Mon 24 Dec 01:10:29 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vp4-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vp4-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vp4-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.2-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 01:10:33 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vp4-3.2-parrot-mrncs/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 716 and 0 Target number of residues in the AU: 716 Target solvent content: 0.6401 Checking the provided sequence file Detected sequence length: 425 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 850 Adjusted target solvent content: 0.57 Input MTZ file: 1vp4-3.2-parrot-mrncs.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: 170 Cell parameters: 164.860 164.860 68.609 90.000 90.000 120.000 Input sequence file: 1vp4-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6800 target number of atoms Had to go as low as 0.80 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: 142.773 3.200 Wilson plot Bfac: 72.01 17764 reflections ( 99.82 % complete ) and 0 restraints for refining 7529 atoms. Observations/parameters ratio is 0.59 ------------------------------------------------------ Starting model: R = 0.3529 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3303 (Rfree = 0.000) for 7529 atoms. Found 67 (67 requested) and removed 97 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 2.95 Search for helices and strands: 0 residues in 0 chains, 7638 seeds are put forward NCS extension: 0 residues added, 7638 seeds are put forward Round 1: 377 peptides, 72 chains. Longest chain 13 peptides. Score 0.323 Round 2: 480 peptides, 73 chains. Longest chain 21 peptides. Score 0.471 Round 3: 504 peptides, 75 chains. Longest chain 30 peptides. Score 0.492 Round 4: 535 peptides, 75 chains. Longest chain 33 peptides. Score 0.532 Round 5: 543 peptides, 72 chains. Longest chain 34 peptides. Score 0.558 Taking the results from Round 5 Chains 74, Residues 471, Estimated correctness of the model 29.2 % 5 chains (61 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 12979 restraints for refining 6208 atoms. 10956 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2833 (Rfree = 0.000) for 6208 atoms. Found 38 (55 requested) and removed 56 (27 requested) atoms. Cycle 2: After refmac, R = 0.2784 (Rfree = 0.000) for 6131 atoms. Found 29 (55 requested) and removed 41 (27 requested) atoms. Cycle 3: After refmac, R = 0.2699 (Rfree = 0.000) for 6099 atoms. Found 22 (54 requested) and removed 45 (27 requested) atoms. Cycle 4: After refmac, R = 0.2535 (Rfree = 0.000) for 6056 atoms. Found 14 (54 requested) and removed 38 (27 requested) atoms. Cycle 5: After refmac, R = 0.2469 (Rfree = 0.000) for 6018 atoms. Found 11 (54 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 6241 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 6275 seeds are put forward Round 1: 496 peptides, 82 chains. Longest chain 25 peptides. Score 0.439 Round 2: 525 peptides, 70 chains. Longest chain 25 peptides. Score 0.547 Round 3: 525 peptides, 65 chains. Longest chain 25 peptides. Score 0.574 Round 4: 536 peptides, 60 chains. Longest chain 38 peptides. Score 0.613 Round 5: 535 peptides, 61 chains. Longest chain 34 peptides. Score 0.606 Taking the results from Round 4 Chains 63, Residues 476, Estimated correctness of the model 44.5 % 5 chains (51 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13070 restraints for refining 6208 atoms. 11057 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2671 (Rfree = 0.000) for 6208 atoms. Found 53 (55 requested) and removed 42 (27 requested) atoms. Cycle 7: After refmac, R = 0.2585 (Rfree = 0.000) for 6188 atoms. Found 20 (55 requested) and removed 33 (27 requested) atoms. Cycle 8: After refmac, R = 0.2540 (Rfree = 0.000) for 6163 atoms. Found 15 (55 requested) and removed 36 (27 requested) atoms. Cycle 9: After refmac, R = 0.2797 (Rfree = 0.000) for 6131 atoms. Found 55 (55 requested) and removed 39 (27 requested) atoms. Cycle 10: After refmac, R = 0.2469 (Rfree = 0.000) for 6132 atoms. Found 29 (55 requested) and removed 33 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 6414 seeds are put forward NCS extension: 40 residues added (7 deleted due to clashes), 6454 seeds are put forward Round 1: 487 peptides, 83 chains. Longest chain 19 peptides. Score 0.420 Round 2: 521 peptides, 72 chains. Longest chain 32 peptides. Score 0.531 Round 3: 535 peptides, 65 chains. Longest chain 41 peptides. Score 0.586 Round 4: 533 peptides, 68 chains. Longest chain 23 peptides. Score 0.567 Round 5: 532 peptides, 70 chains. Longest chain 32 peptides. Score 0.556 Taking the results from Round 3 Chains 68, Residues 470, Estimated correctness of the model 37.2 % 6 chains (109 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 12427 restraints for refining 6207 atoms. 10146 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2656 (Rfree = 0.000) for 6207 atoms. Found 50 (55 requested) and removed 56 (27 requested) atoms. Cycle 12: After refmac, R = 0.2530 (Rfree = 0.000) for 6180 atoms. Found 23 (55 requested) and removed 33 (27 requested) atoms. Cycle 13: After refmac, R = 0.2512 (Rfree = 0.000) for 6156 atoms. Found 12 (55 requested) and removed 29 (27 requested) atoms. Cycle 14: After refmac, R = 0.2537 (Rfree = 0.000) for 6132 atoms. Found 17 (55 requested) and removed 27 (27 requested) atoms. Cycle 15: After refmac, R = 0.2804 (Rfree = 0.000) for 6118 atoms. Found 48 (54 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 6339 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 6371 seeds are put forward Round 1: 488 peptides, 74 chains. Longest chain 33 peptides. Score 0.476 Round 2: 520 peptides, 69 chains. Longest chain 39 peptides. Score 0.546 Round 3: 533 peptides, 67 chains. Longest chain 23 peptides. Score 0.573 Round 4: 521 peptides, 65 chains. Longest chain 24 peptides. Score 0.569 Round 5: 518 peptides, 69 chains. Longest chain 24 peptides. Score 0.544 Taking the results from Round 3 Chains 67, Residues 466, Estimated correctness of the model 33.6 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13559 restraints for refining 6208 atoms. 11708 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2642 (Rfree = 0.000) for 6208 atoms. Found 41 (55 requested) and removed 31 (27 requested) atoms. Cycle 17: After refmac, R = 0.2567 (Rfree = 0.000) for 6194 atoms. Found 34 (55 requested) and removed 29 (27 requested) atoms. Cycle 18: After refmac, R = 0.2534 (Rfree = 0.000) for 6187 atoms. Found 25 (55 requested) and removed 28 (27 requested) atoms. Cycle 19: After refmac, R = 0.2516 (Rfree = 0.000) for 6175 atoms. Found 22 (55 requested) and removed 29 (27 requested) atoms. Cycle 20: After refmac, R = 0.2412 (Rfree = 0.000) for 6163 atoms. Found 16 (55 requested) and removed 27 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.00 Search for helices and strands: 0 residues in 0 chains, 6383 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 6396 seeds are put forward Round 1: 463 peptides, 70 chains. Longest chain 22 peptides. Score 0.466 Round 2: 515 peptides, 68 chains. Longest chain 22 peptides. Score 0.546 Round 3: 503 peptides, 65 chains. Longest chain 24 peptides. Score 0.548 Round 4: 505 peptides, 63 chains. Longest chain 28 peptides. Score 0.561 Round 5: 509 peptides, 62 chains. Longest chain 25 peptides. Score 0.571 Taking the results from Round 5 Chains 62, Residues 447, Estimated correctness of the model 33.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13624 restraints for refining 6208 atoms. 11863 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2564 (Rfree = 0.000) for 6208 atoms. Found 42 (55 requested) and removed 29 (27 requested) atoms. Cycle 22: After refmac, R = 0.2676 (Rfree = 0.000) for 6215 atoms. Found 51 (55 requested) and removed 32 (27 requested) atoms. Cycle 23: After refmac, R = 0.2394 (Rfree = 0.000) for 6222 atoms. Found 28 (55 requested) and removed 28 (27 requested) atoms. Cycle 24: After refmac, R = 0.2360 (Rfree = 0.000) for 6212 atoms. Found 20 (55 requested) and removed 29 (27 requested) atoms. Cycle 25: After refmac, R = 0.2673 (Rfree = 0.000) for 6192 atoms. Found 55 (55 requested) and removed 34 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 6500 seeds are put forward NCS extension: 23 residues added (5 deleted due to clashes), 6523 seeds are put forward Round 1: 466 peptides, 72 chains. Longest chain 23 peptides. Score 0.458 Round 2: 491 peptides, 63 chains. Longest chain 26 peptides. Score 0.544 Round 3: 504 peptides, 66 chains. Longest chain 25 peptides. Score 0.543 Round 4: 504 peptides, 68 chains. Longest chain 23 peptides. Score 0.532 Round 5: 496 peptides, 65 chains. Longest chain 24 peptides. Score 0.539 Taking the results from Round 2 Chains 65, Residues 428, Estimated correctness of the model 25.1 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13594 restraints for refining 6208 atoms. 11847 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2532 (Rfree = 0.000) for 6208 atoms. Found 46 (55 requested) and removed 31 (27 requested) atoms. Cycle 27: After refmac, R = 0.2427 (Rfree = 0.000) for 6220 atoms. Found 23 (55 requested) and removed 28 (27 requested) atoms. Cycle 28: After refmac, R = 0.2574 (Rfree = 0.000) for 6213 atoms. Found 36 (55 requested) and removed 33 (27 requested) atoms. Cycle 29: After refmac, R = 0.2393 (Rfree = 0.000) for 6214 atoms. Found 31 (55 requested) and removed 27 (27 requested) atoms. Cycle 30: After refmac, R = 0.2501 (Rfree = 0.000) for 6206 atoms. Found 55 (55 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 2.94 Search for helices and strands: 0 residues in 0 chains, 6473 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 6502 seeds are put forward Round 1: 423 peptides, 72 chains. Longest chain 25 peptides. Score 0.395 Round 2: 474 peptides, 62 chains. Longest chain 25 peptides. Score 0.528 Round 3: 468 peptides, 65 chains. Longest chain 18 peptides. Score 0.503 Round 4: 462 peptides, 67 chains. Longest chain 19 peptides. Score 0.483 Round 5: 464 peptides, 60 chains. Longest chain 25 peptides. Score 0.527 Taking the results from Round 2 Chains 66, Residues 412, Estimated correctness of the model 20.2 % 4 chains (47 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13281 restraints for refining 6208 atoms. 11515 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2497 (Rfree = 0.000) for 6208 atoms. Found 46 (55 requested) and removed 39 (27 requested) atoms. Cycle 32: After refmac, R = 0.2402 (Rfree = 0.000) for 6205 atoms. Found 25 (55 requested) and removed 29 (27 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2374 (Rfree = 0.000) for 6197 atoms. Found 19 (55 requested) and removed 28 (27 requested) atoms. Cycle 34: After refmac, R = 0.2358 (Rfree = 0.000) for 6186 atoms. Found 12 (55 requested) and removed 27 (27 requested) atoms. Cycle 35: After refmac, R = 0.2363 (Rfree = 0.000) for 6169 atoms. Found 14 (55 requested) and removed 31 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 6401 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 6418 seeds are put forward Round 1: 399 peptides, 72 chains. Longest chain 14 peptides. Score 0.358 Round 2: 452 peptides, 65 chains. Longest chain 27 peptides. Score 0.481 Round 3: 462 peptides, 64 chains. Longest chain 19 peptides. Score 0.501 Round 4: 461 peptides, 63 chains. Longest chain 25 peptides. Score 0.505 Round 5: 447 peptides, 61 chains. Longest chain 27 peptides. Score 0.499 Taking the results from Round 4 Chains 66, Residues 398, Estimated correctness of the model 12.9 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13737 restraints for refining 6207 atoms. 12128 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2512 (Rfree = 0.000) for 6207 atoms. Found 46 (55 requested) and removed 34 (27 requested) atoms. Cycle 37: After refmac, R = 0.2389 (Rfree = 0.000) for 6212 atoms. Found 17 (55 requested) and removed 28 (27 requested) atoms. Cycle 38: After refmac, R = 0.2316 (Rfree = 0.000) for 6193 atoms. Found 13 (55 requested) and removed 27 (27 requested) atoms. Cycle 39: After refmac, R = 0.2448 (Rfree = 0.000) for 6172 atoms. Found 21 (55 requested) and removed 27 (27 requested) atoms. Cycle 40: After refmac, R = 0.2676 (Rfree = 0.000) for 6164 atoms. Found 55 (55 requested) and removed 29 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 2.95 Search for helices and strands: 0 residues in 0 chains, 6436 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 6452 seeds are put forward Round 1: 404 peptides, 76 chains. Longest chain 16 peptides. Score 0.339 Round 2: 443 peptides, 67 chains. Longest chain 19 peptides. Score 0.457 Round 3: 419 peptides, 66 chains. Longest chain 23 peptides. Score 0.428 Round 4: 452 peptides, 71 chains. Longest chain 17 peptides. Score 0.444 Round 5: 444 peptides, 70 chains. Longest chain 16 peptides. Score 0.439 Taking the results from Round 2 Chains 69, Residues 376, Estimated correctness of the model 0.0 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13740 restraints for refining 6208 atoms. 12180 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2582 (Rfree = 0.000) for 6208 atoms. Found 55 (55 requested) and removed 44 (27 requested) atoms. Cycle 42: After refmac, R = 0.2829 (Rfree = 0.000) for 6211 atoms. Found 55 (55 requested) and removed 31 (27 requested) atoms. Cycle 43: After refmac, R = 0.2467 (Rfree = 0.000) for 6225 atoms. Found 46 (55 requested) and removed 34 (27 requested) atoms. Cycle 44: After refmac, R = 0.2465 (Rfree = 0.000) for 6218 atoms. Found 50 (55 requested) and removed 35 (27 requested) atoms. Cycle 45: After refmac, R = 0.2294 (Rfree = 0.000) for 6212 atoms. Found 29 (55 requested) and removed 27 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 6456 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 6479 seeds are put forward Round 1: 365 peptides, 72 chains. Longest chain 11 peptides. Score 0.304 Round 2: 429 peptides, 70 chains. Longest chain 17 peptides. Score 0.417 Round 3: 412 peptides, 67 chains. Longest chain 13 peptides. Score 0.412 Round 4: 412 peptides, 66 chains. Longest chain 14 peptides. Score 0.418 Round 5: 413 peptides, 72 chains. Longest chain 27 peptides. Score 0.380 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 66, Residues 346, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence Sequence coverage is 1 % Consider running further cycles of model building using 1vp4-3_warpNtrace.pdb as input Building loops using Loopy2018 66 chains (346 residues) following loop building 2 chains (6 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17764 reflections ( 99.82 % complete ) and 14204 restraints for refining 6207 atoms. 12873 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2439 (Rfree = 0.000) for 6207 atoms. Found 0 (55 requested) and removed 23 (27 requested) atoms. Cycle 47: After refmac, R = 0.2587 (Rfree = 0.000) for 6171 atoms. Found 0 (55 requested) and removed 16 (27 requested) atoms. Cycle 48: After refmac, R = 0.2409 (Rfree = 0.000) for 6153 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 49: After refmac, R = 0.2730 (Rfree = 0.000) for 6120 atoms. TimeTaking 72.8