null Sun 23 Dec 22:23:05 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 1vp8-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vp8-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vp8-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp8-3.2-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/1vp8-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp8-3.2-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 22:23:15 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/1vp8-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp8-3.2-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 189 and 0 Target number of residues in the AU: 189 Target solvent content: 0.6156 Checking the provided sequence file Detected sequence length: 201 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 201 Adjusted target solvent content: 0.59 Input MTZ file: 1vp8-3.2-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: 182 Cell parameters: 109.749 109.749 76.534 90.000 90.000 120.000 Input sequence file: 1vp8-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1608 target number of atoms Had to go as low as 0.75 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: 18.945 3.200 Wilson plot Bfac: 58.89 4799 reflections ( 99.23 % complete ) and 0 restraints for refining 1771 atoms. Observations/parameters ratio is 0.68 ------------------------------------------------------ Starting model: R = 0.3123 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2184 (Rfree = 0.000) for 1771 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.08 2.73 Search for helices and strands: 0 residues in 0 chains, 1794 seeds are put forward Round 1: 128 peptides, 17 chains. Longest chain 19 peptides. Score 0.544 Round 2: 155 peptides, 14 chains. Longest chain 24 peptides. Score 0.715 Round 3: 162 peptides, 13 chains. Longest chain 30 peptides. Score 0.753 Round 4: 164 peptides, 12 chains. Longest chain 36 peptides. Score 0.773 Round 5: 164 peptides, 11 chains. Longest chain 45 peptides. Score 0.787 Taking the results from Round 5 Chains 13, Residues 153, Estimated correctness of the model 81.4 % 4 chains (74 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 165 A and 169 A 12 chains (156 residues) following loop building 3 chains (77 residues) in sequence following loop building ------------------------------------------------------ 4799 reflections ( 99.23 % complete ) and 2286 restraints for refining 1484 atoms. 1414 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2468 (Rfree = 0.000) for 1484 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 2: After refmac, R = 0.2326 (Rfree = 0.000) for 1447 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 3: After refmac, R = 0.2046 (Rfree = 0.000) for 1436 atoms. Found 7 (12 requested) and removed 11 (6 requested) atoms. Cycle 4: After refmac, R = 0.1995 (Rfree = 0.000) for 1428 atoms. Found 10 (11 requested) and removed 9 (6 requested) atoms. Cycle 5: After refmac, R = 0.2028 (Rfree = 0.000) for 1428 atoms. Found 11 (11 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 2.76 Search for helices and strands: 0 residues in 0 chains, 1470 seeds are put forward Round 1: 165 peptides, 9 chains. Longest chain 51 peptides. Score 0.816 Round 2: 173 peptides, 10 chains. Longest chain 51 peptides. Score 0.822 Round 3: 168 peptides, 10 chains. Longest chain 40 peptides. Score 0.810 Round 4: 163 peptides, 11 chains. Longest chain 43 peptides. Score 0.784 Round 5: 162 peptides, 14 chains. Longest chain 22 peptides. Score 0.738 Taking the results from Round 2 Chains 11, Residues 163, Estimated correctness of the model 86.6 % 4 chains (128 residues) have been docked in sequence Building loops using Loopy2018 11 chains (163 residues) following loop building 4 chains (128 residues) in sequence following loop building ------------------------------------------------------ 4799 reflections ( 99.23 % complete ) and 1898 restraints for refining 1504 atoms. 741 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2468 (Rfree = 0.000) for 1504 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 7: After refmac, R = 0.2232 (Rfree = 0.000) for 1484 atoms. Found 10 (11 requested) and removed 12 (6 requested) atoms. Cycle 8: After refmac, R = 0.2072 (Rfree = 0.000) for 1474 atoms. Found 7 (11 requested) and removed 13 (6 requested) atoms. Cycle 9: After refmac, R = 0.2083 (Rfree = 0.000) for 1463 atoms. Found 9 (11 requested) and removed 10 (6 requested) atoms. Cycle 10: After refmac, R = 0.1996 (Rfree = 0.000) for 1457 atoms. Found 7 (11 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.09 2.74 Search for helices and strands: 0 residues in 0 chains, 1493 seeds are put forward Round 1: 165 peptides, 9 chains. Longest chain 32 peptides. Score 0.816 Round 2: 166 peptides, 10 chains. Longest chain 33 peptides. Score 0.805 Round 3: 172 peptides, 8 chains. Longest chain 53 peptides. Score 0.843 Round 4: 175 peptides, 10 chains. Longest chain 59 peptides. Score 0.826 Round 5: 166 peptides, 13 chains. Longest chain 22 peptides. Score 0.765 Taking the results from Round 3 Chains 10, Residues 164, Estimated correctness of the model 89.4 % 5 chains (138 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 64 A and 68 A 9 chains (167 residues) following loop building 4 chains (141 residues) in sequence following loop building ------------------------------------------------------ 4799 reflections ( 99.23 % complete ) and 1877 restraints for refining 1516 atoms. 658 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2416 (Rfree = 0.000) for 1516 atoms. Found 10 (10 requested) and removed 23 (6 requested) atoms. Cycle 12: After refmac, R = 0.2247 (Rfree = 0.000) for 1497 atoms. Found 10 (10 requested) and removed 10 (6 requested) atoms. Cycle 13: After refmac, R = 0.2119 (Rfree = 0.000) for 1492 atoms. Found 10 (10 requested) and removed 11 (6 requested) atoms. Cycle 14: After refmac, R = 0.1876 (Rfree = 0.000) for 1489 atoms. Found 10 (10 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.1768 (Rfree = 0.000) for 1490 atoms. Found 8 (9 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.10 2.75 Search for helices and strands: 0 residues in 0 chains, 1531 seeds are put forward Round 1: 160 peptides, 9 chains. Longest chain 51 peptides. Score 0.804 Round 2: 168 peptides, 8 chains. Longest chain 51 peptides. Score 0.834 Round 3: 169 peptides, 8 chains. Longest chain 63 peptides. Score 0.837 Round 4: 156 peptides, 12 chains. Longest chain 29 peptides. Score 0.750 Round 5: 157 peptides, 12 chains. Longest chain 27 peptides. Score 0.753 Taking the results from Round 3 Chains 9, Residues 161, Estimated correctness of the model 88.6 % 3 chains (110 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 138 A 8 chains (167 residues) following loop building 2 chains (116 residues) in sequence following loop building ------------------------------------------------------ 4799 reflections ( 99.23 % complete ) and 2009 restraints for refining 1468 atoms. 933 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2358 (Rfree = 0.000) for 1468 atoms. Found 9 (9 requested) and removed 23 (6 requested) atoms. Cycle 17: After refmac, R = 0.2103 (Rfree = 0.000) for 1445 atoms. Found 9 (9 requested) and removed 9 (6 requested) atoms. Cycle 18: After refmac, R = 0.2035 (Rfree = 0.000) for 1445 atoms. Found 7 (8 requested) and removed 8 (6 requested) atoms. Cycle 19: After refmac, R = 0.2010 (Rfree = 0.000) for 1442 atoms. Found 8 (8 requested) and removed 8 (6 requested) atoms. Cycle 20: After refmac, R = 0.1918 (Rfree = 0.000) for 1440 atoms. Found 5 (7 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.07 2.72 Search for helices and strands: 0 residues in 0 chains, 1468 seeds are put forward Round 1: 168 peptides, 8 chains. Longest chain 28 peptides. Score 0.834 Round 2: 165 peptides, 6 chains. Longest chain 66 peptides. Score 0.851 Round 3: 167 peptides, 9 chains. Longest chain 47 peptides. Score 0.820 Round 4: 169 peptides, 10 chains. Longest chain 29 peptides. Score 0.813 Round 5: 164 peptides, 10 chains. Longest chain 23 peptides. Score 0.800 Taking the results from Round 2 Chains 8, Residues 159, Estimated correctness of the model 90.3 % 4 chains (118 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 A and 44 A 7 chains (161 residues) following loop building 3 chains (120 residues) in sequence following loop building ------------------------------------------------------ 4799 reflections ( 99.23 % complete ) and 2051 restraints for refining 1468 atoms. 956 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2208 (Rfree = 0.000) for 1468 atoms. Found 7 (8 requested) and removed 13 (6 requested) atoms. Cycle 22: After refmac, R = 0.2035 (Rfree = 0.000) for 1458 atoms. Found 8 (8 requested) and removed 13 (6 requested) atoms. Cycle 23: After refmac, R = 0.1986 (Rfree = 0.000) for 1452 atoms. Found 7 (7 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.1883 (Rfree = 0.000) for 1449 atoms. Found 7 (7 requested) and removed 7 (6 requested) atoms. Cycle 25: After refmac, R = 0.1727 (Rfree = 0.000) for 1448 atoms. Found 7 (7 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.05 2.70 Search for helices and strands: 0 residues in 0 chains, 1508 seeds are put forward Round 1: 166 peptides, 9 chains. Longest chain 55 peptides. Score 0.818 Round 2: 172 peptides, 9 chains. Longest chain 34 peptides. Score 0.831 Round 3: 176 peptides, 10 chains. Longest chain 37 peptides. Score 0.828 Round 4: 179 peptides, 7 chains. Longest chain 61 peptides. Score 0.867 Round 5: 176 peptides, 9 chains. Longest chain 44 peptides. Score 0.840 Taking the results from Round 4 Chains 8, Residues 172, Estimated correctness of the model 92.1 % 4 chains (133 residues) have been docked in sequence Building loops using Loopy2018 8 chains (172 residues) following loop building 4 chains (133 residues) in sequence following loop building ------------------------------------------------------ 4799 reflections ( 99.23 % complete ) and 1830 restraints for refining 1468 atoms. 661 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2371 (Rfree = 0.000) for 1468 atoms. Found 6 (6 requested) and removed 29 (6 requested) atoms. Cycle 27: After refmac, R = 0.2172 (Rfree = 0.000) for 1439 atoms. Found 6 (6 requested) and removed 13 (6 requested) atoms. Cycle 28: After refmac, R = 0.2207 (Rfree = 0.000) for 1426 atoms. Found 6 (6 requested) and removed 8 (6 requested) atoms. Cycle 29: After refmac, R = 0.2082 (Rfree = 0.000) for 1423 atoms. Found 6 (6 requested) and removed 9 (6 requested) atoms. Cycle 30: After refmac, R = 0.2087 (Rfree = 0.000) for 1417 atoms. Found 6 (6 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.09 2.74 Search for helices and strands: 0 residues in 0 chains, 1466 seeds are put forward Round 1: 165 peptides, 11 chains. Longest chain 31 peptides. Score 0.790 Round 2: 179 peptides, 10 chains. Longest chain 43 peptides. Score 0.835 Round 3: 172 peptides, 9 chains. Longest chain 54 peptides. Score 0.831 Round 4: 178 peptides, 8 chains. Longest chain 62 peptides. Score 0.854 Round 5: 161 peptides, 10 chains. Longest chain 39 peptides. Score 0.793 Taking the results from Round 4 Chains 10, Residues 170, Estimated correctness of the model 90.7 % 4 chains (127 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 A and 93 A Built loop between residues 140 A and 146 A 6 chains (174 residues) following loop building 2 chains (135 residues) in sequence following loop building ------------------------------------------------------ 4799 reflections ( 99.23 % complete ) and 1843 restraints for refining 1468 atoms. 658 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2288 (Rfree = 0.000) for 1468 atoms. Found 6 (6 requested) and removed 22 (6 requested) atoms. Cycle 32: After refmac, R = 0.2099 (Rfree = 0.000) for 1449 atoms. Found 6 (6 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.2131 (Rfree = 0.000) for 1446 atoms. Found 6 (6 requested) and removed 9 (6 requested) atoms. Cycle 34: After refmac, R = 0.2022 (Rfree = 0.000) for 1441 atoms. Found 6 (6 requested) and removed 9 (6 requested) atoms. Cycle 35: After refmac, R = 0.1977 (Rfree = 0.000) for 1435 atoms. Found 6 (6 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.09 2.74 Search for helices and strands: 0 residues in 0 chains, 1473 seeds are put forward Round 1: 164 peptides, 11 chains. Longest chain 35 peptides. Score 0.787 Round 2: 173 peptides, 7 chains. Longest chain 67 peptides. Score 0.856 Round 3: 167 peptides, 11 chains. Longest chain 45 peptides. Score 0.795 Round 4: 156 peptides, 11 chains. Longest chain 36 peptides. Score 0.765 Round 5: 165 peptides, 10 chains. Longest chain 44 peptides. Score 0.803 Taking the results from Round 2 Chains 7, Residues 166, Estimated correctness of the model 90.9 % 4 chains (137 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 54 A and 59 A Built loop between residues 167 A and 170 A 5 chains (172 residues) following loop building 2 chains (143 residues) in sequence following loop building ------------------------------------------------------ 4799 reflections ( 99.23 % complete ) and 1852 restraints for refining 1481 atoms. 642 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2369 (Rfree = 0.000) for 1481 atoms. Found 6 (6 requested) and removed 16 (6 requested) atoms. Cycle 37: After refmac, R = 0.2190 (Rfree = 0.000) for 1466 atoms. Found 6 (6 requested) and removed 13 (6 requested) atoms. Cycle 38: After refmac, R = 0.2082 (Rfree = 0.000) for 1456 atoms. Found 6 (6 requested) and removed 8 (6 requested) atoms. Cycle 39: After refmac, R = 0.2054 (Rfree = 0.000) for 1451 atoms. Found 6 (6 requested) and removed 7 (6 requested) atoms. Cycle 40: After refmac, R = 0.2019 (Rfree = 0.000) for 1447 atoms. Found 6 (6 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.08 2.73 Search for helices and strands: 0 residues in 0 chains, 1471 seeds are put forward Round 1: 173 peptides, 9 chains. Longest chain 46 peptides. Score 0.833 Round 2: 168 peptides, 11 chains. Longest chain 46 peptides. Score 0.797 Round 3: 169 peptides, 11 chains. Longest chain 42 peptides. Score 0.800 Round 4: 169 peptides, 10 chains. Longest chain 43 peptides. Score 0.813 Round 5: 174 peptides, 8 chains. Longest chain 40 peptides. Score 0.847 Taking the results from Round 5 Chains 8, Residues 166, Estimated correctness of the model 89.8 % 5 chains (128 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 53 A and 59 A Built loop between residues 87 A and 90 A Built loop between residues 111 A and 115 A 5 chains (176 residues) following loop building 2 chains (138 residues) in sequence following loop building ------------------------------------------------------ 4799 reflections ( 99.23 % complete ) and 1789 restraints for refining 1468 atoms. 570 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2515 (Rfree = 0.000) for 1468 atoms. Found 6 (6 requested) and removed 23 (6 requested) atoms. Cycle 42: After refmac, R = 0.2281 (Rfree = 0.000) for 1449 atoms. Found 6 (6 requested) and removed 11 (6 requested) atoms. Cycle 43: After refmac, R = 0.2243 (Rfree = 0.000) for 1443 atoms. Found 6 (6 requested) and removed 11 (6 requested) atoms. Cycle 44: After refmac, R = 0.2168 (Rfree = 0.000) for 1437 atoms. Found 6 (6 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.2053 (Rfree = 0.000) for 1436 atoms. Found 6 (6 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.11 2.76 Search for helices and strands: 0 residues in 0 chains, 1490 seeds are put forward Round 1: 161 peptides, 13 chains. Longest chain 23 peptides. Score 0.750 Round 2: 169 peptides, 9 chains. Longest chain 48 peptides. Score 0.825 Round 3: 164 peptides, 13 chains. Longest chain 30 peptides. Score 0.759 Round 4: 165 peptides, 10 chains. Longest chain 43 peptides. Score 0.803 Round 5: 169 peptides, 11 chains. Longest chain 31 peptides. Score 0.800 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 160, Estimated correctness of the model 87.0 % 3 chains (99 residues) have been docked in sequence Sequence coverage is 61 % Consider running further cycles of model building using 1vp8-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 136 A and 150 A 8 chains (168 residues) following loop building 2 chains (112 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4799 reflections ( 99.23 % complete ) and 2090 restraints for refining 1468 atoms. 1026 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2468 (Rfree = 0.000) for 1468 atoms. Found 0 (6 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2309 (Rfree = 0.000) for 1461 atoms. Found 0 (6 requested) and removed 3 (6 requested) atoms. Cycle 48: After refmac, R = 0.2274 (Rfree = 0.000) for 1453 atoms. Found 0 (6 requested) and removed 3 (6 requested) atoms. Cycle 49: After refmac, R = 0.2282 (Rfree = 0.000) for 1449 atoms. Found 0 (6 requested) and removed 1 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:10:43 GMT 2018 Job finished. TimeTaking 47.64 Used memory is bytes: 10133984