null Sun 23 Dec 22:22:43 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 2o2g-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o2g-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o2g-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2g-3.4-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/2o2g-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2g-3.4-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 22:22:53 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/2o2g-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o2g-3.4-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 141 and 0 Target number of residues in the AU: 141 Target solvent content: 0.6247 Checking the provided sequence file Detected sequence length: 223 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 223 Adjusted target solvent content: 0.41 Input MTZ file: 2o2g-3.4-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: 47.887 62.444 67.988 90.000 90.000 90.000 Input sequence file: 2o2g-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1784 target number of atoms Had to go as low as 0.60 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: 45.990 3.400 Wilson plot Bfac: 63.43 2827 reflections ( 92.63 % complete ) and 0 restraints for refining 1968 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3707 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3145 (Rfree = 0.000) for 1968 atoms. Found 14 (14 requested) and removed 48 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.70 Search for helices and strands: 0 residues in 0 chains, 1964 seeds are put forward Round 1: 57 peptides, 13 chains. Longest chain 5 peptides. Score 0.217 Round 2: 78 peptides, 16 chains. Longest chain 7 peptides. Score 0.295 Round 3: 82 peptides, 17 chains. Longest chain 7 peptides. Score 0.293 Round 4: 93 peptides, 17 chains. Longest chain 8 peptides. Score 0.384 Round 5: 100 peptides, 18 chains. Longest chain 9 peptides. Score 0.405 Taking the results from Round 5 Chains 18, Residues 82, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 2827 reflections ( 92.63 % complete ) and 3759 restraints for refining 1622 atoms. 3419 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3021 (Rfree = 0.000) for 1622 atoms. Found 7 (12 requested) and removed 12 (6 requested) atoms. Cycle 2: After refmac, R = 0.3073 (Rfree = 0.000) for 1604 atoms. Found 5 (12 requested) and removed 10 (6 requested) atoms. Cycle 3: After refmac, R = 0.2694 (Rfree = 0.000) for 1580 atoms. Found 7 (12 requested) and removed 10 (6 requested) atoms. Cycle 4: After refmac, R = 0.2857 (Rfree = 0.000) for 1569 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 5: After refmac, R = 0.2411 (Rfree = 0.000) for 1559 atoms. Found 1 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.61 Search for helices and strands: 0 residues in 0 chains, 1611 seeds are put forward Round 1: 70 peptides, 15 chains. Longest chain 8 peptides. Score 0.261 Round 2: 74 peptides, 13 chains. Longest chain 12 peptides. Score 0.369 Round 3: 78 peptides, 12 chains. Longest chain 16 peptides. Score 0.436 Round 4: 79 peptides, 14 chains. Longest chain 15 peptides. Score 0.374 Round 5: 81 peptides, 13 chains. Longest chain 16 peptides. Score 0.425 Taking the results from Round 3 Chains 12, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2827 reflections ( 92.63 % complete ) and 3586 restraints for refining 1496 atoms. 3334 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2825 (Rfree = 0.000) for 1496 atoms. Found 6 (11 requested) and removed 10 (5 requested) atoms. Cycle 7: After refmac, R = 0.3010 (Rfree = 0.000) for 1489 atoms. Found 10 (11 requested) and removed 9 (5 requested) atoms. Cycle 8: After refmac, R = 0.2599 (Rfree = 0.000) for 1482 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. Cycle 9: After refmac, R = 0.2856 (Rfree = 0.000) for 1478 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 10: After refmac, R = 0.2636 (Rfree = 0.000) for 1472 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.23 3.65 Search for helices and strands: 0 residues in 0 chains, 1524 seeds are put forward Round 1: 75 peptides, 17 chains. Longest chain 6 peptides. Score 0.231 Round 2: 81 peptides, 15 chains. Longest chain 11 peptides. Score 0.356 Round 3: 89 peptides, 18 chains. Longest chain 9 peptides. Score 0.317 Round 4: 86 peptides, 15 chains. Longest chain 16 peptides. Score 0.396 Round 5: 82 peptides, 15 chains. Longest chain 8 peptides. Score 0.364 Taking the results from Round 4 Chains 17, Residues 71, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 2827 reflections ( 92.63 % complete ) and 3381 restraints for refining 1548 atoms. 3059 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2726 (Rfree = 0.000) for 1548 atoms. Found 6 (11 requested) and removed 19 (5 requested) atoms. Cycle 12: After refmac, R = 0.2687 (Rfree = 0.000) for 1529 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 13: After refmac, R = 0.2572 (Rfree = 0.000) for 1528 atoms. Found 7 (11 requested) and removed 8 (5 requested) atoms. Cycle 14: After refmac, R = 0.2502 (Rfree = 0.000) for 1522 atoms. Found 11 (11 requested) and removed 24 (5 requested) atoms. Cycle 15: After refmac, R = 0.2440 (Rfree = 0.000) for 1504 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.68 Search for helices and strands: 0 residues in 0 chains, 1539 seeds are put forward Round 1: 49 peptides, 10 chains. Longest chain 7 peptides. Score 0.261 Round 2: 63 peptides, 12 chains. Longest chain 9 peptides. Score 0.311 Round 3: 62 peptides, 12 chains. Longest chain 8 peptides. Score 0.302 Round 4: 70 peptides, 11 chains. Longest chain 12 peptides. Score 0.408 Round 5: 74 peptides, 12 chains. Longest chain 12 peptides. Score 0.404 Taking the results from Round 4 Chains 11, Residues 59, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2827 reflections ( 92.63 % complete ) and 3504 restraints for refining 1546 atoms. 3257 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2555 (Rfree = 0.000) for 1546 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 17: After refmac, R = 0.2550 (Rfree = 0.000) for 1536 atoms. Found 9 (11 requested) and removed 7 (5 requested) atoms. Cycle 18: After refmac, R = 0.2469 (Rfree = 0.000) for 1535 atoms. Found 6 (11 requested) and removed 9 (5 requested) atoms. Cycle 19: After refmac, R = 0.2377 (Rfree = 0.000) for 1530 atoms. Found 10 (11 requested) and removed 6 (5 requested) atoms. Cycle 20: After refmac, R = 0.2048 (Rfree = 0.000) for 1530 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 3.67 Search for helices and strands: 0 residues in 0 chains, 1556 seeds are put forward Round 1: 69 peptides, 14 chains. Longest chain 7 peptides. Score 0.289 Round 2: 68 peptides, 11 chains. Longest chain 11 peptides. Score 0.391 Round 3: 69 peptides, 13 chains. Longest chain 10 peptides. Score 0.326 Round 4: 70 peptides, 12 chains. Longest chain 11 peptides. Score 0.371 Round 5: 74 peptides, 12 chains. Longest chain 12 peptides. Score 0.404 Taking the results from Round 5 Chains 12, Residues 62, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2827 reflections ( 92.63 % complete ) and 3398 restraints for refining 1531 atoms. 3124 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2578 (Rfree = 0.000) for 1531 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 22: After refmac, R = 0.2655 (Rfree = 0.000) for 1521 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 23: After refmac, R = 0.2653 (Rfree = 0.000) for 1517 atoms. Found 8 (11 requested) and removed 10 (5 requested) atoms. Cycle 24: After refmac, R = 0.2593 (Rfree = 0.000) for 1513 atoms. Found 10 (11 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.2138 (Rfree = 0.000) for 1516 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 3.63 Search for helices and strands: 0 residues in 0 chains, 1542 seeds are put forward Round 1: 65 peptides, 15 chains. Longest chain 7 peptides. Score 0.215 Round 2: 66 peptides, 11 chains. Longest chain 14 peptides. Score 0.375 Round 3: 67 peptides, 12 chains. Longest chain 15 peptides. Score 0.346 Round 4: 64 peptides, 12 chains. Longest chain 12 peptides. Score 0.320 Round 5: 68 peptides, 12 chains. Longest chain 14 peptides. Score 0.355 Taking the results from Round 2 Chains 11, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2827 reflections ( 92.63 % complete ) and 3401 restraints for refining 1465 atoms. 3192 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2884 (Rfree = 0.000) for 1465 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 27: After refmac, R = 0.2838 (Rfree = 0.000) for 1456 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 28: After refmac, R = 0.2745 (Rfree = 0.000) for 1458 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 29: After refmac, R = 0.2597 (Rfree = 0.000) for 1459 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 30: After refmac, R = 0.2312 (Rfree = 0.000) for 1463 atoms. Found 6 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.69 Search for helices and strands: 0 residues in 0 chains, 1512 seeds are put forward Round 1: 68 peptides, 15 chains. Longest chain 9 peptides. Score 0.243 Round 2: 76 peptides, 15 chains. Longest chain 9 peptides. Score 0.314 Round 3: 71 peptides, 14 chains. Longest chain 8 peptides. Score 0.307 Round 4: 75 peptides, 14 chains. Longest chain 10 peptides. Score 0.341 Round 5: 68 peptides, 13 chains. Longest chain 7 peptides. Score 0.318 Taking the results from Round 4 Chains 14, Residues 61, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2827 reflections ( 92.63 % complete ) and 3406 restraints for refining 1495 atoms. 3157 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2996 (Rfree = 0.000) for 1495 atoms. Found 11 (11 requested) and removed 29 (5 requested) atoms. Cycle 32: After refmac, R = 0.2628 (Rfree = 0.000) for 1471 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 33: After refmac, R = 0.2529 (Rfree = 0.000) for 1468 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 34: After refmac, R = 0.2516 (Rfree = 0.000) for 1470 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 35: After refmac, R = 0.2560 (Rfree = 0.000) for 1471 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.66 Search for helices and strands: 0 residues in 0 chains, 1520 seeds are put forward Round 1: 58 peptides, 13 chains. Longest chain 6 peptides. Score 0.226 Round 2: 72 peptides, 14 chains. Longest chain 8 peptides. Score 0.315 Round 3: 71 peptides, 13 chains. Longest chain 10 peptides. Score 0.344 Round 4: 66 peptides, 10 chains. Longest chain 13 peptides. Score 0.411 Round 5: 79 peptides, 13 chains. Longest chain 12 peptides. Score 0.409 Taking the results from Round 4 Chains 11, Residues 56, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2827 reflections ( 92.63 % complete ) and 3270 restraints for refining 1497 atoms. 3026 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2801 (Rfree = 0.000) for 1497 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 37: After refmac, R = 0.2606 (Rfree = 0.000) for 1490 atoms. Found 9 (11 requested) and removed 10 (5 requested) atoms. Cycle 38: After refmac, R = 0.2607 (Rfree = 0.000) for 1483 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 39: After refmac, R = 0.2473 (Rfree = 0.000) for 1475 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 40: After refmac, R = 0.2573 (Rfree = 0.000) for 1477 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 3.70 Search for helices and strands: 0 residues in 0 chains, 1506 seeds are put forward Round 1: 37 peptides, 7 chains. Longest chain 8 peptides. Score 0.271 Round 2: 54 peptides, 10 chains. Longest chain 8 peptides. Score 0.308 Round 3: 57 peptides, 11 chains. Longest chain 7 peptides. Score 0.296 Round 4: 52 peptides, 11 chains. Longest chain 7 peptides. Score 0.249 Round 5: 56 peptides, 11 chains. Longest chain 8 peptides. Score 0.287 Taking the results from Round 2 Chains 10, Residues 44, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2827 reflections ( 92.63 % complete ) and 3040 restraints for refining 1408 atoms. 2855 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2310 (Rfree = 0.000) for 1408 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 42: After refmac, R = 0.2409 (Rfree = 0.000) for 1408 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 43: After refmac, R = 0.2371 (Rfree = 0.000) for 1408 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.2318 (Rfree = 0.000) for 1412 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 45: After refmac, R = 0.1816 (Rfree = 0.000) for 1411 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 3.67 Search for helices and strands: 0 residues in 0 chains, 1432 seeds are put forward Round 1: 51 peptides, 10 chains. Longest chain 10 peptides. Score 0.280 Round 2: 59 peptides, 11 chains. Longest chain 12 peptides. Score 0.314 Round 3: 64 peptides, 11 chains. Longest chain 9 peptides. Score 0.358 Round 4: 62 peptides, 12 chains. Longest chain 10 peptides. Score 0.302 Round 5: 64 peptides, 12 chains. Longest chain 9 peptides. Score 0.320 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 53, 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 2o2g-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2827 reflections ( 92.63 % complete ) and 3038 restraints for refining 1403 atoms. 2837 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2152 (Rfree = 0.000) for 1403 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1893 (Rfree = 0.000) for 1390 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1923 (Rfree = 0.000) for 1385 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1776 (Rfree = 0.000) for 1377 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:50:40 GMT 2018 Job finished. TimeTaking 27.95 Used memory is bytes: 13490744