Sun 23 Dec 22:23:02 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 1vjx-2.3-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjx-2.3-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjx-2.3-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjx-2.3-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/1vjx-2.3-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjx-2.3-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 22:23:12 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/1vjx-2.3-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjx-2.3-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 174 and 0 Target number of residues in the AU: 174 Target solvent content: 0.5430 Checking the provided sequence file Detected sequence length: 157 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 157 Adjusted target solvent content: 0.59 Input MTZ file: 1vjx-2.3-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: 98 Cell parameters: 82.326 82.326 121.618 90.000 90.000 90.000 Input sequence file: 1vjx-2.3-parrot-hancs.fasta_lf Building free atoms model in initial map for 1256 target number of atoms Had to go as low as 0.70 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 3 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 Loops will be built when appropriate and at the last cycle Resolution range: 68.175 2.300 Wilson plot Bfac: 33.53 9304 reflections ( 96.55 % complete ) and 0 restraints for refining 1388 atoms. Observations/parameters ratio is 1.68 ------------------------------------------------------ Starting model: R = 0.3658 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3066 (Rfree = 0.000) for 1388 atoms. Found 22 (31 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.40 2.13 Round 1: 91 peptides, 17 chains. Longest chain 8 peptides. Score 0.366 Round 2: 101 peptides, 14 chains. Longest chain 12 peptides. Score 0.532 Round 3: 96 peptides, 11 chains. Longest chain 18 peptides. Score 0.586 Round 4: 111 peptides, 10 chains. Longest chain 19 peptides. Score 0.693 Round 5: 115 peptides, 12 chains. Longest chain 16 peptides. Score 0.666 Taking the results from Round 4 Chains 10, Residues 101, Estimated correctness of the model 87.2 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 9304 reflections ( 96.55 % complete ) and 2293 restraints for refining 1193 atoms. 1822 conditional restraints added. Observations/parameters ratio is 1.95 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3533 (Rfree = 0.000) for 1193 atoms. Found 17 (27 requested) and removed 14 (13 requested) atoms. Cycle 2: After refmac, R = 0.3294 (Rfree = 0.000) for 1192 atoms. Found 5 (27 requested) and removed 14 (13 requested) atoms. Cycle 3: After refmac, R = 0.3326 (Rfree = 0.000) for 1179 atoms. Found 8 (27 requested) and removed 14 (13 requested) atoms. Cycle 4: After refmac, R = 0.3427 (Rfree = 0.000) for 1170 atoms. Found 8 (26 requested) and removed 13 (13 requested) atoms. Cycle 5: After refmac, R = 0.3346 (Rfree = 0.000) for 1163 atoms. Found 12 (26 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.37 2.10 Round 1: 101 peptides, 11 chains. Longest chain 18 peptides. Score 0.616 Round 2: 111 peptides, 9 chains. Longest chain 23 peptides. Score 0.715 Round 3: 110 peptides, 11 chains. Longest chain 41 peptides. Score 0.664 Round 4: 110 peptides, 6 chains. Longest chain 51 peptides. Score 0.773 Round 5: 111 peptides, 8 chains. Longest chain 37 peptides. Score 0.736 Taking the results from Round 4 Chains 6, Residues 104, Estimated correctness of the model 92.7 % 2 chains (71 residues) have been docked in sequence Building loops using Loopy2018 6 chains (104 residues) following loop building 2 chains (71 residues) in sequence following loop building ------------------------------------------------------ 9304 reflections ( 96.55 % complete ) and 1774 restraints for refining 1202 atoms. 1052 conditional restraints added. Observations/parameters ratio is 1.94 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3356 (Rfree = 0.000) for 1202 atoms. Found 24 (27 requested) and removed 13 (13 requested) atoms. Cycle 7: After refmac, R = 0.3177 (Rfree = 0.000) for 1207 atoms. Found 12 (26 requested) and removed 14 (13 requested) atoms. Cycle 8: After refmac, R = 0.3151 (Rfree = 0.000) for 1202 atoms. Found 11 (26 requested) and removed 13 (13 requested) atoms. Cycle 9: After refmac, R = 0.3040 (Rfree = 0.000) for 1199 atoms. Found 12 (25 requested) and removed 13 (13 requested) atoms. Cycle 10: After refmac, R = 0.3050 (Rfree = 0.000) for 1195 atoms. Found 6 (25 requested) and removed 7 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.34 2.07 Round 1: 112 peptides, 10 chains. Longest chain 24 peptides. Score 0.697 Round 2: 111 peptides, 7 chains. Longest chain 28 peptides. Score 0.757 Round 3: 117 peptides, 9 chains. Longest chain 27 peptides. Score 0.741 Round 4: 123 peptides, 14 chains. Longest chain 26 peptides. Score 0.659 Round 5: 118 peptides, 10 chains. Longest chain 34 peptides. Score 0.724 Taking the results from Round 2 Chains 8, Residues 104, Estimated correctness of the model 91.7 % 2 chains (49 residues) have been docked in sequence Building loops using Loopy2018 8 chains (104 residues) following loop building 2 chains (49 residues) in sequence following loop building ------------------------------------------------------ 9304 reflections ( 96.55 % complete ) and 1989 restraints for refining 1201 atoms. 1363 conditional restraints added. Observations/parameters ratio is 1.94 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3206 (Rfree = 0.000) for 1201 atoms. Found 24 (24 requested) and removed 18 (13 requested) atoms. Cycle 12: After refmac, R = 0.3037 (Rfree = 0.000) for 1204 atoms. Found 7 (24 requested) and removed 13 (13 requested) atoms. Cycle 13: After refmac, R = 0.2966 (Rfree = 0.000) for 1195 atoms. Found 5 (23 requested) and removed 15 (13 requested) atoms. Cycle 14: After refmac, R = 0.2968 (Rfree = 0.000) for 1183 atoms. Found 10 (23 requested) and removed 13 (13 requested) atoms. Cycle 15: After refmac, R = 0.3058 (Rfree = 0.000) for 1177 atoms. Found 15 (22 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.35 2.08 Round 1: 116 peptides, 9 chains. Longest chain 29 peptides. Score 0.736 Round 2: 116 peptides, 7 chains. Longest chain 41 peptides. Score 0.776 Round 3: 120 peptides, 8 chains. Longest chain 49 peptides. Score 0.772 Round 4: 122 peptides, 7 chains. Longest chain 46 peptides. Score 0.797 Round 5: 118 peptides, 11 chains. Longest chain 24 peptides. Score 0.703 Taking the results from Round 4 Chains 9, Residues 115, Estimated correctness of the model 94.0 % 3 chains (85 residues) have been docked in sequence Building loops using Loopy2018 9 chains (115 residues) following loop building 3 chains (85 residues) in sequence following loop building ------------------------------------------------------ 9304 reflections ( 96.55 % complete ) and 1597 restraints for refining 1214 atoms. 761 conditional restraints added. Observations/parameters ratio is 1.92 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3058 (Rfree = 0.000) for 1214 atoms. Found 22 (22 requested) and removed 15 (13 requested) atoms. Cycle 17: After refmac, R = 0.2919 (Rfree = 0.000) for 1219 atoms. Found 16 (22 requested) and removed 14 (14 requested) atoms. Cycle 18: After refmac, R = 0.2893 (Rfree = 0.000) for 1217 atoms. Found 13 (21 requested) and removed 8 (13 requested) atoms. Cycle 19: After refmac, R = 0.2843 (Rfree = 0.000) for 1221 atoms. Found 5 (21 requested) and removed 5 (14 requested) atoms. Cycle 20: After refmac, R = 0.2852 (Rfree = 0.000) for 1220 atoms. Found 7 (20 requested) and removed 4 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.34 2.07 Round 1: 118 peptides, 9 chains. Longest chain 28 peptides. Score 0.745 Round 2: 117 peptides, 7 chains. Longest chain 29 peptides. Score 0.780 Round 3: 117 peptides, 9 chains. Longest chain 24 peptides. Score 0.741 Round 4: 119 peptides, 9 chains. Longest chain 38 peptides. Score 0.749 Round 5: 116 peptides, 8 chains. Longest chain 31 peptides. Score 0.757 Taking the results from Round 2 Chains 9, Residues 110, Estimated correctness of the model 93.1 % 4 chains (93 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 127 A and 131 A 8 chains (113 residues) following loop building 3 chains (96 residues) in sequence following loop building ------------------------------------------------------ 9304 reflections ( 96.55 % complete ) and 1619 restraints for refining 1247 atoms. 755 conditional restraints added. Observations/parameters ratio is 1.87 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2882 (Rfree = 0.000) for 1247 atoms. Found 20 (20 requested) and removed 16 (14 requested) atoms. Cycle 22: After refmac, R = 0.2777 (Rfree = 0.000) for 1251 atoms. Found 14 (19 requested) and removed 13 (14 requested) atoms. Cycle 23: After refmac, R = 0.2789 (Rfree = 0.000) for 1251 atoms. Found 6 (18 requested) and removed 7 (14 requested) atoms. Cycle 24: After refmac, R = 0.2767 (Rfree = 0.000) for 1249 atoms. Found 12 (18 requested) and removed 2 (14 requested) atoms. Cycle 25: After refmac, R = 0.2785 (Rfree = 0.000) for 1258 atoms. Found 11 (18 requested) and removed 7 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.34 2.07 Round 1: 119 peptides, 8 chains. Longest chain 30 peptides. Score 0.768 Round 2: 120 peptides, 9 chains. Longest chain 28 peptides. Score 0.753 Round 3: 118 peptides, 12 chains. Longest chain 23 peptides. Score 0.681 Round 4: 116 peptides, 14 chains. Longest chain 25 peptides. Score 0.623 Round 5: 123 peptides, 9 chains. Longest chain 37 peptides. Score 0.764 Taking the results from Round 1 Chains 12, Residues 111, Estimated correctness of the model 92.4 % 4 chains (88 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 127 A and 132 A 9 chains (112 residues) following loop building 3 chains (92 residues) in sequence following loop building ------------------------------------------------------ 9304 reflections ( 96.55 % complete ) and 1681 restraints for refining 1275 atoms. 835 conditional restraints added. Observations/parameters ratio is 1.82 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2865 (Rfree = 0.000) for 1275 atoms. Found 18 (18 requested) and removed 21 (14 requested) atoms. Cycle 27: After refmac, R = 0.2728 (Rfree = 0.000) for 1270 atoms. Found 12 (17 requested) and removed 14 (14 requested) atoms. Cycle 28: After refmac, R = 0.2678 (Rfree = 0.000) for 1266 atoms. Found 16 (17 requested) and removed 10 (14 requested) atoms. Cycle 29: After refmac, R = 0.2615 (Rfree = 0.000) for 1270 atoms. Found 10 (16 requested) and removed 6 (14 requested) atoms. Cycle 30: After refmac, R = 0.2585 (Rfree = 0.000) for 1274 atoms. Found 8 (16 requested) and removed 3 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.35 2.08 Round 1: 119 peptides, 9 chains. Longest chain 30 peptides. Score 0.749 Round 2: 125 peptides, 7 chains. Longest chain 55 peptides. Score 0.807 Round 3: 123 peptides, 9 chains. Longest chain 42 peptides. Score 0.764 Round 4: 124 peptides, 10 chains. Longest chain 28 peptides. Score 0.749 Round 5: 121 peptides, 12 chains. Longest chain 23 peptides. Score 0.695 Taking the results from Round 2 Chains 9, Residues 118, Estimated correctness of the model 94.5 % 3 chains (94 residues) have been docked in sequence Building loops using Loopy2018 9 chains (118 residues) following loop building 3 chains (94 residues) in sequence following loop building ------------------------------------------------------ 9304 reflections ( 96.55 % complete ) and 1613 restraints for refining 1277 atoms. 734 conditional restraints added. Observations/parameters ratio is 1.82 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2761 (Rfree = 0.000) for 1277 atoms. Found 16 (16 requested) and removed 17 (14 requested) atoms. Cycle 32: After refmac, R = 0.2697 (Rfree = 0.000) for 1276 atoms. Found 11 (15 requested) and removed 14 (14 requested) atoms. Cycle 33: After refmac, R = 0.2673 (Rfree = 0.000) for 1272 atoms. Found 8 (14 requested) and removed 11 (14 requested) atoms. Cycle 34: After refmac, R = 0.2640 (Rfree = 0.000) for 1267 atoms. Found 3 (14 requested) and removed 6 (14 requested) atoms. Cycle 35: After refmac, R = 0.2652 (Rfree = 0.000) for 1264 atoms. Found 5 (14 requested) and removed 1 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.35 2.08 Round 1: 120 peptides, 9 chains. Longest chain 27 peptides. Score 0.753 Round 2: 120 peptides, 9 chains. Longest chain 24 peptides. Score 0.753 Round 3: 129 peptides, 8 chains. Longest chain 42 peptides. Score 0.803 Round 4: 130 peptides, 9 chains. Longest chain 40 peptides. Score 0.789 Round 5: 126 peptides, 8 chains. Longest chain 44 peptides. Score 0.793 Taking the results from Round 3 Chains 8, Residues 121, Estimated correctness of the model 94.3 % 3 chains (85 residues) have been docked in sequence Building loops using Loopy2018 8 chains (121 residues) following loop building 3 chains (85 residues) in sequence following loop building ------------------------------------------------------ 9304 reflections ( 96.55 % complete ) and 1700 restraints for refining 1252 atoms. 864 conditional restraints added. Observations/parameters ratio is 1.86 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2811 (Rfree = 0.000) for 1252 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 37: After refmac, R = 0.2724 (Rfree = 0.000) for 1252 atoms. Found 14 (14 requested) and removed 14 (14 requested) atoms. Cycle 38: After refmac, R = 0.2662 (Rfree = 0.000) for 1251 atoms. Found 12 (14 requested) and removed 11 (14 requested) atoms. Cycle 39: After refmac, R = 0.2625 (Rfree = 0.000) for 1252 atoms. Found 2 (14 requested) and removed 5 (14 requested) atoms. Cycle 40: After refmac, R = 0.2619 (Rfree = 0.000) for 1249 atoms. Found 2 (14 requested) and removed 3 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.34 2.07 Round 1: 122 peptides, 10 chains. Longest chain 33 peptides. Score 0.741 Round 2: 128 peptides, 11 chains. Longest chain 24 peptides. Score 0.745 Round 3: 128 peptides, 8 chains. Longest chain 54 peptides. Score 0.799 Round 4: 122 peptides, 11 chains. Longest chain 23 peptides. Score 0.721 Round 5: 124 peptides, 7 chains. Longest chain 48 peptides. Score 0.803 Taking the results from Round 5 Chains 10, Residues 117, Estimated correctness of the model 94.3 % 3 chains (77 residues) have been docked in sequence Building loops using Loopy2018 10 chains (117 residues) following loop building 3 chains (77 residues) in sequence following loop building ------------------------------------------------------ 9304 reflections ( 96.55 % complete ) and 1766 restraints for refining 1253 atoms. 960 conditional restraints added. Observations/parameters ratio is 1.86 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2863 (Rfree = 0.000) for 1253 atoms. Found 14 (14 requested) and removed 16 (14 requested) atoms. Cycle 42: After refmac, R = 0.2784 (Rfree = 0.000) for 1250 atoms. Found 14 (14 requested) and removed 16 (14 requested) atoms. Cycle 43: After refmac, R = 0.2750 (Rfree = 0.000) for 1246 atoms. Found 7 (14 requested) and removed 13 (14 requested) atoms. Cycle 44: After refmac, R = 0.2739 (Rfree = 0.000) for 1237 atoms. Found 3 (14 requested) and removed 7 (14 requested) atoms. Cycle 45: After refmac, R = 0.2688 (Rfree = 0.000) for 1232 atoms. Found 6 (14 requested) and removed 6 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.35 2.08 Round 1: 127 peptides, 9 chains. Longest chain 36 peptides. Score 0.779 Round 2: 133 peptides, 8 chains. Longest chain 44 peptides. Score 0.815 Round 3: 125 peptides, 9 chains. Longest chain 31 peptides. Score 0.771 Round 4: 124 peptides, 10 chains. Longest chain 39 peptides. Score 0.749 Round 5: 119 peptides, 9 chains. Longest chain 26 peptides. Score 0.749 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 125, Estimated correctness of the model 94.9 % 3 chains (94 residues) have been docked in sequence Sequence coverage is 74 % Consider running further cycles of model building using 1vjx-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 92 A and 97 A 7 chains (129 residues) following loop building 2 chains (98 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9304 reflections ( 96.55 % complete ) and 1701 restraints for refining 1308 atoms. 773 conditional restraints added. Observations/parameters ratio is 1.78 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2814 (Rfree = 0.000) for 1308 atoms. Found 0 (15 requested) and removed 1 (15 requested) atoms. Cycle 47: After refmac, R = 0.2809 (Rfree = 0.000) for 1305 atoms. Found 0 (15 requested) and removed 0 (15 requested) atoms. Cycle 48: After refmac, R = 0.2806 (Rfree = 0.000) for 1304 atoms. Found 0 (15 requested) and removed 1 (15 requested) atoms. Cycle 49: After refmac, R = 0.2757 (Rfree = 0.000) for 1303 atoms. Found 0 (14 requested) and removed 1 (14 requested) atoms. Writing output files ... TimeTaking 32.55