Mon 24 Dec 01:01:04 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 1vpz-2.1-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vpz-2.1-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vpz-2.1-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-2.1-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/1vpz-2.1-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-2.1-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 01:01:09 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/1vpz-2.1-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vpz-2.1-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 114 and 0 Target number of residues in the AU: 114 Target solvent content: 0.5492 Checking the provided sequence file Detected sequence length: 73 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 146 Adjusted target solvent content: 0.42 Input MTZ file: 1vpz-2.1-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: 20 Cell parameters: 49.075 56.647 98.468 90.000 90.000 90.000 Input sequence file: 1vpz-2.1-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1168 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: 24.580 2.051 Wilson plot Bfac: 35.03 8798 reflections ( 98.63 % complete ) and 0 restraints for refining 1292 atoms. Observations/parameters ratio is 1.70 ------------------------------------------------------ Starting model: R = 0.3596 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3441 (Rfree = 0.000) for 1292 atoms. Found 12 (41 requested) and removed 35 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.52 2.81 NCS extension: 0 residues added, 1269 seeds are put forward Round 1: 63 peptides, 11 chains. Longest chain 8 peptides. Score 0.411 Round 2: 80 peptides, 9 chains. Longest chain 17 peptides. Score 0.658 Round 3: 91 peptides, 9 chains. Longest chain 18 peptides. Score 0.734 Round 4: 96 peptides, 8 chains. Longest chain 24 peptides. Score 0.788 Round 5: 94 peptides, 9 chains. Longest chain 20 peptides. Score 0.751 Taking the results from Round 4 Chains 8, Residues 88, Estimated correctness of the model 95.5 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 8798 reflections ( 98.63 % complete ) and 2235 restraints for refining 1128 atoms. 1790 conditional restraints added. Observations/parameters ratio is 1.95 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3767 (Rfree = 0.000) for 1128 atoms. Found 27 (35 requested) and removed 25 (17 requested) atoms. Cycle 2: After refmac, R = 0.3680 (Rfree = 0.000) for 1122 atoms. Found 14 (34 requested) and removed 24 (17 requested) atoms. Cycle 3: After refmac, R = 0.3510 (Rfree = 0.000) for 1098 atoms. Found 9 (34 requested) and removed 19 (17 requested) atoms. Cycle 4: After refmac, R = 0.3523 (Rfree = 0.000) for 1075 atoms. Found 16 (32 requested) and removed 20 (17 requested) atoms. Cycle 5: After refmac, R = 0.3365 (Rfree = 0.000) for 1063 atoms. Found 12 (31 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.42 2.69 NCS extension: 11 residues added (3 deleted due to clashes), 1075 seeds are put forward Round 1: 93 peptides, 8 chains. Longest chain 24 peptides. Score 0.772 Round 2: 100 peptides, 5 chains. Longest chain 31 peptides. Score 0.867 Round 3: 99 peptides, 6 chains. Longest chain 27 peptides. Score 0.845 Round 4: 98 peptides, 8 chains. Longest chain 24 peptides. Score 0.797 Round 5: 97 peptides, 6 chains. Longest chain 24 peptides. Score 0.837 Taking the results from Round 2 Chains 5, Residues 95, Estimated correctness of the model 98.1 % 3 chains (76 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 35 A and 41 A 4 chains (100 residues) following loop building 2 chains (81 residues) in sequence following loop building ------------------------------------------------------ 8798 reflections ( 98.63 % complete ) and 1408 restraints for refining 1086 atoms. 699 conditional restraints added. Observations/parameters ratio is 2.03 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3571 (Rfree = 0.000) for 1086 atoms. Found 24 (31 requested) and removed 26 (17 requested) atoms. Cycle 7: After refmac, R = 0.3304 (Rfree = 0.000) for 1077 atoms. Found 17 (30 requested) and removed 20 (17 requested) atoms. Cycle 8: After refmac, R = 0.3194 (Rfree = 0.000) for 1063 atoms. Found 13 (29 requested) and removed 18 (17 requested) atoms. Cycle 9: After refmac, R = 0.3135 (Rfree = 0.000) for 1053 atoms. Found 9 (28 requested) and removed 16 (16 requested) atoms. Cycle 10: After refmac, R = 0.3023 (Rfree = 0.000) for 1043 atoms. Found 8 (27 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.38 2.65 NCS extension: 49 residues added (18 deleted due to clashes), 1086 seeds are put forward Round 1: 98 peptides, 5 chains. Longest chain 30 peptides. Score 0.861 Round 2: 100 peptides, 5 chains. Longest chain 27 peptides. Score 0.867 Round 3: 96 peptides, 7 chains. Longest chain 23 peptides. Score 0.811 Round 4: 97 peptides, 7 chains. Longest chain 23 peptides. Score 0.816 Round 5: 94 peptides, 8 chains. Longest chain 19 peptides. Score 0.778 Taking the results from Round 2 Chains 7, Residues 95, Estimated correctness of the model 98.1 % 3 chains (65 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 35 A and 42 A 6 chains (101 residues) following loop building 2 chains (71 residues) in sequence following loop building ------------------------------------------------------ 8798 reflections ( 98.63 % complete ) and 1499 restraints for refining 1062 atoms. 818 conditional restraints added. Observations/parameters ratio is 2.07 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3373 (Rfree = 0.000) for 1062 atoms. Found 26 (26 requested) and removed 20 (16 requested) atoms. Cycle 12: After refmac, R = 0.3190 (Rfree = 0.000) for 1068 atoms. Found 11 (27 requested) and removed 17 (17 requested) atoms. Cycle 13: After refmac, R = 0.3132 (Rfree = 0.000) for 1058 atoms. Found 11 (25 requested) and removed 16 (16 requested) atoms. Cycle 14: After refmac, R = 0.3001 (Rfree = 0.000) for 1049 atoms. Found 11 (24 requested) and removed 16 (16 requested) atoms. Cycle 15: After refmac, R = 0.2928 (Rfree = 0.000) for 1041 atoms. Found 12 (24 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.37 2.64 NCS extension: 28 residues added (40 deleted due to clashes), 1065 seeds are put forward Round 1: 100 peptides, 4 chains. Longest chain 28 peptides. Score 0.885 Round 2: 99 peptides, 5 chains. Longest chain 36 peptides. Score 0.864 Round 3: 101 peptides, 4 chains. Longest chain 31 peptides. Score 0.888 Round 4: 103 peptides, 5 chains. Longest chain 28 peptides. Score 0.877 Round 5: 100 peptides, 6 chains. Longest chain 34 peptides. Score 0.848 Taking the results from Round 3 Chains 5, Residues 97, Estimated correctness of the model 98.6 % 4 chains (96 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 42 A Built loop between residues 36 B and 42 B 3 chains (105 residues) following loop building 2 chains (104 residues) in sequence following loop building ------------------------------------------------------ 8798 reflections ( 98.63 % complete ) and 1179 restraints for refining 1087 atoms. 352 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3150 (Rfree = 0.000) for 1087 atoms. Found 22 (24 requested) and removed 21 (17 requested) atoms. Cycle 17: After refmac, R = 0.2972 (Rfree = 0.000) for 1083 atoms. Found 10 (23 requested) and removed 17 (17 requested) atoms. Cycle 18: After refmac, R = 0.2824 (Rfree = 0.000) for 1073 atoms. Found 4 (22 requested) and removed 17 (17 requested) atoms. Cycle 19: After refmac, R = 0.2727 (Rfree = 0.000) for 1057 atoms. Found 11 (21 requested) and removed 16 (16 requested) atoms. Cycle 20: After refmac, R = 0.2661 (Rfree = 0.000) for 1051 atoms. Found 8 (20 requested) and removed 11 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.38 2.65 NCS extension: 4 residues added (0 deleted due to clashes), 1052 seeds are put forward Round 1: 102 peptides, 4 chains. Longest chain 29 peptides. Score 0.891 Round 2: 102 peptides, 4 chains. Longest chain 54 peptides. Score 0.891 Round 3: 98 peptides, 5 chains. Longest chain 27 peptides. Score 0.861 Round 4: 101 peptides, 4 chains. Longest chain 51 peptides. Score 0.888 Round 5: 104 peptides, 4 chains. Longest chain 30 peptides. Score 0.896 Taking the results from Round 5 Chains 6, Residues 100, Estimated correctness of the model 98.8 % 4 chains (98 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 42 A Built loop between residues 38 B and 42 B 3 chains (105 residues) following loop building 2 chains (104 residues) in sequence following loop building ------------------------------------------------------ 8798 reflections ( 98.63 % complete ) and 1136 restraints for refining 1074 atoms. 312 conditional restraints added. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2976 (Rfree = 0.000) for 1074 atoms. Found 20 (20 requested) and removed 19 (17 requested) atoms. Cycle 22: After refmac, R = 0.2827 (Rfree = 0.000) for 1071 atoms. Found 13 (20 requested) and removed 17 (17 requested) atoms. Cycle 23: After refmac, R = 0.2711 (Rfree = 0.000) for 1061 atoms. Found 11 (19 requested) and removed 17 (17 requested) atoms. Cycle 24: After refmac, R = 0.2625 (Rfree = 0.000) for 1052 atoms. Found 5 (18 requested) and removed 16 (16 requested) atoms. Cycle 25: After refmac, R = 0.2577 (Rfree = 0.000) for 1036 atoms. Found 10 (17 requested) and removed 10 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.39 2.66 NCS extension: 3 residues added (0 deleted due to clashes), 1040 seeds are put forward Round 1: 102 peptides, 2 chains. Longest chain 51 peptides. Score 0.921 Round 2: 105 peptides, 3 chains. Longest chain 51 peptides. Score 0.913 Round 3: 105 peptides, 3 chains. Longest chain 54 peptides. Score 0.913 Round 4: 106 peptides, 4 chains. Longest chain 48 peptides. Score 0.901 Round 5: 105 peptides, 5 chains. Longest chain 42 peptides. Score 0.882 Taking the results from Round 1 Chains 2, Residues 100, Estimated correctness of the model 99.3 % 2 chains (100 residues) have been docked in sequence Building loops using Loopy2018 2 chains (100 residues) following loop building 2 chains (100 residues) in sequence following loop building ------------------------------------------------------ 8798 reflections ( 98.63 % complete ) and 1201 restraints for refining 1040 atoms. 421 conditional restraints added. Observations/parameters ratio is 2.11 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2785 (Rfree = 0.000) for 1040 atoms. Found 16 (16 requested) and removed 19 (16 requested) atoms. Cycle 27: After refmac, R = 0.2630 (Rfree = 0.000) for 1037 atoms. Found 11 (16 requested) and removed 16 (16 requested) atoms. Cycle 28: After refmac, R = 0.2622 (Rfree = 0.000) for 1028 atoms. Found 7 (16 requested) and removed 7 (16 requested) atoms. Cycle 29: After refmac, R = 0.2556 (Rfree = 0.000) for 1027 atoms. Found 8 (16 requested) and removed 2 (16 requested) atoms. Cycle 30: After refmac, R = 0.2533 (Rfree = 0.000) for 1032 atoms. Found 4 (16 requested) and removed 2 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.38 2.65 NCS extension: 0 residues added, 1034 seeds are put forward Round 1: 105 peptides, 3 chains. Longest chain 51 peptides. Score 0.913 Round 2: 106 peptides, 2 chains. Longest chain 55 peptides. Score 0.929 Round 3: 105 peptides, 3 chains. Longest chain 54 peptides. Score 0.913 Round 4: 107 peptides, 4 chains. Longest chain 28 peptides. Score 0.903 Round 5: 108 peptides, 2 chains. Longest chain 54 peptides. Score 0.933 Taking the results from Round 5 Chains 2, Residues 106, Estimated correctness of the model 99.5 % 2 chains (106 residues) have been docked in sequence Building loops using Loopy2018 2 chains (106 residues) following loop building 2 chains (106 residues) in sequence following loop building ------------------------------------------------------ 8798 reflections ( 98.63 % complete ) and 1097 restraints for refining 1038 atoms. 258 conditional restraints added. Observations/parameters ratio is 2.12 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2701 (Rfree = 0.000) for 1038 atoms. Found 16 (16 requested) and removed 16 (16 requested) atoms. Cycle 32: After refmac, R = 0.2585 (Rfree = 0.000) for 1037 atoms. Found 16 (16 requested) and removed 16 (16 requested) atoms. Cycle 33: After refmac, R = 0.2561 (Rfree = 0.000) for 1030 atoms. Found 14 (16 requested) and removed 11 (16 requested) atoms. Cycle 34: After refmac, R = 0.2491 (Rfree = 0.000) for 1030 atoms. Found 13 (16 requested) and removed 9 (16 requested) atoms. Cycle 35: After refmac, R = 0.2441 (Rfree = 0.000) for 1033 atoms. Found 15 (16 requested) and removed 11 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.37 2.64 NCS extension: 6 residues added (0 deleted due to clashes), 1043 seeds are put forward Round 1: 107 peptides, 3 chains. Longest chain 54 peptides. Score 0.918 Round 2: 107 peptides, 3 chains. Longest chain 55 peptides. Score 0.918 Round 3: 110 peptides, 4 chains. Longest chain 56 peptides. Score 0.910 Round 4: 108 peptides, 3 chains. Longest chain 55 peptides. Score 0.920 Round 5: 108 peptides, 4 chains. Longest chain 56 peptides. Score 0.906 Taking the results from Round 4 Chains 3, Residues 105, Estimated correctness of the model 99.2 % 3 chains (105 residues) have been docked in sequence Building loops using Loopy2018 3 chains (105 residues) following loop building 3 chains (105 residues) in sequence following loop building ------------------------------------------------------ 8798 reflections ( 98.63 % complete ) and 1100 restraints for refining 1053 atoms. 257 conditional restraints added. Observations/parameters ratio is 2.09 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2722 (Rfree = 0.000) for 1053 atoms. Found 16 (16 requested) and removed 16 (16 requested) atoms. Cycle 37: After refmac, R = 0.2606 (Rfree = 0.000) for 1051 atoms. Found 16 (16 requested) and removed 16 (16 requested) atoms. Cycle 38: After refmac, R = 0.2556 (Rfree = 0.000) for 1047 atoms. Found 16 (16 requested) and removed 16 (16 requested) atoms. Cycle 39: After refmac, R = 0.2510 (Rfree = 0.000) for 1041 atoms. Found 7 (16 requested) and removed 14 (16 requested) atoms. Cycle 40: After refmac, R = 0.2479 (Rfree = 0.000) for 1032 atoms. Found 9 (16 requested) and removed 3 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.38 2.65 NCS extension: 14 residues added (48 deleted due to clashes), 1053 seeds are put forward Round 1: 111 peptides, 4 chains. Longest chain 32 peptides. Score 0.912 Round 2: 111 peptides, 2 chains. Longest chain 56 peptides. Score 0.938 Round 3: 108 peptides, 4 chains. Longest chain 29 peptides. Score 0.906 Round 4: 110 peptides, 4 chains. Longest chain 51 peptides. Score 0.910 Round 5: 110 peptides, 4 chains. Longest chain 43 peptides. Score 0.910 Taking the results from Round 2 Chains 2, Residues 109, Estimated correctness of the model 99.5 % 2 chains (109 residues) have been docked in sequence Building loops using Loopy2018 2 chains (109 residues) following loop building 2 chains (109 residues) in sequence following loop building ------------------------------------------------------ 8798 reflections ( 98.63 % complete ) and 1100 restraints for refining 1068 atoms. 230 conditional restraints added. Observations/parameters ratio is 2.06 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2705 (Rfree = 0.000) for 1068 atoms. Found 17 (17 requested) and removed 19 (17 requested) atoms. Cycle 42: After refmac, R = 0.2605 (Rfree = 0.000) for 1063 atoms. Found 16 (16 requested) and removed 17 (16 requested) atoms. Cycle 43: After refmac, R = 0.2554 (Rfree = 0.000) for 1059 atoms. Found 14 (16 requested) and removed 16 (16 requested) atoms. Cycle 44: After refmac, R = 0.2479 (Rfree = 0.000) for 1050 atoms. Found 11 (16 requested) and removed 16 (16 requested) atoms. Cycle 45: After refmac, R = 0.2432 (Rfree = 0.000) for 1042 atoms. Found 12 (16 requested) and removed 9 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.38 2.65 NCS extension: 8 residues added (1 deleted due to clashes), 1053 seeds are put forward Round 1: 108 peptides, 3 chains. Longest chain 55 peptides. Score 0.920 Round 2: 109 peptides, 3 chains. Longest chain 54 peptides. Score 0.922 Round 3: 107 peptides, 3 chains. Longest chain 55 peptides. Score 0.918 Round 4: 107 peptides, 5 chains. Longest chain 54 peptides. Score 0.888 Round 5: 108 peptides, 3 chains. Longest chain 55 peptides. Score 0.920 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 106, Estimated correctness of the model 99.3 % 3 chains (103 residues) have been docked in sequence Sequence coverage is 96 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 34 A and 40 A 2 chains (108 residues) following loop building 2 chains (108 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 8798 reflections ( 98.63 % complete ) and 858 restraints for refining 850 atoms. Observations/parameters ratio is 2.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3041 (Rfree = 0.000) for 850 atoms. Found 1 (13 requested) and removed 0 (13 requested) atoms. Cycle 47: After refmac, R = 0.2864 (Rfree = 0.000) for 850 atoms. Found 0 (13 requested) and removed 0 (13 requested) atoms. Cycle 48: After refmac, R = 0.2776 (Rfree = 0.000) for 850 atoms. Found 0 (13 requested) and removed 0 (13 requested) atoms. Cycle 49: After refmac, R = 0.2719 (Rfree = 0.000) for 850 atoms. Found 0 (13 requested) and removed 0 (13 requested) atoms. Writing output files ... TimeTaking 24.02