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 1vk2-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk2-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk2-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk2-3.6-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/1vk2-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk2-3.6-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/1vk2-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk2-3.6-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 150 and 0 Target number of residues in the AU: 150 Target solvent content: 0.6591 Checking the provided sequence file Detected sequence length: 204 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 204 Adjusted target solvent content: 0.54 Input MTZ file: 1vk2-3.6-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: 96 Cell parameters: 61.120 61.120 127.494 90.000 90.000 90.000 Input sequence file: 1vk2-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1632 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: 55.114 3.600 Wilson plot Bfac: 83.67 3100 reflections ( 99.81 % complete ) and 0 restraints for refining 1822 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3468 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3583 (Rfree = 0.000) for 1822 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.63 3.44 Search for helices and strands: 0 residues in 0 chains, 1845 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 9 peptides. Score 0.305 Round 2: 95 peptides, 14 chains. Longest chain 13 peptides. Score 0.461 Round 3: 115 peptides, 16 chains. Longest chain 14 peptides. Score 0.528 Round 4: 118 peptides, 15 chains. Longest chain 19 peptides. Score 0.570 Round 5: 122 peptides, 15 chains. Longest chain 18 peptides. Score 0.591 Taking the results from Round 5 Chains 15, Residues 107, Estimated correctness of the model 11.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3100 reflections ( 99.81 % complete ) and 3395 restraints for refining 1478 atoms. 2982 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2905 (Rfree = 0.000) for 1478 atoms. Found 7 (9 requested) and removed 11 (4 requested) atoms. Cycle 2: After refmac, R = 0.2956 (Rfree = 0.000) for 1431 atoms. Found 5 (9 requested) and removed 13 (4 requested) atoms. Cycle 3: After refmac, R = 0.2747 (Rfree = 0.000) for 1402 atoms. Found 4 (9 requested) and removed 8 (4 requested) atoms. Cycle 4: After refmac, R = 0.2658 (Rfree = 0.000) for 1385 atoms. Found 6 (8 requested) and removed 6 (4 requested) atoms. Cycle 5: After refmac, R = 0.2324 (Rfree = 0.000) for 1378 atoms. Found 5 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 1443 seeds are put forward Round 1: 93 peptides, 16 chains. Longest chain 13 peptides. Score 0.390 Round 2: 109 peptides, 13 chains. Longest chain 27 peptides. Score 0.570 Round 3: 107 peptides, 14 chains. Longest chain 15 peptides. Score 0.534 Round 4: 114 peptides, 16 chains. Longest chain 15 peptides. Score 0.522 Round 5: 118 peptides, 18 chains. Longest chain 15 peptides. Score 0.494 Taking the results from Round 2 Chains 15, Residues 96, Estimated correctness of the model 2.6 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3100 reflections ( 99.81 % complete ) and 2952 restraints for refining 1358 atoms. 2550 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2601 (Rfree = 0.000) for 1358 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 7: After refmac, R = 0.2364 (Rfree = 0.000) for 1348 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 8: After refmac, R = 0.2341 (Rfree = 0.000) for 1346 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 9: After refmac, R = 0.2205 (Rfree = 0.000) for 1341 atoms. Found 4 (8 requested) and removed 7 (4 requested) atoms. Cycle 10: After refmac, R = 0.2103 (Rfree = 0.000) for 1336 atoms. Found 5 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 1389 seeds are put forward Round 1: 101 peptides, 18 chains. Longest chain 9 peptides. Score 0.386 Round 2: 124 peptides, 16 chains. Longest chain 15 peptides. Score 0.577 Round 3: 121 peptides, 16 chains. Longest chain 15 peptides. Score 0.561 Round 4: 131 peptides, 17 chains. Longest chain 21 peptides. Score 0.591 Round 5: 117 peptides, 16 chains. Longest chain 15 peptides. Score 0.539 Taking the results from Round 4 Chains 17, Residues 114, Estimated correctness of the model 11.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3100 reflections ( 99.81 % complete ) and 2917 restraints for refining 1371 atoms. 2478 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2485 (Rfree = 0.000) for 1371 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 12: After refmac, R = 0.2295 (Rfree = 0.000) for 1363 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 13: After refmac, R = 0.2152 (Rfree = 0.000) for 1363 atoms. Found 4 (8 requested) and removed 7 (4 requested) atoms. Cycle 14: After refmac, R = 0.2155 (Rfree = 0.000) for 1359 atoms. Found 2 (8 requested) and removed 5 (4 requested) atoms. Cycle 15: After refmac, R = 0.2159 (Rfree = 0.000) for 1355 atoms. Found 6 (8 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 1416 seeds are put forward Round 1: 100 peptides, 16 chains. Longest chain 14 peptides. Score 0.436 Round 2: 114 peptides, 14 chains. Longest chain 28 peptides. Score 0.572 Round 3: 107 peptides, 15 chains. Longest chain 19 peptides. Score 0.507 Round 4: 115 peptides, 16 chains. Longest chain 17 peptides. Score 0.528 Round 5: 115 peptides, 15 chains. Longest chain 22 peptides. Score 0.553 Taking the results from Round 2 Chains 14, Residues 100, Estimated correctness of the model 3.4 % 1 chains (27 residues) have been docked in sequence ------------------------------------------------------ 3100 reflections ( 99.81 % complete ) and 2878 restraints for refining 1461 atoms. 2380 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2451 (Rfree = 0.000) for 1461 atoms. Found 8 (9 requested) and removed 19 (4 requested) atoms. Cycle 17: After refmac, R = 0.2248 (Rfree = 0.000) for 1444 atoms. Found 6 (9 requested) and removed 13 (4 requested) atoms. Cycle 18: After refmac, R = 0.2179 (Rfree = 0.000) for 1434 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.2133 (Rfree = 0.000) for 1433 atoms. Found 5 (9 requested) and removed 5 (4 requested) atoms. Cycle 20: After refmac, R = 0.2068 (Rfree = 0.000) for 1432 atoms. Found 1 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.59 3.40 Search for helices and strands: 0 residues in 0 chains, 1465 seeds are put forward Round 1: 89 peptides, 15 chains. Longest chain 11 peptides. Score 0.392 Round 2: 97 peptides, 14 chains. Longest chain 20 peptides. Score 0.474 Round 3: 113 peptides, 18 chains. Longest chain 11 peptides. Score 0.464 Round 4: 118 peptides, 16 chains. Longest chain 20 peptides. Score 0.545 Round 5: 119 peptides, 15 chains. Longest chain 19 peptides. Score 0.575 Taking the results from Round 5 Chains 16, Residues 104, Estimated correctness of the model 4.6 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 3100 reflections ( 99.81 % complete ) and 3116 restraints for refining 1478 atoms. 2653 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2554 (Rfree = 0.000) for 1478 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 22: After refmac, R = 0.2334 (Rfree = 0.000) for 1465 atoms. Found 8 (9 requested) and removed 6 (4 requested) atoms. Cycle 23: After refmac, R = 0.2243 (Rfree = 0.000) for 1463 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.2205 (Rfree = 0.000) for 1462 atoms. Found 3 (9 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.2156 (Rfree = 0.000) for 1459 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.37 Search for helices and strands: 0 residues in 0 chains, 1514 seeds are put forward Round 1: 89 peptides, 18 chains. Longest chain 9 peptides. Score 0.300 Round 2: 113 peptides, 19 chains. Longest chain 12 peptides. Score 0.436 Round 3: 121 peptides, 17 chains. Longest chain 15 peptides. Score 0.537 Round 4: 104 peptides, 14 chains. Longest chain 15 peptides. Score 0.516 Round 5: 122 peptides, 16 chains. Longest chain 15 peptides. Score 0.567 Taking the results from Round 5 Chains 16, Residues 106, Estimated correctness of the model 1.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3100 reflections ( 99.81 % complete ) and 3319 restraints for refining 1479 atoms. 2911 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2328 (Rfree = 0.000) for 1479 atoms. Found 8 (9 requested) and removed 6 (4 requested) atoms. Cycle 27: After refmac, R = 0.2214 (Rfree = 0.000) for 1475 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 28: After refmac, R = 0.2524 (Rfree = 0.000) for 1471 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 29: After refmac, R = 0.2178 (Rfree = 0.000) for 1470 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 30: After refmac, R = 0.2219 (Rfree = 0.000) for 1462 atoms. Found 7 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 1515 seeds are put forward Round 1: 99 peptides, 17 chains. Longest chain 20 peptides. Score 0.401 Round 2: 102 peptides, 14 chains. Longest chain 22 peptides. Score 0.504 Round 3: 101 peptides, 14 chains. Longest chain 20 peptides. Score 0.498 Round 4: 109 peptides, 14 chains. Longest chain 21 peptides. Score 0.545 Round 5: 110 peptides, 13 chains. Longest chain 21 peptides. Score 0.576 Taking the results from Round 5 Chains 13, Residues 97, Estimated correctness of the model 5.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3100 reflections ( 99.81 % complete ) and 3300 restraints for refining 1479 atoms. 2925 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2241 (Rfree = 0.000) for 1479 atoms. Found 8 (9 requested) and removed 7 (4 requested) atoms. Cycle 32: After refmac, R = 0.2412 (Rfree = 0.000) for 1474 atoms. Found 7 (9 requested) and removed 6 (4 requested) atoms. Cycle 33: After refmac, R = 0.2350 (Rfree = 0.000) for 1471 atoms. Found 7 (9 requested) and removed 11 (4 requested) atoms. Cycle 34: After refmac, R = 0.2074 (Rfree = 0.000) for 1467 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.2196 (Rfree = 0.000) for 1464 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 1517 seeds are put forward Round 1: 80 peptides, 14 chains. Longest chain 10 peptides. Score 0.359 Round 2: 94 peptides, 13 chains. Longest chain 22 peptides. Score 0.483 Round 3: 93 peptides, 10 chains. Longest chain 28 peptides. Score 0.559 Round 4: 100 peptides, 13 chains. Longest chain 28 peptides. Score 0.519 Round 5: 91 peptides, 12 chains. Longest chain 18 peptides. Score 0.492 Taking the results from Round 3 Chains 11, Residues 83, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 3100 reflections ( 99.81 % complete ) and 3177 restraints for refining 1479 atoms. 2817 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2308 (Rfree = 0.000) for 1479 atoms. Found 6 (9 requested) and removed 6 (4 requested) atoms. Cycle 37: After refmac, R = 0.2336 (Rfree = 0.000) for 1473 atoms. Found 5 (9 requested) and removed 8 (4 requested) atoms. Cycle 38: After refmac, R = 0.2040 (Rfree = 0.000) for 1467 atoms. Found 2 (9 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.2119 (Rfree = 0.000) for 1458 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 40: After refmac, R = 0.2095 (Rfree = 0.000) for 1456 atoms. Found 5 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 1489 seeds are put forward Round 1: 85 peptides, 13 chains. Longest chain 16 peptides. Score 0.425 Round 2: 100 peptides, 11 chains. Longest chain 25 peptides. Score 0.572 Round 3: 97 peptides, 12 chains. Longest chain 19 peptides. Score 0.529 Round 4: 101 peptides, 12 chains. Longest chain 20 peptides. Score 0.551 Round 5: 102 peptides, 9 chains. Longest chain 39 peptides. Score 0.631 Taking the results from Round 5 Chains 9, Residues 93, Estimated correctness of the model 26.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3100 reflections ( 99.81 % complete ) and 3253 restraints for refining 1479 atoms. 2890 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2094 (Rfree = 0.000) for 1479 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 42: After refmac, R = 0.2047 (Rfree = 0.000) for 1477 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 43: After refmac, R = 0.1944 (Rfree = 0.000) for 1474 atoms. Found 5 (9 requested) and removed 6 (4 requested) atoms. Cycle 44: After refmac, R = 0.1940 (Rfree = 0.000) for 1469 atoms. Found 6 (9 requested) and removed 5 (4 requested) atoms. Cycle 45: After refmac, R = 0.1904 (Rfree = 0.000) for 1470 atoms. Found 4 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 3.37 Search for helices and strands: 0 residues in 0 chains, 1516 seeds are put forward Round 1: 70 peptides, 12 chains. Longest chain 12 peptides. Score 0.350 Round 2: 85 peptides, 13 chains. Longest chain 16 peptides. Score 0.425 Round 3: 102 peptides, 15 chains. Longest chain 20 peptides. Score 0.477 Round 4: 109 peptides, 16 chains. Longest chain 14 peptides. Score 0.493 Round 5: 106 peptides, 17 chains. Longest chain 16 peptides. Score 0.447 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 93, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1vk2-3_warpNtrace.pdb as input Building loops using Loopy2018 16 chains (93 residues) following loop building 2 chains (6 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3100 reflections ( 99.81 % complete ) and 3286 restraints for refining 1479 atoms. 2920 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2121 (Rfree = 0.000) for 1479 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2001 (Rfree = 0.000) for 1468 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.1997 (Rfree = 0.000) for 1460 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.1878 (Rfree = 0.000) for 1455 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:52:28 GMT 2018 Job finished. TimeTaking 29.39 Used memory is bytes: 12929240