Sun 23 Dec 22:23:10 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 2prr-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2prr-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2prr-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-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/2prr-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-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 ============================================================ Sun 23 Dec 22:23:19 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/2prr-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prr-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 1687 and 0 Target number of residues in the AU: 1687 Target solvent content: 0.6799 Checking the provided sequence file Detected sequence length: 197 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 12 Adjusted target number of residues: 2364 Adjusted target solvent content: 0.55 Input MTZ file: 2prr-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: 1 Cell parameters: 65.105 93.953 120.898 84.262 81.638 77.734 Input sequence file: 2prr-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 18912 target number of atoms Had to go as low as 0.85 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: 119.307 4.000 Wilson plot Bfac: 101.00 Failed to save intermediate PDB 22829 reflections ( 97.72 % complete ) and 0 restraints for refining 20904 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3267 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2939 (Rfree = 0.000) for 20904 atoms. Found 99 (99 requested) and removed 127 (49 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.95 3.69 Search for helices and strands: 0 residues in 0 chains, 21515 seeds are put forward NCS extension: 0 residues added, 21515 seeds are put forward Round 1: 974 peptides, 185 chains. Longest chain 15 peptides. Score 0.323 Round 2: 1148 peptides, 162 chains. Longest chain 21 peptides. Score 0.479 Round 3: 1189 peptides, 163 chains. Longest chain 23 peptides. Score 0.498 Round 4: 1191 peptides, 149 chains. Longest chain 25 peptides. Score 0.530 Round 5: 1204 peptides, 142 chains. Longest chain 29 peptides. Score 0.552 Taking the results from Round 5 Chains 146, Residues 1062, Estimated correctness of the model 0.0 % 5 chains (63 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 39382 restraints for refining 17066 atoms. 35027 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2093 (Rfree = 0.000) for 17066 atoms. Found 28 (81 requested) and removed 96 (40 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.1948 (Rfree = 0.000) for 16786 atoms. Found 34 (80 requested) and removed 78 (40 requested) atoms. Cycle 3: After refmac, R = 0.1853 (Rfree = 0.000) for 16646 atoms. Found 22 (79 requested) and removed 84 (39 requested) atoms. Cycle 4: After refmac, R = 0.1823 (Rfree = 0.000) for 16496 atoms. Found 29 (78 requested) and removed 79 (39 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.1787 (Rfree = 0.000) for 16389 atoms. Found 53 (78 requested) and removed 84 (39 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.91 3.66 Search for helices and strands: 0 residues in 0 chains, 17156 seeds are put forward NCS extension: 36 residues added (0 deleted due to clashes), 17192 seeds are put forward Round 1: 1040 peptides, 182 chains. Longest chain 15 peptides. Score 0.371 Round 2: 1171 peptides, 157 chains. Longest chain 23 peptides. Score 0.503 Round 3: 1195 peptides, 152 chains. Longest chain 19 peptides. Score 0.526 Round 4: 1194 peptides, 146 chains. Longest chain 28 peptides. Score 0.538 Round 5: 1202 peptides, 158 chains. Longest chain 19 peptides. Score 0.516 Taking the results from Round 4 Chains 147, Residues 1048, Estimated correctness of the model 0.0 % 3 chains (38 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 22829 reflections ( 97.72 % complete ) and 38927 restraints for refining 17077 atoms. 34715 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1921 (Rfree = 0.000) for 17077 atoms. Found 39 (81 requested) and removed 134 (40 requested) atoms. Cycle 7: After refmac, R = 0.1891 (Rfree = 0.000) for 16834 atoms. Found 52 (80 requested) and removed 107 (40 requested) atoms. Cycle 8: After refmac, R = 0.1717 (Rfree = 0.000) for 16710 atoms. Found 28 (79 requested) and removed 89 (39 requested) atoms. Cycle 9: After refmac, R = 0.1675 (Rfree = 0.000) for 16602 atoms. Found 38 (79 requested) and removed 68 (39 requested) atoms. Cycle 10: After refmac, R = 0.1377 (Rfree = 0.000) for 16531 atoms. Found 9 (78 requested) and removed 63 (39 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.92 3.67 Search for helices and strands: 0 residues in 0 chains, 17225 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 17253 seeds are put forward Round 1: 1058 peptides, 172 chains. Longest chain 17 peptides. Score 0.406 Round 2: 1173 peptides, 158 chains. Longest chain 21 peptides. Score 0.501 Round 3: 1150 peptides, 158 chains. Longest chain 21 peptides. Score 0.490 Round 4: 1187 peptides, 158 chains. Longest chain 20 peptides. Score 0.508 Round 5: 1180 peptides, 158 chains. Longest chain 21 peptides. Score 0.505 Taking the results from Round 4 Chains 160, Residues 1029, Estimated correctness of the model 0.0 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 39003 restraints for refining 17073 atoms. 34939 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1810 (Rfree = 0.000) for 17073 atoms. Found 36 (81 requested) and removed 97 (40 requested) atoms. Cycle 12: After refmac, R = 0.1806 (Rfree = 0.000) for 16886 atoms. Found 29 (80 requested) and removed 95 (40 requested) atoms. Cycle 13: After refmac, R = 0.1759 (Rfree = 0.000) for 16763 atoms. Found 48 (79 requested) and removed 73 (39 requested) atoms. Cycle 14: After refmac, R = 0.1685 (Rfree = 0.000) for 16684 atoms. Found 33 (79 requested) and removed 67 (39 requested) atoms. Cycle 15: After refmac, R = 0.1350 (Rfree = 0.000) for 16602 atoms. Found 6 (79 requested) and removed 60 (39 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.92 3.67 Search for helices and strands: 0 residues in 0 chains, 17248 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 17266 seeds are put forward Round 1: 1037 peptides, 189 chains. Longest chain 13 peptides. Score 0.351 Round 2: 1134 peptides, 166 chains. Longest chain 17 peptides. Score 0.463 Round 3: 1178 peptides, 163 chains. Longest chain 17 peptides. Score 0.492 Round 4: 1171 peptides, 161 chains. Longest chain 21 peptides. Score 0.493 Round 5: 1199 peptides, 161 chains. Longest chain 21 peptides. Score 0.508 Taking the results from Round 5 Chains 164, Residues 1038, Estimated correctness of the model 0.0 % 5 chains (41 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 39020 restraints for refining 17078 atoms. 34849 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1870 (Rfree = 0.000) for 17078 atoms. Found 31 (81 requested) and removed 93 (40 requested) atoms. Cycle 17: After refmac, R = 0.1811 (Rfree = 0.000) for 16895 atoms. Found 41 (80 requested) and removed 81 (40 requested) atoms. Cycle 18: After refmac, R = 0.1710 (Rfree = 0.000) for 16777 atoms. Found 36 (80 requested) and removed 82 (40 requested) atoms. Cycle 19: After refmac, R = 0.1696 (Rfree = 0.000) for 16683 atoms. Found 35 (79 requested) and removed 73 (39 requested) atoms. Cycle 20: After refmac, R = 0.1643 (Rfree = 0.000) for 16599 atoms. Found 38 (79 requested) and removed 67 (39 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.92 3.67 Search for helices and strands: 0 residues in 0 chains, 17303 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 17328 seeds are put forward Round 1: 996 peptides, 187 chains. Longest chain 14 peptides. Score 0.331 Round 2: 1133 peptides, 164 chains. Longest chain 19 peptides. Score 0.467 Round 3: 1113 peptides, 153 chains. Longest chain 22 peptides. Score 0.482 Round 4: 1113 peptides, 155 chains. Longest chain 22 peptides. Score 0.477 Round 5: 1139 peptides, 158 chains. Longest chain 19 peptides. Score 0.484 Taking the results from Round 5 Chains 163, Residues 981, Estimated correctness of the model 0.0 % 5 chains (38 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 39330 restraints for refining 17076 atoms. 35424 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1918 (Rfree = 0.000) for 17076 atoms. Found 59 (81 requested) and removed 100 (40 requested) atoms. Cycle 22: After refmac, R = 0.1776 (Rfree = 0.000) for 16921 atoms. Found 55 (80 requested) and removed 79 (40 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1713 (Rfree = 0.000) for 16841 atoms. Found 43 (80 requested) and removed 77 (40 requested) atoms. Cycle 24: After refmac, R = 0.1665 (Rfree = 0.000) for 16768 atoms. Found 41 (79 requested) and removed 72 (39 requested) atoms. Cycle 25: After refmac, R = 0.1338 (Rfree = 0.000) for 16709 atoms. Found 2 (79 requested) and removed 54 (39 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.94 3.69 Search for helices and strands: 0 residues in 0 chains, 17301 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 17324 seeds are put forward Round 1: 928 peptides, 176 chains. Longest chain 13 peptides. Score 0.318 Round 2: 1065 peptides, 171 chains. Longest chain 20 peptides. Score 0.413 Round 3: 1059 peptides, 161 chains. Longest chain 23 peptides. Score 0.434 Round 4: 1075 peptides, 151 chains. Longest chain 31 peptides. Score 0.467 Round 5: 1075 peptides, 154 chains. Longest chain 19 peptides. Score 0.460 Taking the results from Round 4 Chains 151, Residues 924, Estimated correctness of the model 0.0 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 39393 restraints for refining 17071 atoms. 35680 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1882 (Rfree = 0.000) for 17071 atoms. Found 59 (81 requested) and removed 81 (40 requested) atoms. Cycle 27: After refmac, R = 0.1811 (Rfree = 0.000) for 16957 atoms. Found 69 (81 requested) and removed 72 (40 requested) atoms. Cycle 28: After refmac, R = 0.1732 (Rfree = 0.000) for 16900 atoms. Found 69 (80 requested) and removed 70 (40 requested) atoms. Cycle 29: After refmac, R = 0.1663 (Rfree = 0.000) for 16854 atoms. Found 72 (80 requested) and removed 63 (40 requested) atoms. Cycle 30: After refmac, R = 0.1281 (Rfree = 0.000) for 16836 atoms. Found 11 (80 requested) and removed 53 (40 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.91 3.66 Search for helices and strands: 0 residues in 0 chains, 17374 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 17397 seeds are put forward Round 1: 886 peptides, 170 chains. Longest chain 14 peptides. Score 0.308 Round 2: 999 peptides, 152 chains. Longest chain 18 peptides. Score 0.423 Round 3: 996 peptides, 158 chains. Longest chain 25 peptides. Score 0.406 Round 4: 1021 peptides, 158 chains. Longest chain 18 peptides. Score 0.420 Round 5: 1034 peptides, 154 chains. Longest chain 25 peptides. Score 0.437 Taking the results from Round 5 Chains 156, Residues 880, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 40047 restraints for refining 17076 atoms. 36657 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1856 (Rfree = 0.000) for 17076 atoms. Found 40 (81 requested) and removed 65 (40 requested) atoms. Cycle 32: After refmac, R = 0.1783 (Rfree = 0.000) for 16969 atoms. Found 69 (81 requested) and removed 72 (40 requested) atoms. Cycle 33: After refmac, R = 0.1789 (Rfree = 0.000) for 16923 atoms. Found 72 (80 requested) and removed 65 (40 requested) atoms. Cycle 34: After refmac, R = 0.1683 (Rfree = 0.000) for 16884 atoms. Found 70 (80 requested) and removed 62 (40 requested) atoms. Cycle 35: After refmac, R = 0.1291 (Rfree = 0.000) for 16852 atoms. Found 10 (80 requested) and removed 49 (40 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.93 3.68 Search for helices and strands: 0 residues in 0 chains, 17428 seeds are put forward NCS extension: 54 residues added (2 deleted due to clashes), 17482 seeds are put forward Round 1: 813 peptides, 167 chains. Longest chain 9 peptides. Score 0.269 Round 2: 977 peptides, 173 chains. Longest chain 15 peptides. Score 0.356 Round 3: 989 peptides, 163 chains. Longest chain 15 peptides. Score 0.389 Round 4: 980 peptides, 157 chains. Longest chain 19 peptides. Score 0.399 Round 5: 968 peptides, 161 chains. Longest chain 15 peptides. Score 0.382 Taking the results from Round 4 Chains 157, Residues 823, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 40680 restraints for refining 17079 atoms. 37529 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1745 (Rfree = 0.000) for 17079 atoms. Found 43 (81 requested) and removed 67 (40 requested) atoms. Cycle 37: After refmac, R = 0.1735 (Rfree = 0.000) for 16973 atoms. Found 81 (81 requested) and removed 70 (40 requested) atoms. Cycle 38: After refmac, R = 0.1729 (Rfree = 0.000) for 16954 atoms. Found 75 (80 requested) and removed 71 (40 requested) atoms. Cycle 39: After refmac, R = 0.1642 (Rfree = 0.000) for 16913 atoms. Found 70 (80 requested) and removed 66 (40 requested) atoms. Cycle 40: After refmac, R = 0.1605 (Rfree = 0.000) for 16890 atoms. Found 61 (80 requested) and removed 72 (40 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.90 3.65 Search for helices and strands: 0 residues in 0 chains, 17475 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 17491 seeds are put forward Round 1: 808 peptides, 171 chains. Longest chain 12 peptides. Score 0.254 Round 2: 887 peptides, 153 chains. Longest chain 13 peptides. Score 0.355 Round 3: 902 peptides, 156 chains. Longest chain 14 peptides. Score 0.356 Round 4: 903 peptides, 150 chains. Longest chain 14 peptides. Score 0.372 Round 5: 941 peptides, 154 chains. Longest chain 14 peptides. Score 0.384 Taking the results from Round 5 Chains 154, Residues 787, Estimated correctness of the model 0.0 % 5 chains (30 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 40574 restraints for refining 17079 atoms. 37463 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1646 (Rfree = 0.000) for 17079 atoms. Found 42 (81 requested) and removed 56 (40 requested) atoms. Cycle 42: After refmac, R = 0.1678 (Rfree = 0.000) for 17002 atoms. Found 81 (81 requested) and removed 52 (40 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1610 (Rfree = 0.000) for 16998 atoms. Found 76 (80 requested) and removed 65 (40 requested) atoms. Cycle 44: After refmac, R = 0.1227 (Rfree = 0.000) for 16993 atoms. Found 14 (80 requested) and removed 51 (40 requested) atoms. Cycle 45: After refmac, R = 0.1163 (Rfree = 0.000) for 16940 atoms. Found 15 (80 requested) and removed 44 (40 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.93 3.68 Search for helices and strands: 0 residues in 0 chains, 17411 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 17423 seeds are put forward Round 1: 758 peptides, 152 chains. Longest chain 15 peptides. Score 0.275 Round 2: 779 peptides, 141 chains. Longest chain 13 peptides. Score 0.320 Round 3: 852 peptides, 151 chains. Longest chain 14 peptides. Score 0.338 Round 4: 834 peptides, 144 chains. Longest chain 17 peptides. Score 0.346 Round 5: 865 peptides, 144 chains. Longest chain 18 peptides. Score 0.365 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 144, Residues 721, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2prr-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 22829 reflections ( 97.72 % complete ) and 40930 restraints for refining 17076 atoms. 38190 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1597 (Rfree = 0.000) for 17076 atoms. Found 0 (81 requested) and removed 40 (40 requested) atoms. Cycle 47: After refmac, R = 0.1788 (Rfree = 0.000) for 16983 atoms. Found 0 (80 requested) and removed 40 (40 requested) atoms. Cycle 48: After refmac, R = 0.1819 (Rfree = 0.000) for 16913 atoms. Found 0 (80 requested) and removed 40 (40 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1262 (Rfree = 0.000) for 16836 atoms. TimeTaking 170.92