Mon 24 Dec 00:58:17 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 1vmf-1.7-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vmf-1.7-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vmf-1.7-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-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/1vmf-1.7-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-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 ============================================================ Mon 24 Dec 00:58:22 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/1vmf-1.7-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vmf-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 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-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: 19 Cell parameters: 57.443 58.601 135.061 90.000 90.000 90.000 Input sequence file: 1vmf-1.7-parrot-mrncs.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 3833 atoms. Observations/parameters ratio is 3.16 ------------------------------------------------------ Starting model: R = 0.3015 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2541 (Rfree = 0.000) for 3833 atoms. Found 198 (198 requested) and removed 102 (99 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.68 1.73 NCS extension: 0 residues added, 3929 seeds are put forward Round 1: 370 peptides, 18 chains. Longest chain 51 peptides. Score 0.892 Round 2: 387 peptides, 11 chains. Longest chain 102 peptides. Score 0.931 Round 3: 395 peptides, 9 chains. Longest chain 120 peptides. Score 0.942 Round 4: 392 peptides, 10 chains. Longest chain 120 peptides. Score 0.937 Round 5: 395 peptides, 8 chains. Longest chain 120 peptides. Score 0.945 Taking the results from Round 5 Chains 8, Residues 387, Estimated correctness of the model 99.8 % 5 chains (352 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 111 C and 115 C Built loop between residues 88 B and 91 B 6 chains (392 residues) following loop building 3 chains (357 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4000 restraints for refining 3647 atoms. 976 conditional restraints added. Observations/parameters ratio is 3.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2588 (Rfree = 0.000) for 3647 atoms. Found 148 (188 requested) and removed 63 (94 requested) atoms. Cycle 2: After refmac, R = 0.2372 (Rfree = 0.000) for 3728 atoms. Found 99 (193 requested) and removed 28 (96 requested) atoms. Cycle 3: After refmac, R = 0.2115 (Rfree = 0.000) for 3794 atoms. Found 104 (196 requested) and removed 35 (98 requested) atoms. Cycle 4: After refmac, R = 0.2013 (Rfree = 0.000) for 3846 atoms. Found 92 (200 requested) and removed 31 (100 requested) atoms. Cycle 5: After refmac, R = 0.1918 (Rfree = 0.000) for 3898 atoms. Found 98 (202 requested) and removed 22 (101 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.66 1.70 NCS extension: 0 residues added (3 deleted due to clashes), 3975 seeds are put forward Round 1: 397 peptides, 7 chains. Longest chain 120 peptides. Score 0.949 Round 2: 399 peptides, 7 chains. Longest chain 121 peptides. Score 0.950 Round 3: 400 peptides, 6 chains. Longest chain 121 peptides. Score 0.953 Round 4: 399 peptides, 7 chains. Longest chain 122 peptides. Score 0.950 Round 5: 397 peptides, 8 chains. Longest chain 120 peptides. Score 0.946 Taking the results from Round 3 Chains 6, Residues 394, Estimated correctness of the model 99.8 % 3 chains (359 residues) have been docked in sequence Building loops using Loopy2018 6 chains (394 residues) following loop building 3 chains (359 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4027 restraints for refining 3776 atoms. 984 conditional restraints added. Observations/parameters ratio is 3.21 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2025 (Rfree = 0.000) for 3776 atoms. Found 163 (195 requested) and removed 54 (97 requested) atoms. Cycle 7: After refmac, R = 0.1888 (Rfree = 0.000) for 3882 atoms. Found 119 (201 requested) and removed 41 (100 requested) atoms. Cycle 8: After refmac, R = 0.1838 (Rfree = 0.000) for 3954 atoms. Found 124 (205 requested) and removed 43 (102 requested) atoms. Cycle 9: After refmac, R = 0.1786 (Rfree = 0.000) for 4027 atoms. Found 96 (208 requested) and removed 64 (104 requested) atoms. Cycle 10: After refmac, R = 0.1759 (Rfree = 0.000) for 4052 atoms. Found 109 (206 requested) and removed 66 (105 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.65 1.69 NCS extension: 0 residues added, 4096 seeds are put forward Round 1: 394 peptides, 8 chains. Longest chain 119 peptides. Score 0.944 Round 2: 396 peptides, 8 chains. Longest chain 122 peptides. Score 0.945 Round 3: 396 peptides, 7 chains. Longest chain 122 peptides. Score 0.948 Round 4: 395 peptides, 9 chains. Longest chain 101 peptides. Score 0.942 Round 5: 393 peptides, 8 chains. Longest chain 123 peptides. Score 0.944 Taking the results from Round 3 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 130 B and 133 B 5 chains (394 residues) following loop building 3 chains (372 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4011 restraints for refining 3855 atoms. 907 conditional restraints added. Observations/parameters ratio is 3.14 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1915 (Rfree = 0.000) for 3855 atoms. Found 180 (191 requested) and removed 59 (99 requested) atoms. Cycle 12: After refmac, R = 0.1851 (Rfree = 0.000) for 3970 atoms. Found 128 (197 requested) and removed 53 (102 requested) atoms. Cycle 13: After refmac, R = 0.1798 (Rfree = 0.000) for 4039 atoms. Found 107 (201 requested) and removed 66 (104 requested) atoms. Cycle 14: After refmac, R = 0.1757 (Rfree = 0.000) for 4073 atoms. Found 116 (198 requested) and removed 51 (105 requested) atoms. Cycle 15: After refmac, R = 0.1726 (Rfree = 0.000) for 4128 atoms. Found 96 (201 requested) and removed 69 (107 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.64 1.68 NCS extension: 3 residues added (13 deleted due to clashes), 4158 seeds are put forward Round 1: 395 peptides, 8 chains. Longest chain 120 peptides. Score 0.945 Round 2: 394 peptides, 10 chains. Longest chain 119 peptides. Score 0.938 Round 3: 395 peptides, 7 chains. Longest chain 120 peptides. Score 0.948 Round 4: 395 peptides, 8 chains. Longest chain 120 peptides. Score 0.945 Round 5: 395 peptides, 9 chains. Longest chain 119 peptides. Score 0.942 Taking the results from Round 3 Chains 7, Residues 388, Estimated correctness of the model 99.8 % 5 chains (365 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 134 B 5 chains (394 residues) following loop building 3 chains (371 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4102 restraints for refining 3910 atoms. 1002 conditional restraints added. Observations/parameters ratio is 3.10 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1885 (Rfree = 0.000) for 3910 atoms. Found 186 (186 requested) and removed 66 (101 requested) atoms. Cycle 17: After refmac, R = 0.1803 (Rfree = 0.000) for 4022 atoms. Found 115 (191 requested) and removed 62 (104 requested) atoms. Cycle 18: After refmac, R = 0.1755 (Rfree = 0.000) for 4071 atoms. Found 123 (190 requested) and removed 65 (105 requested) atoms. Cycle 19: After refmac, R = 0.1755 (Rfree = 0.000) for 4118 atoms. Found 111 (187 requested) and removed 74 (106 requested) atoms. Cycle 20: After refmac, R = 0.1725 (Rfree = 0.000) for 4147 atoms. Found 120 (185 requested) and removed 79 (107 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.65 1.69 NCS extension: 0 residues added (28 deleted due to clashes), 4188 seeds are put forward Round 1: 399 peptides, 7 chains. Longest chain 121 peptides. Score 0.950 Round 2: 396 peptides, 9 chains. Longest chain 122 peptides. Score 0.942 Round 3: 395 peptides, 9 chains. Longest chain 101 peptides. Score 0.942 Round 4: 397 peptides, 8 chains. Longest chain 119 peptides. Score 0.946 Round 5: 398 peptides, 8 chains. Longest chain 122 peptides. Score 0.946 Taking the results from Round 1 Chains 7, Residues 392, Estimated correctness of the model 99.8 % 5 chains (370 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 C and 46 C Built loop between residues 130 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 4078 restraints for refining 3911 atoms. 959 conditional restraints added. Observations/parameters ratio is 3.10 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1878 (Rfree = 0.000) for 3911 atoms. Found 167 (170 requested) and removed 43 (101 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1818 (Rfree = 0.000) for 4017 atoms. Found 95 (175 requested) and removed 58 (104 requested) atoms. Cycle 23: After refmac, R = 0.1751 (Rfree = 0.000) for 4047 atoms. Found 113 (171 requested) and removed 35 (104 requested) atoms. Cycle 24: After refmac, R = 0.1732 (Rfree = 0.000) for 4114 atoms. Found 97 (175 requested) and removed 70 (106 requested) atoms. Cycle 25: After refmac, R = 0.1712 (Rfree = 0.000) for 4133 atoms. Found 116 (171 requested) and removed 63 (107 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.66 1.70 NCS extension: 6 residues added (19 deleted due to clashes), 4192 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 120 peptides. Score 0.946 Round 3: 396 peptides, 9 chains. Longest chain 122 peptides. Score 0.942 Round 4: 398 peptides, 6 chains. Longest chain 122 peptides. Score 0.952 Round 5: 396 peptides, 9 chains. Longest chain 120 peptides. Score 0.942 Taking the results from Round 4 Chains 6, Residues 392, 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 (394 residues) following loop building 3 chains (372 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4078 restraints for refining 3899 atoms. 974 conditional restraints added. Observations/parameters ratio is 3.10 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1876 (Rfree = 0.000) for 3899 atoms. Found 157 (157 requested) and removed 49 (100 requested) atoms. Cycle 27: After refmac, R = 0.1809 (Rfree = 0.000) for 3990 atoms. Found 103 (161 requested) and removed 47 (103 requested) atoms. Cycle 28: After refmac, R = 0.1739 (Rfree = 0.000) for 4040 atoms. Found 104 (163 requested) and removed 49 (104 requested) atoms. Cycle 29: After refmac, R = 0.1712 (Rfree = 0.000) for 4088 atoms. Found 100 (165 requested) and removed 52 (106 requested) atoms. Cycle 30: After refmac, R = 0.1694 (Rfree = 0.000) for 4130 atoms. Found 102 (163 requested) and removed 81 (107 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.65 1.69 NCS extension: 5 residues added (26 deleted due to clashes), 4156 seeds are put forward Round 1: 394 peptides, 8 chains. Longest chain 121 peptides. Score 0.944 Round 2: 395 peptides, 8 chains. Longest chain 121 peptides. Score 0.945 Round 3: 394 peptides, 9 chains. Longest chain 121 peptides. Score 0.941 Round 4: 395 peptides, 8 chains. Longest chain 121 peptides. Score 0.945 Round 5: 396 peptides, 8 chains. Longest chain 122 peptides. Score 0.945 Taking the results from Round 5 Chains 8, Residues 388, Estimated correctness of the model 99.8 % 5 chains (355 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 C and 47 C Built loop between residues 55 C and 58 C 6 chains (392 residues) following loop building 3 chains (359 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4181 restraints for refining 3879 atoms. 1146 conditional restraints added. Observations/parameters ratio is 3.12 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1874 (Rfree = 0.000) for 3879 atoms. Found 148 (148 requested) and removed 57 (100 requested) atoms. Cycle 32: After refmac, R = 0.1800 (Rfree = 0.000) for 3960 atoms. Found 123 (152 requested) and removed 42 (102 requested) atoms. Cycle 33: After refmac, R = 0.1752 (Rfree = 0.000) for 4037 atoms. Found 120 (155 requested) and removed 57 (104 requested) atoms. Cycle 34: After refmac, R = 0.1736 (Rfree = 0.000) for 4093 atoms. Found 122 (157 requested) and removed 72 (106 requested) atoms. Cycle 35: After refmac, R = 0.1741 (Rfree = 0.000) for 4133 atoms. Found 120 (154 requested) and removed 100 (107 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.66 1.70 NCS extension: 2 residues added (1 deleted due to clashes), 4155 seeds are put forward Round 1: 392 peptides, 8 chains. Longest chain 118 peptides. Score 0.944 Round 2: 394 peptides, 9 chains. Longest chain 121 peptides. Score 0.941 Round 3: 396 peptides, 7 chains. Longest chain 122 peptides. Score 0.948 Round 4: 394 peptides, 10 chains. Longest chain 122 peptides. Score 0.938 Round 5: 394 peptides, 9 chains. Longest chain 121 peptides. Score 0.941 Taking the results from Round 3 Chains 7, Residues 389, 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 (392 residues) following loop building 3 chains (359 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4176 restraints for refining 3878 atoms. 1148 conditional restraints added. Observations/parameters ratio is 3.12 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1881 (Rfree = 0.000) for 3878 atoms. Found 140 (140 requested) and removed 48 (100 requested) atoms. Cycle 37: After refmac, R = 0.1811 (Rfree = 0.000) for 3957 atoms. Found 113 (143 requested) and removed 27 (102 requested) atoms. Cycle 38: After refmac, R = 0.1769 (Rfree = 0.000) for 4035 atoms. Found 112 (146 requested) and removed 49 (104 requested) atoms. Cycle 39: After refmac, R = 0.1744 (Rfree = 0.000) for 4091 atoms. Found 111 (148 requested) and removed 76 (106 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1741 (Rfree = 0.000) for 4117 atoms. Found 129 (145 requested) and removed 77 (106 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.65 1.69 NCS extension: 0 residues added, 4169 seeds are put forward Round 1: 396 peptides, 7 chains. Longest chain 121 peptides. Score 0.948 Round 2: 395 peptides, 8 chains. Longest chain 120 peptides. Score 0.945 Round 3: 398 peptides, 6 chains. Longest chain 133 peptides. Score 0.952 Round 4: 394 peptides, 8 chains. Longest chain 121 peptides. Score 0.944 Round 5: 396 peptides, 8 chains. Longest chain 119 peptides. Score 0.945 Taking the results from Round 3 Chains 6, Residues 392, Estimated correctness of the model 99.8 % 4 chains (369 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 C and 32 C 5 chains (394 residues) following loop building 3 chains (371 residues) in sequence following loop building ------------------------------------------------------ 48424 reflections ( 99.96 % complete ) and 4078 restraints for refining 3893 atoms. 981 conditional restraints added. Observations/parameters ratio is 3.11 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1878 (Rfree = 0.000) for 3893 atoms. Found 133 (133 requested) and removed 51 (100 requested) atoms. Cycle 42: After refmac, R = 0.1792 (Rfree = 0.000) for 3968 atoms. Found 112 (135 requested) and removed 45 (102 requested) atoms. Cycle 43: After refmac, R = 0.1757 (Rfree = 0.000) for 4023 atoms. Found 102 (137 requested) and removed 63 (104 requested) atoms. Cycle 44: After refmac, R = 0.1733 (Rfree = 0.000) for 4053 atoms. Found 109 (134 requested) and removed 51 (105 requested) atoms. Cycle 45: After refmac, R = 0.1728 (Rfree = 0.000) for 4101 atoms. Found 101 (136 requested) and removed 70 (106 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.66 1.70 NCS extension: 1 residues added (26 deleted due to clashes), 4133 seeds are put forward Round 1: 394 peptides, 7 chains. Longest chain 120 peptides. Score 0.948 Round 2: 396 peptides, 8 chains. Longest chain 120 peptides. Score 0.945 Round 3: 393 peptides, 8 chains. Longest chain 121 peptides. Score 0.944 Round 4: 395 peptides, 6 chains. Longest chain 121 peptides. Score 0.951 Round 5: 397 peptides, 7 chains. Longest chain 120 peptides. Score 0.949 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 389, Estimated correctness of the model 99.8 % 3 chains (358 residues) have been docked in sequence Sequence coverage is 91 % All DUM atoms will be removed Building loops using Loopy2018 6 chains (389 residues) following loop building 3 chains (358 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 48424 reflections ( 99.96 % complete ) and 3016 restraints for refining 2960 atoms. Observations/parameters ratio is 4.09 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2734 (Rfree = 0.000) for 2960 atoms. Found 95 (95 requested) and removed 0 (95 requested) atoms. Cycle 47: After refmac, R = 0.2521 (Rfree = 0.000) for 2960 atoms. Found 95 (98 requested) and removed 1 (79 requested) atoms. Cycle 48: After refmac, R = 0.2344 (Rfree = 0.000) for 2960 atoms. Found 75 (101 requested) and removed 3 (81 requested) atoms. Cycle 49: After refmac, R = 0.2217 (Rfree = 0.000) for 2960 atoms. TimeTaking 53.3