms. Cycle 37: After refmac, R = 0.1829 (Rfree = 0.000) for 3979 atoms. Found 105 (157 requested) and removed 32 (103 requested) atoms. Cycle 38: After refmac, R = 0.1763 (Rfree = 0.000) for 4047 atoms. Found 101 (159 requested) and removed 40 (104 requested) atoms. Cycle 39: After refmac, R = 0.1733 (Rfree = 0.000) for 4101 atoms. Found 82 (161 requested) and removed 63 (106 requested) atoms. Cycle 40: After refmac, R = 0.1718 (Rfree = 0.000) for 4113 atoms. Found 85 (158 requested) and removed 53 (106 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.66 1.70 NCS extension: 2 residues added (56 deleted due to clashes), 4149 seeds are put forward Round 1: 396 peptides, 8 chains. Longest chain 122 peptides. Score 0.945 Round 2: 398 peptides, 6 chains. Longest chain 133 peptides. Score 0.952 Round 3: 395 peptides, 8 chains. Longest chain 122 peptides. Score 0.945 Round 4: 399 peptides, 6 chains. Longest chain 133 peptides. Score 0.953 Round 5: 399 peptides, 6 chains. Longest chain 123 peptides. Score 0.953 Taking the results from Round 5 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 43 B and 46 B 5 chains (395 residues) following loop building 3 chains (373 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4112 restraints for refining 3906 atoms. 1004 conditional restraints added. Observations/parameters ratio is 3.10 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1918 (Rfree = 0.000) for 3906 atoms. Found 145 (145 requested) and removed 49 (101 requested) atoms. Cycle 42: After refmac, R = 0.1827 (Rfree = 0.000) for 3994 atoms. Found 101 (149 requested) and removed 33 (103 requested) atoms. Cycle 43: After refmac, R = 0.1777 (Rfree = 0.000) for 4056 atoms. Found 82 (151 requested) and removed 45 (105 requested) atoms. Cycle 44: After refmac, R = 0.1748 (Rfree = 0.000) for 4087 atoms. Found 84 (148 requested) and removed 47 (105 requested) atoms. Cycle 45: After refmac, R = 0.1733 (Rfree = 0.000) for 4116 atoms. Found 88 (145 requested) and removed 45 (106 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.66 1.70 NCS extension: 4 residues added (26 deleted due to clashes), 4164 seeds are put forward Round 1: 396 peptides, 8 chains. Longest chain 122 peptides. Score 0.945 Round 2: 397 peptides, 7 chains. Longest chain 122 peptides. Score 0.949 Round 3: 395 peptides, 8 chains. Longest chain 122 peptides. Score 0.945 Round 4: 395 peptides, 9 chains. Longest chain 123 peptides. Score 0.942 Round 5: 395 peptides, 9 chains. Longest chain 123 peptides. Score 0.942 Taking the results from Round 2 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 35 B and 38 B Built loop between residues 111 B and 114 B 5 chains (394 residues) following loop building 3 chains (371 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 48424 reflections ( 99.96 % complete ) and 3104 restraints for refining 3046 atoms. Observations/parameters ratio is 3.97 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2707 (Rfree = 0.000) for 3046 atoms. Found 104 (104 requested) and removed 0 (104 requested) atoms. Cycle 47: After refmac, R = 0.2569 (Rfree = 0.000) for 3046 atoms. Found 57 (108 requested) and removed 0 (81 requested) atoms. Cycle 48: After refmac, R = 0.2455 (Rfree = 0.000) for 3046 atoms. Found 36 (110 requested) and removed 3 (83 requested) atoms. Cycle 49: After refmac, R = 0.2360 (Rfree = 0.000) for 3046 atoms. TimeTaking 72.48