Tue 25 Dec 19:27:57 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 2f4l-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2f4l-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2f4l-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4l-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/2f4l-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4l-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 19:28:07 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/2f4l-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4l-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 828 and 0 Target number of residues in the AU: 828 Target solvent content: 0.6529 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1188 Adjusted target solvent content: 0.50 Input MTZ file: 2f4l-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: 80.030 103.980 155.130 90.000 90.000 90.000 Input sequence file: 2f4l-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 9504 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: 86.372 4.000 Wilson plot Bfac: 80.01 11382 reflections ( 99.54 % complete ) and 0 restraints for refining 10518 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3139 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3241 (Rfree = 0.000) for 10518 atoms. Found 49 (49 requested) and removed 146 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.66 3.66 Search for helices and strands: 0 residues in 0 chains, 10554 seeds are put forward NCS extension: 0 residues added, 10554 seeds are put forward Round 1: 475 peptides, 95 chains. Longest chain 13 peptides. Score 0.305 Round 2: 614 peptides, 90 chains. Longest chain 34 peptides. Score 0.502 Round 3: 681 peptides, 92 chains. Longest chain 34 peptides. Score 0.562 Round 4: 691 peptides, 85 chains. Longest chain 30 peptides. Score 0.602 Round 5: 713 peptides, 84 chains. Longest chain 34 peptides. Score 0.626 Taking the results from Round 5 Chains 88, Residues 629, Estimated correctness of the model 0.0 % 7 chains (62 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 19170 restraints for refining 8578 atoms. 16544 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2473 (Rfree = 0.000) for 8578 atoms. Found 40 (40 requested) and removed 80 (20 requested) atoms. Cycle 2: After refmac, R = 0.2251 (Rfree = 0.000) for 8358 atoms. Found 26 (40 requested) and removed 49 (20 requested) atoms. Cycle 3: After refmac, R = 0.2152 (Rfree = 0.000) for 8287 atoms. Found 11 (39 requested) and removed 29 (19 requested) atoms. Cycle 4: After refmac, R = 0.2138 (Rfree = 0.000) for 8259 atoms. Found 5 (39 requested) and removed 20 (19 requested) atoms. Cycle 5: After refmac, R = 0.2106 (Rfree = 0.000) for 8238 atoms. Found 3 (39 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.69 3.69 Search for helices and strands: 0 residues in 0 chains, 8395 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 8414 seeds are put forward Round 1: 557 peptides, 99 chains. Longest chain 18 peptides. Score 0.389 Round 2: 647 peptides, 97 chains. Longest chain 16 peptides. Score 0.504 Round 3: 663 peptides, 91 chains. Longest chain 26 peptides. Score 0.549 Round 4: 658 peptides, 89 chains. Longest chain 28 peptides. Score 0.553 Round 5: 661 peptides, 84 chains. Longest chain 23 peptides. Score 0.578 Taking the results from Round 5 Chains 88, Residues 577, Estimated correctness of the model 0.0 % 7 chains (57 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 19450 restraints for refining 8580 atoms. 17033 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2357 (Rfree = 0.000) for 8580 atoms. Found 32 (40 requested) and removed 72 (20 requested) atoms. Cycle 7: After refmac, R = 0.2323 (Rfree = 0.000) for 8411 atoms. Found 32 (40 requested) and removed 44 (20 requested) atoms. Cycle 8: After refmac, R = 0.2457 (Rfree = 0.000) for 8319 atoms. Found 39 (39 requested) and removed 78 (19 requested) atoms. Cycle 9: After refmac, R = 0.2275 (Rfree = 0.000) for 8212 atoms. Found 35 (39 requested) and removed 34 (19 requested) atoms. Cycle 10: After refmac, R = 0.1876 (Rfree = 0.000) for 8165 atoms. Found 12 (39 requested) and removed 36 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.73 3.73 Search for helices and strands: 0 residues in 0 chains, 8309 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 8324 seeds are put forward Round 1: 550 peptides, 97 chains. Longest chain 22 peptides. Score 0.391 Round 2: 630 peptides, 93 chains. Longest chain 24 peptides. Score 0.505 Round 3: 634 peptides, 82 chains. Longest chain 19 peptides. Score 0.560 Round 4: 647 peptides, 81 chains. Longest chain 22 peptides. Score 0.577 Round 5: 661 peptides, 81 chains. Longest chain 27 peptides. Score 0.591 Taking the results from Round 5 Chains 84, Residues 580, Estimated correctness of the model 0.0 % 6 chains (87 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 18821 restraints for refining 8569 atoms. 16275 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2272 (Rfree = 0.000) for 8569 atoms. Found 36 (40 requested) and removed 68 (20 requested) atoms. Cycle 12: After refmac, R = 0.2073 (Rfree = 0.000) for 8486 atoms. Found 17 (40 requested) and removed 37 (20 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2009 (Rfree = 0.000) for 8446 atoms. Found 10 (40 requested) and removed 37 (20 requested) atoms. Cycle 14: After refmac, R = 0.2045 (Rfree = 0.000) for 8404 atoms. Found 20 (40 requested) and removed 37 (20 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1855 (Rfree = 0.000) for 8371 atoms. Found 6 (39 requested) and removed 26 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 3.68 Search for helices and strands: 0 residues in 0 chains, 8542 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 8567 seeds are put forward Round 1: 538 peptides, 99 chains. Longest chain 14 peptides. Score 0.365 Round 2: 603 peptides, 85 chains. Longest chain 18 peptides. Score 0.514 Round 3: 599 peptides, 82 chains. Longest chain 20 peptides. Score 0.524 Round 4: 620 peptides, 88 chains. Longest chain 19 peptides. Score 0.518 Round 5: 641 peptides, 83 chains. Longest chain 33 peptides. Score 0.563 Taking the results from Round 5 Chains 85, Residues 558, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 20020 restraints for refining 8582 atoms. 17820 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2076 (Rfree = 0.000) for 8582 atoms. Found 28 (40 requested) and removed 65 (20 requested) atoms. Cycle 17: After refmac, R = 0.2006 (Rfree = 0.000) for 8490 atoms. Found 12 (40 requested) and removed 30 (20 requested) atoms. Cycle 18: After refmac, R = 0.2061 (Rfree = 0.000) for 8437 atoms. Found 23 (40 requested) and removed 37 (20 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2000 (Rfree = 0.000) for 8398 atoms. Found 22 (40 requested) and removed 29 (20 requested) atoms. Cycle 20: After refmac, R = 0.1966 (Rfree = 0.000) for 8371 atoms. Found 23 (39 requested) and removed 37 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 3.62 Search for helices and strands: 0 residues in 0 chains, 8568 seeds are put forward NCS extension: 36 residues added (3 deleted due to clashes), 8604 seeds are put forward Round 1: 521 peptides, 99 chains. Longest chain 10 peptides. Score 0.343 Round 2: 594 peptides, 93 chains. Longest chain 16 peptides. Score 0.465 Round 3: 604 peptides, 88 chains. Longest chain 18 peptides. Score 0.501 Round 4: 615 peptides, 87 chains. Longest chain 22 peptides. Score 0.517 Round 5: 601 peptides, 87 chains. Longest chain 14 peptides. Score 0.502 Taking the results from Round 4 Chains 87, Residues 528, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 19990 restraints for refining 8582 atoms. 17928 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2202 (Rfree = 0.000) for 8582 atoms. Found 40 (40 requested) and removed 84 (20 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2161 (Rfree = 0.000) for 8485 atoms. Found 40 (40 requested) and removed 46 (20 requested) atoms. Cycle 23: After refmac, R = 0.2061 (Rfree = 0.000) for 8443 atoms. Found 40 (40 requested) and removed 36 (20 requested) atoms. Cycle 24: After refmac, R = 0.1992 (Rfree = 0.000) for 8423 atoms. Found 40 (40 requested) and removed 33 (20 requested) atoms. Cycle 25: After refmac, R = 0.1690 (Rfree = 0.000) for 8408 atoms. Found 14 (40 requested) and removed 24 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 3.63 Search for helices and strands: 0 residues in 0 chains, 8601 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 8634 seeds are put forward Round 1: 437 peptides, 90 chains. Longest chain 8 peptides. Score 0.281 Round 2: 514 peptides, 92 chains. Longest chain 15 peptides. Score 0.373 Round 3: 512 peptides, 84 chains. Longest chain 14 peptides. Score 0.414 Round 4: 542 peptides, 87 chains. Longest chain 19 peptides. Score 0.435 Round 5: 576 peptides, 90 chains. Longest chain 18 peptides. Score 0.459 Taking the results from Round 5 Chains 90, Residues 486, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 20406 restraints for refining 8582 atoms. 18552 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1988 (Rfree = 0.000) for 8582 atoms. Found 39 (40 requested) and removed 63 (20 requested) atoms. Cycle 27: After refmac, R = 0.1881 (Rfree = 0.000) for 8491 atoms. Found 31 (40 requested) and removed 30 (20 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1703 (Rfree = 0.000) for 8463 atoms. Found 9 (40 requested) and removed 26 (20 requested) atoms. Cycle 29: After refmac, R = 0.1579 (Rfree = 0.000) for 8415 atoms. Found 14 (40 requested) and removed 26 (20 requested) atoms. Cycle 30: After refmac, R = 0.1573 (Rfree = 0.000) for 8389 atoms. Found 10 (39 requested) and removed 26 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 3.69 Search for helices and strands: 0 residues in 0 chains, 8543 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 8568 seeds are put forward Round 1: 410 peptides, 89 chains. Longest chain 8 peptides. Score 0.248 Round 2: 475 peptides, 87 chains. Longest chain 13 peptides. Score 0.350 Round 3: 475 peptides, 82 chains. Longest chain 15 peptides. Score 0.378 Round 4: 519 peptides, 89 chains. Longest chain 15 peptides. Score 0.396 Round 5: 501 peptides, 82 chains. Longest chain 16 peptides. Score 0.411 Taking the results from Round 5 Chains 83, Residues 419, Estimated correctness of the model 0.0 % 5 chains (31 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 20398 restraints for refining 8583 atoms. 18714 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2038 (Rfree = 0.000) for 8583 atoms. Found 35 (40 requested) and removed 53 (20 requested) atoms. Cycle 32: After refmac, R = 0.2024 (Rfree = 0.000) for 8530 atoms. Found 17 (40 requested) and removed 31 (20 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1905 (Rfree = 0.000) for 8495 atoms. Found 10 (40 requested) and removed 22 (20 requested) atoms. Cycle 34: After refmac, R = 0.1760 (Rfree = 0.000) for 8467 atoms. Found 7 (40 requested) and removed 28 (20 requested) atoms. Cycle 35: After refmac, R = 0.1748 (Rfree = 0.000) for 8437 atoms. Found 9 (40 requested) and removed 26 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 3.68 Search for helices and strands: 0 residues in 0 chains, 8605 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8620 seeds are put forward Round 1: 390 peptides, 79 chains. Longest chain 11 peptides. Score 0.280 Round 2: 448 peptides, 82 chains. Longest chain 19 peptides. Score 0.343 Round 3: 460 peptides, 77 chains. Longest chain 15 peptides. Score 0.387 Round 4: 467 peptides, 80 chains. Longest chain 15 peptides. Score 0.379 Round 5: 468 peptides, 72 chains. Longest chain 22 peptides. Score 0.425 Taking the results from Round 5 Chains 72, Residues 396, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 11382 reflections ( 99.54 % complete ) and 20722 restraints for refining 8583 atoms. 19194 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2056 (Rfree = 0.000) for 8583 atoms. Found 40 (40 requested) and removed 40 (20 requested) atoms. Cycle 37: After refmac, R = 0.1936 (Rfree = 0.000) for 8551 atoms. Found 12 (40 requested) and removed 22 (20 requested) atoms. Cycle 38: After refmac, R = 0.1902 (Rfree = 0.000) for 8528 atoms. Found 11 (40 requested) and removed 22 (20 requested) atoms. Cycle 39: After refmac, R = 0.1861 (Rfree = 0.000) for 8514 atoms. Found 10 (40 requested) and removed 22 (20 requested) atoms. Cycle 40: After refmac, R = 0.1791 (Rfree = 0.000) for 8498 atoms. Found 5 (40 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 3.71 Search for helices and strands: 0 residues in 0 chains, 8642 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 8673 seeds are put forward Round 1: 352 peptides, 73 chains. Longest chain 11 peptides. Score 0.261 Round 2: 412 peptides, 71 chains. Longest chain 13 peptides. Score 0.358 Round 3: 436 peptides, 73 chains. Longest chain 16 peptides. Score 0.379 Round 4: 440 peptides, 70 chains. Longest chain 18 peptides. Score 0.401 Round 5: 427 peptides, 72 chains. Longest chain 17 peptides. Score 0.373 Taking the results from Round 4 Chains 70, Residues 370, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 20895 restraints for refining 8582 atoms. 19458 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2011 (Rfree = 0.000) for 8582 atoms. Found 36 (40 requested) and removed 50 (20 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1863 (Rfree = 0.000) for 8537 atoms. Found 22 (40 requested) and removed 24 (20 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1769 (Rfree = 0.000) for 8511 atoms. Found 13 (40 requested) and removed 24 (20 requested) atoms. Cycle 44: After refmac, R = 0.1742 (Rfree = 0.000) for 8484 atoms. Found 11 (40 requested) and removed 23 (20 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1739 (Rfree = 0.000) for 8459 atoms. Found 11 (40 requested) and removed 24 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.72 Search for helices and strands: 0 residues in 0 chains, 8565 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 8591 seeds are put forward Round 1: 332 peptides, 72 chains. Longest chain 10 peptides. Score 0.238 Round 2: 375 peptides, 68 chains. Longest chain 12 peptides. Score 0.326 Round 3: 367 peptides, 66 chains. Longest chain 12 peptides. Score 0.327 Round 4: 397 peptides, 69 chains. Longest chain 12 peptides. Score 0.350 Round 5: 397 peptides, 67 chains. Longest chain 13 peptides. Score 0.362 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 67, Residues 330, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2f4l-4_warpNtrace.pdb as input Building loops using Loopy2018 67 chains (330 residues) following loop building 2 chains (15 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11382 reflections ( 99.54 % complete ) and 20987 restraints for refining 8568 atoms. 19691 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2070 (Rfree = 0.000) for 8568 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2288 (Rfree = 0.000) for 8522 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.2181 (Rfree = 0.000) for 8481 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.2132 (Rfree = 0.000) for 8428 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 21:24:15 GMT 2018 Job finished. TimeTaking 116.3