Tue 25 Dec 19:27:58 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 1vkd-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkd-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkd-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-4.0-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/1vkd-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-4.0-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 ============================================================ Tue 25 Dec 19:28:06 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/1vkd-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-4.0-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 1592 and 0 Target number of residues in the AU: 1592 Target solvent content: 0.6169 Checking the provided sequence file Detected sequence length: 338 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 2028 Adjusted target solvent content: 0.51 Input MTZ file: 1vkd-4.0-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: 86.922 101.512 254.880 90.000 90.000 90.000 Input sequence file: 1vkd-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 16224 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 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: 127.440 4.000 Wilson plot Bfac: 59.94 19706 reflections ( 99.63 % complete ) and 0 restraints for refining 17881 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3050 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2999 (Rfree = 0.000) for 17881 atoms. Found 84 (84 requested) and removed 84 (42 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.38 Search for helices and strands: 0 residues in 0 chains, 18074 seeds are put forward NCS extension: 0 residues added, 18074 seeds are put forward Round 1: 806 peptides, 158 chains. Longest chain 13 peptides. Score 0.312 Round 2: 1049 peptides, 175 chains. Longest chain 19 peptides. Score 0.437 Round 3: 1138 peptides, 174 chains. Longest chain 17 peptides. Score 0.497 Round 4: 1200 peptides, 173 chains. Longest chain 19 peptides. Score 0.538 Round 5: 1259 peptides, 170 chains. Longest chain 31 peptides. Score 0.579 Taking the results from Round 5 Chains 172, Residues 1089, Estimated correctness of the model 0.0 % 9 chains (76 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 19706 reflections ( 99.63 % complete ) and 32392 restraints for refining 14649 atoms. 27955 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2286 (Rfree = 0.000) for 14649 atoms. Found 34 (69 requested) and removed 108 (34 requested) atoms. Cycle 2: After refmac, R = 0.2199 (Rfree = 0.000) for 14327 atoms. Found 33 (69 requested) and removed 91 (34 requested) atoms. Cycle 3: After refmac, R = 0.2134 (Rfree = 0.000) for 14160 atoms. Found 43 (67 requested) and removed 65 (33 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2069 (Rfree = 0.000) for 14048 atoms. Found 36 (67 requested) and removed 75 (33 requested) atoms. Cycle 5: After refmac, R = 0.2039 (Rfree = 0.000) for 13968 atoms. Found 55 (66 requested) and removed 73 (33 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.36 Search for helices and strands: 0 residues in 0 chains, 14270 seeds are put forward NCS extension: 27 residues added (5 deleted due to clashes), 14297 seeds are put forward Round 1: 1030 peptides, 186 chains. Longest chain 14 peptides. Score 0.391 Round 2: 1160 peptides, 181 chains. Longest chain 21 peptides. Score 0.492 Round 3: 1190 peptides, 164 chains. Longest chain 23 peptides. Score 0.555 Round 4: 1201 peptides, 164 chains. Longest chain 25 peptides. Score 0.561 Round 5: 1199 peptides, 168 chains. Longest chain 20 peptides. Score 0.550 Taking the results from Round 4 Chains 170, Residues 1037, Estimated correctness of the model 0.0 % 14 chains (116 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 19706 reflections ( 99.63 % complete ) and 32246 restraints for refining 14650 atoms. 27832 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2089 (Rfree = 0.000) for 14650 atoms. Found 47 (69 requested) and removed 123 (34 requested) atoms. Cycle 7: After refmac, R = 0.1968 (Rfree = 0.000) for 14447 atoms. Found 31 (69 requested) and removed 87 (34 requested) atoms. Cycle 8: After refmac, R = 0.1882 (Rfree = 0.000) for 14324 atoms. Found 24 (68 requested) and removed 89 (34 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1821 (Rfree = 0.000) for 14224 atoms. Found 28 (67 requested) and removed 69 (33 requested) atoms. Cycle 10: After refmac, R = 0.1820 (Rfree = 0.000) for 14140 atoms. Found 35 (67 requested) and removed 67 (33 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.36 Search for helices and strands: 0 residues in 0 chains, 14379 seeds are put forward NCS extension: 35 residues added (4 deleted due to clashes), 14414 seeds are put forward Round 1: 1055 peptides, 186 chains. Longest chain 16 peptides. Score 0.408 Round 2: 1110 peptides, 167 chains. Longest chain 16 peptides. Score 0.499 Round 3: 1156 peptides, 169 chains. Longest chain 23 peptides. Score 0.522 Round 4: 1188 peptides, 164 chains. Longest chain 23 peptides. Score 0.554 Round 5: 1182 peptides, 165 chains. Longest chain 20 peptides. Score 0.548 Taking the results from Round 4 Chains 165, Residues 1024, Estimated correctness of the model 0.0 % 9 chains (56 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 32464 restraints for refining 14651 atoms. 28344 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2003 (Rfree = 0.000) for 14651 atoms. Found 48 (69 requested) and removed 90 (34 requested) atoms. Cycle 12: After refmac, R = 0.1940 (Rfree = 0.000) for 14533 atoms. Found 46 (69 requested) and removed 95 (34 requested) atoms. Cycle 13: After refmac, R = 0.1948 (Rfree = 0.000) for 14440 atoms. Found 66 (68 requested) and removed 85 (34 requested) atoms. Cycle 14: After refmac, R = 0.1855 (Rfree = 0.000) for 14394 atoms. Found 44 (68 requested) and removed 83 (34 requested) atoms. Cycle 15: After refmac, R = 0.1779 (Rfree = 0.000) for 14338 atoms. Found 43 (68 requested) and removed 74 (34 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 3.39 Search for helices and strands: 0 residues in 0 chains, 14570 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 14585 seeds are put forward Round 1: 991 peptides, 178 chains. Longest chain 14 peptides. Score 0.387 Round 2: 1103 peptides, 174 chains. Longest chain 22 peptides. Score 0.475 Round 3: 1124 peptides, 171 chains. Longest chain 23 peptides. Score 0.497 Round 4: 1140 peptides, 169 chains. Longest chain 21 peptides. Score 0.512 Round 5: 1152 peptides, 172 chains. Longest chain 19 peptides. Score 0.512 Taking the results from Round 5 Chains 172, Residues 980, Estimated correctness of the model 0.0 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 33255 restraints for refining 14652 atoms. 29346 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2124 (Rfree = 0.000) for 14652 atoms. Found 59 (69 requested) and removed 83 (34 requested) atoms. Cycle 17: After refmac, R = 0.2016 (Rfree = 0.000) for 14489 atoms. Found 57 (69 requested) and removed 62 (34 requested) atoms. Cycle 18: After refmac, R = 0.1646 (Rfree = 0.000) for 14400 atoms. Found 34 (68 requested) and removed 53 (34 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 19: After refmac, R = 0.1528 (Rfree = 0.000) for 14343 atoms. Found 14 (68 requested) and removed 53 (34 requested) atoms. Cycle 20: After refmac, R = 0.1497 (Rfree = 0.000) for 14284 atoms. Found 12 (67 requested) and removed 48 (33 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.42 Search for helices and strands: 0 residues in 0 chains, 14520 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 14539 seeds are put forward Round 1: 974 peptides, 184 chains. Longest chain 12 peptides. Score 0.357 Round 2: 1073 peptides, 170 chains. Longest chain 20 peptides. Score 0.467 Round 3: 1060 peptides, 162 chains. Longest chain 16 peptides. Score 0.481 Round 4: 1096 peptides, 172 chains. Longest chain 15 peptides. Score 0.476 Round 5: 1091 peptides, 164 chains. Longest chain 21 peptides. Score 0.495 Taking the results from Round 5 Chains 165, Residues 927, Estimated correctness of the model 0.0 % 8 chains (53 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 33651 restraints for refining 14649 atoms. 29923 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2074 (Rfree = 0.000) for 14649 atoms. Found 42 (69 requested) and removed 72 (34 requested) atoms. Cycle 22: After refmac, R = 0.2018 (Rfree = 0.000) for 14512 atoms. Found 68 (69 requested) and removed 84 (34 requested) atoms. Cycle 23: After refmac, R = 0.1887 (Rfree = 0.000) for 14448 atoms. Found 60 (68 requested) and removed 88 (34 requested) atoms. Cycle 24: After refmac, R = 0.1809 (Rfree = 0.000) for 14383 atoms. Found 51 (68 requested) and removed 68 (34 requested) atoms. Cycle 25: After refmac, R = 0.1798 (Rfree = 0.000) for 14339 atoms. Found 68 (68 requested) and removed 60 (34 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 14595 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 14612 seeds are put forward Round 1: 886 peptides, 171 chains. Longest chain 15 peptides. Score 0.332 Round 2: 974 peptides, 156 chains. Longest chain 23 peptides. Score 0.442 Round 3: 1019 peptides, 162 chains. Longest chain 15 peptides. Score 0.454 Round 4: 1032 peptides, 153 chains. Longest chain 20 peptides. Score 0.489 Round 5: 1027 peptides, 144 chains. Longest chain 24 peptides. Score 0.511 Taking the results from Round 5 Chains 146, Residues 883, Estimated correctness of the model 0.0 % 8 chains (50 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 19706 reflections ( 99.63 % complete ) and 33487 restraints for refining 14652 atoms. 29937 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2005 (Rfree = 0.000) for 14652 atoms. Found 53 (69 requested) and removed 85 (34 requested) atoms. Cycle 27: After refmac, R = 0.1906 (Rfree = 0.000) for 14519 atoms. Found 69 (69 requested) and removed 78 (34 requested) atoms. Cycle 28: After refmac, R = 0.1849 (Rfree = 0.000) for 14458 atoms. Found 68 (68 requested) and removed 64 (34 requested) atoms. Cycle 29: After refmac, R = 0.1712 (Rfree = 0.000) for 14425 atoms. Found 65 (68 requested) and removed 67 (34 requested) atoms. Cycle 30: After refmac, R = 0.1445 (Rfree = 0.000) for 14395 atoms. Found 16 (68 requested) and removed 49 (34 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 3.41 Search for helices and strands: 0 residues in 0 chains, 14631 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 14666 seeds are put forward Round 1: 858 peptides, 170 chains. Longest chain 14 peptides. Score 0.314 Round 2: 939 peptides, 161 chains. Longest chain 14 peptides. Score 0.402 Round 3: 975 peptides, 157 chains. Longest chain 15 peptides. Score 0.439 Round 4: 1016 peptides, 167 chains. Longest chain 18 peptides. Score 0.438 Round 5: 1049 peptides, 155 chains. Longest chain 21 peptides. Score 0.494 Taking the results from Round 5 Chains 155, Residues 894, Estimated correctness of the model 0.0 % 6 chains (41 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 33664 restraints for refining 14652 atoms. 30085 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2118 (Rfree = 0.000) for 14652 atoms. Found 69 (69 requested) and removed 80 (34 requested) atoms. Cycle 32: After refmac, R = 0.2031 (Rfree = 0.000) for 14535 atoms. Found 69 (69 requested) and removed 66 (34 requested) atoms. Cycle 33: After refmac, R = 0.1885 (Rfree = 0.000) for 14478 atoms. Found 69 (69 requested) and removed 63 (34 requested) atoms. Cycle 34: After refmac, R = 0.1488 (Rfree = 0.000) for 14450 atoms. Found 27 (68 requested) and removed 57 (34 requested) atoms. Cycle 35: After refmac, R = 0.1387 (Rfree = 0.000) for 14395 atoms. Found 13 (68 requested) and removed 47 (34 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 3.43 Search for helices and strands: 0 residues in 0 chains, 14531 seeds are put forward NCS extension: 35 residues added (1 deleted due to clashes), 14566 seeds are put forward Round 1: 813 peptides, 166 chains. Longest chain 15 peptides. Score 0.292 Round 2: 898 peptides, 151 chains. Longest chain 16 peptides. Score 0.404 Round 3: 906 peptides, 151 chains. Longest chain 18 peptides. Score 0.410 Round 4: 916 peptides, 150 chains. Longest chain 13 peptides. Score 0.420 Round 5: 955 peptides, 146 chains. Longest chain 23 peptides. Score 0.458 Taking the results from Round 5 Chains 146, Residues 809, Estimated correctness of the model 0.0 % 6 chains (27 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 34153 restraints for refining 14649 atoms. 30968 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2009 (Rfree = 0.000) for 14649 atoms. Found 69 (69 requested) and removed 79 (34 requested) atoms. Cycle 37: After refmac, R = 0.1927 (Rfree = 0.000) for 14560 atoms. Found 69 (69 requested) and removed 70 (34 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1883 (Rfree = 0.000) for 14507 atoms. Found 69 (69 requested) and removed 74 (34 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1816 (Rfree = 0.000) for 14471 atoms. Found 68 (68 requested) and removed 56 (34 requested) atoms. Cycle 40: After refmac, R = 0.1815 (Rfree = 0.000) for 14438 atoms. Found 68 (68 requested) and removed 53 (34 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.39 Search for helices and strands: 0 residues in 0 chains, 14666 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 14682 seeds are put forward Round 1: 718 peptides, 145 chains. Longest chain 10 peptides. Score 0.286 Round 2: 817 peptides, 145 chains. Longest chain 12 peptides. Score 0.364 Round 3: 824 peptides, 140 chains. Longest chain 15 peptides. Score 0.385 Round 4: 819 peptides, 136 chains. Longest chain 21 peptides. Score 0.394 Round 5: 810 peptides, 131 chains. Longest chain 15 peptides. Score 0.403 Taking the results from Round 5 Chains 132, Residues 679, Estimated correctness of the model 0.0 % 9 chains (52 residues) have been docked in sequence ------------------------------------------------------ 19706 reflections ( 99.63 % complete ) and 34524 restraints for refining 14650 atoms. 31738 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1990 (Rfree = 0.000) for 14650 atoms. Found 69 (69 requested) and removed 79 (34 requested) atoms. Cycle 42: After refmac, R = 0.1893 (Rfree = 0.000) for 14577 atoms. Found 69 (69 requested) and removed 69 (34 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 43: After refmac, R = 0.1760 (Rfree = 0.000) for 14536 atoms. Found 69 (69 requested) and removed 57 (34 requested) atoms. Cycle 44: After refmac, R = 0.1352 (Rfree = 0.000) for 14513 atoms. Found 28 (69 requested) and removed 43 (34 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1260 (Rfree = 0.000) for 14477 atoms. Found 12 (68 requested) and removed 41 (34 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 3.40 Search for helices and strands: 0 residues in 0 chains, 14625 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 14643 seeds are put forward Round 1: 665 peptides, 137 chains. Longest chain 11 peptides. Score 0.270 Round 2: 774 peptides, 138 chains. Longest chain 18 peptides. Score 0.354 Round 3: 791 peptides, 135 chains. Longest chain 16 peptides. Score 0.377 Round 4: 772 peptides, 128 chains. Longest chain 17 peptides. Score 0.385 Round 5: 769 peptides, 122 chains. Longest chain 18 peptides. Score 0.403 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 123, Residues 647, Estimated correctness of the model 0.0 % 9 chains (50 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vkd-4_warpNtrace.pdb as input Building loops using Loopy2018 123 chains (647 residues) following loop building 9 chains (50 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 19706 reflections ( 99.63 % complete ) and 34571 restraints for refining 14652 atoms. 31932 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1956 (Rfree = 0.000) for 14652 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.1897 (Rfree = 0.000) for 14557 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.1829 (Rfree = 0.000) for 14466 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Cycle 49: After refmac, R = 0.1742 (Rfree = 0.000) for 14383 atoms. Found 0 (68 requested) and removed 34 (34 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 22:36:02 GMT 2018 Job finished. TimeTaking 188.08