Mon 24 Dec 01:00:20 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 1ztc-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1ztc-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1ztc-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.8-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/1ztc-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.8-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 01:00:25 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/1ztc-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.8-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 1095 and 0 Target number of residues in the AU: 1095 Target solvent content: 0.6595 Checking the provided sequence file Detected sequence length: 221 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 884 Adjusted target solvent content: 0.73 Input MTZ file: 1ztc-3.8-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: 19 Cell parameters: 89.783 127.343 152.224 90.000 90.000 90.000 Input sequence file: 1ztc-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7072 target number of atoms Had to go as low as 1.10 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: 97.673 3.800 Wilson plot Bfac: 84.57 17528 reflections ( 98.52 % complete ) and 0 restraints for refining 7851 atoms. Observations/parameters ratio is 0.56 ------------------------------------------------------ Starting model: R = 0.3362 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3207 (Rfree = 0.000) for 7851 atoms. Found 43 (43 requested) and removed 26 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 2.62 Search for helices and strands: 0 residues in 0 chains, 8028 seeds are put forward NCS extension: 0 residues added, 8028 seeds are put forward Round 1: 542 peptides, 72 chains. Longest chain 18 peptides. Score 0.447 Round 2: 632 peptides, 65 chains. Longest chain 25 peptides. Score 0.551 Round 3: 635 peptides, 55 chains. Longest chain 45 peptides. Score 0.590 Round 4: 621 peptides, 51 chains. Longest chain 44 peptides. Score 0.595 Round 5: 619 peptides, 52 chains. Longest chain 37 peptides. Score 0.589 Taking the results from Round 4 Chains 55, Residues 570, Estimated correctness of the model 0.0 % 3 chains (63 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 12982 restraints for refining 6397 atoms. 10500 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2756 (Rfree = 0.000) for 6397 atoms. Found 35 (35 requested) and removed 36 (17 requested) atoms. Cycle 2: After refmac, R = 0.2594 (Rfree = 0.000) for 6286 atoms. Found 35 (35 requested) and removed 25 (17 requested) atoms. Cycle 3: After refmac, R = 0.2480 (Rfree = 0.000) for 6243 atoms. Found 34 (34 requested) and removed 23 (17 requested) atoms. Cycle 4: After refmac, R = 0.2400 (Rfree = 0.000) for 6217 atoms. Found 34 (34 requested) and removed 26 (17 requested) atoms. Cycle 5: After refmac, R = 0.2307 (Rfree = 0.000) for 6202 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.69 2.65 Search for helices and strands: 0 residues in 0 chains, 6451 seeds are put forward NCS extension: 29 residues added (13 deleted due to clashes), 6480 seeds are put forward Round 1: 592 peptides, 57 chains. Longest chain 24 peptides. Score 0.550 Round 2: 615 peptides, 50 chains. Longest chain 30 peptides. Score 0.594 Round 3: 652 peptides, 60 chains. Longest chain 44 peptides. Score 0.585 Round 4: 628 peptides, 56 chains. Longest chain 34 peptides. Score 0.582 Round 5: 640 peptides, 53 chains. Longest chain 42 peptides. Score 0.601 Taking the results from Round 5 Chains 53, Residues 587, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13659 restraints for refining 6395 atoms. 11364 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2736 (Rfree = 0.000) for 6395 atoms. Found 35 (35 requested) and removed 26 (17 requested) atoms. Cycle 7: After refmac, R = 0.2583 (Rfree = 0.000) for 6319 atoms. Found 35 (35 requested) and removed 28 (17 requested) atoms. Cycle 8: After refmac, R = 0.2527 (Rfree = 0.000) for 6271 atoms. Found 34 (34 requested) and removed 23 (17 requested) atoms. Cycle 9: After refmac, R = 0.2444 (Rfree = 0.000) for 6252 atoms. Found 34 (34 requested) and removed 26 (17 requested) atoms. Cycle 10: After refmac, R = 0.2440 (Rfree = 0.000) for 6235 atoms. Found 34 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 2.62 Search for helices and strands: 0 residues in 0 chains, 6553 seeds are put forward NCS extension: 25 residues added (7 deleted due to clashes), 6578 seeds are put forward Round 1: 614 peptides, 70 chains. Longest chain 22 peptides. Score 0.518 Round 2: 660 peptides, 61 chains. Longest chain 37 peptides. Score 0.587 Round 3: 643 peptides, 58 chains. Longest chain 54 peptides. Score 0.585 Round 4: 645 peptides, 58 chains. Longest chain 42 peptides. Score 0.587 Round 5: 629 peptides, 58 chains. Longest chain 29 peptides. Score 0.575 Taking the results from Round 4 Chains 58, Residues 587, Estimated correctness of the model 0.0 % 2 chains (53 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13165 restraints for refining 6397 atoms. 10655 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2754 (Rfree = 0.000) for 6397 atoms. Found 35 (35 requested) and removed 36 (17 requested) atoms. Cycle 12: After refmac, R = 0.2653 (Rfree = 0.000) for 6329 atoms. Found 35 (35 requested) and removed 26 (17 requested) atoms. Cycle 13: After refmac, R = 0.2609 (Rfree = 0.000) for 6310 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. Cycle 14: After refmac, R = 0.2560 (Rfree = 0.000) for 6293 atoms. Found 34 (34 requested) and removed 25 (17 requested) atoms. Cycle 15: After refmac, R = 0.2569 (Rfree = 0.000) for 6284 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 2.66 Search for helices and strands: 0 residues in 0 chains, 6565 seeds are put forward NCS extension: 47 residues added (3 deleted due to clashes), 6612 seeds are put forward Round 1: 580 peptides, 62 chains. Longest chain 26 peptides. Score 0.521 Round 2: 627 peptides, 63 chains. Longest chain 27 peptides. Score 0.555 Round 3: 626 peptides, 53 chains. Longest chain 33 peptides. Score 0.591 Round 4: 632 peptides, 55 chains. Longest chain 32 peptides. Score 0.588 Round 5: 618 peptides, 53 chains. Longest chain 34 peptides. Score 0.585 Taking the results from Round 3 Chains 57, Residues 573, Estimated correctness of the model 0.0 % 5 chains (88 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 12750 restraints for refining 6397 atoms. 10095 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2812 (Rfree = 0.000) for 6397 atoms. Found 35 (35 requested) and removed 27 (17 requested) atoms. Cycle 17: After refmac, R = 0.2641 (Rfree = 0.000) for 6341 atoms. Found 35 (35 requested) and removed 29 (17 requested) atoms. Cycle 18: After refmac, R = 0.2639 (Rfree = 0.000) for 6303 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. Cycle 19: After refmac, R = 0.2566 (Rfree = 0.000) for 6281 atoms. Found 34 (34 requested) and removed 30 (17 requested) atoms. Cycle 20: After refmac, R = 0.2557 (Rfree = 0.000) for 6264 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.68 2.64 Search for helices and strands: 0 residues in 0 chains, 6498 seeds are put forward NCS extension: 20 residues added (6 deleted due to clashes), 6518 seeds are put forward Round 1: 583 peptides, 65 chains. Longest chain 25 peptides. Score 0.512 Round 2: 605 peptides, 57 chains. Longest chain 32 peptides. Score 0.560 Round 3: 612 peptides, 61 chains. Longest chain 33 peptides. Score 0.551 Round 4: 614 peptides, 61 chains. Longest chain 23 peptides. Score 0.552 Round 5: 628 peptides, 55 chains. Longest chain 28 peptides. Score 0.585 Taking the results from Round 5 Chains 56, Residues 573, Estimated correctness of the model 0.0 % 2 chains (35 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13514 restraints for refining 6394 atoms. 11102 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2648 (Rfree = 0.000) for 6394 atoms. Found 35 (35 requested) and removed 33 (17 requested) atoms. Cycle 22: After refmac, R = 0.2646 (Rfree = 0.000) for 6341 atoms. Found 35 (35 requested) and removed 30 (17 requested) atoms. Cycle 23: After refmac, R = 0.2519 (Rfree = 0.000) for 6312 atoms. Found 34 (34 requested) and removed 40 (17 requested) atoms. Cycle 24: After refmac, R = 0.2477 (Rfree = 0.000) for 6280 atoms. Found 34 (34 requested) and removed 34 (17 requested) atoms. Cycle 25: After refmac, R = 0.2450 (Rfree = 0.000) for 6270 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.68 2.64 Search for helices and strands: 0 residues in 0 chains, 6485 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 6501 seeds are put forward Round 1: 596 peptides, 71 chains. Longest chain 27 peptides. Score 0.499 Round 2: 629 peptides, 58 chains. Longest chain 30 peptides. Score 0.575 Round 3: 590 peptides, 59 chains. Longest chain 27 peptides. Score 0.541 Round 4: 624 peptides, 63 chains. Longest chain 49 peptides. Score 0.553 Round 5: 627 peptides, 62 chains. Longest chain 30 peptides. Score 0.559 Taking the results from Round 2 Chains 58, Residues 571, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13841 restraints for refining 6396 atoms. 11587 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2547 (Rfree = 0.000) for 6396 atoms. Found 35 (35 requested) and removed 22 (17 requested) atoms. Cycle 27: After refmac, R = 0.2495 (Rfree = 0.000) for 6373 atoms. Found 35 (35 requested) and removed 26 (17 requested) atoms. Cycle 28: After refmac, R = 0.2475 (Rfree = 0.000) for 6356 atoms. Found 35 (35 requested) and removed 27 (17 requested) atoms. Cycle 29: After refmac, R = 0.2398 (Rfree = 0.000) for 6345 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. Cycle 30: After refmac, R = 0.2185 (Rfree = 0.000) for 6332 atoms. Found 14 (34 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.68 2.64 Search for helices and strands: 0 residues in 0 chains, 6558 seeds are put forward NCS extension: 11 residues added (7 deleted due to clashes), 6569 seeds are put forward Round 1: 589 peptides, 73 chains. Longest chain 22 peptides. Score 0.485 Round 2: 626 peptides, 59 chains. Longest chain 35 peptides. Score 0.569 Round 3: 624 peptides, 65 chains. Longest chain 34 peptides. Score 0.545 Round 4: 631 peptides, 58 chains. Longest chain 34 peptides. Score 0.576 Round 5: 642 peptides, 62 chains. Longest chain 38 peptides. Score 0.570 Taking the results from Round 4 Chains 59, Residues 573, Estimated correctness of the model 0.0 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13373 restraints for refining 6397 atoms. 10994 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2609 (Rfree = 0.000) for 6397 atoms. Found 35 (35 requested) and removed 23 (17 requested) atoms. Cycle 32: After refmac, R = 0.2550 (Rfree = 0.000) for 6386 atoms. Found 35 (35 requested) and removed 29 (17 requested) atoms. Cycle 33: After refmac, R = 0.2445 (Rfree = 0.000) for 6379 atoms. Found 28 (35 requested) and removed 25 (17 requested) atoms. Cycle 34: After refmac, R = 0.2384 (Rfree = 0.000) for 6368 atoms. Found 21 (35 requested) and removed 20 (17 requested) atoms. Cycle 35: After refmac, R = 0.2357 (Rfree = 0.000) for 6359 atoms. Found 19 (35 requested) and removed 23 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 2.61 Search for helices and strands: 0 residues in 0 chains, 6559 seeds are put forward NCS extension: 15 residues added (7 deleted due to clashes), 6574 seeds are put forward Round 1: 556 peptides, 68 chains. Longest chain 26 peptides. Score 0.477 Round 2: 623 peptides, 60 chains. Longest chain 34 peptides. Score 0.563 Round 3: 615 peptides, 64 chains. Longest chain 33 peptides. Score 0.542 Round 4: 585 peptides, 60 chains. Longest chain 27 peptides. Score 0.533 Round 5: 584 peptides, 61 chains. Longest chain 36 peptides. Score 0.528 Taking the results from Round 2 Chains 63, Residues 563, Estimated correctness of the model 0.0 % 2 chains (41 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13559 restraints for refining 6394 atoms. 11200 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2538 (Rfree = 0.000) for 6394 atoms. Found 35 (35 requested) and removed 28 (17 requested) atoms. Cycle 37: After refmac, R = 0.2458 (Rfree = 0.000) for 6366 atoms. Found 35 (35 requested) and removed 19 (17 requested) atoms. Cycle 38: After refmac, R = 0.2419 (Rfree = 0.000) for 6355 atoms. Found 31 (35 requested) and removed 19 (17 requested) atoms. Cycle 39: After refmac, R = 0.2331 (Rfree = 0.000) for 6347 atoms. Found 24 (35 requested) and removed 20 (17 requested) atoms. Cycle 40: After refmac, R = 0.2282 (Rfree = 0.000) for 6338 atoms. Found 26 (34 requested) and removed 28 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 2.63 Search for helices and strands: 0 residues in 0 chains, 6523 seeds are put forward NCS extension: 21 residues added (10 deleted due to clashes), 6544 seeds are put forward Round 1: 561 peptides, 71 chains. Longest chain 23 peptides. Score 0.469 Round 2: 593 peptides, 67 chains. Longest chain 30 peptides. Score 0.512 Round 3: 579 peptides, 64 chains. Longest chain 22 peptides. Score 0.512 Round 4: 589 peptides, 64 chains. Longest chain 30 peptides. Score 0.521 Round 5: 591 peptides, 64 chains. Longest chain 24 peptides. Score 0.522 Taking the results from Round 5 Chains 64, Residues 527, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 14322 restraints for refining 6397 atoms. 12278 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2699 (Rfree = 0.000) for 6397 atoms. Found 35 (35 requested) and removed 18 (17 requested) atoms. Cycle 42: After refmac, R = 0.2591 (Rfree = 0.000) for 6384 atoms. Found 35 (35 requested) and removed 23 (17 requested) atoms. Cycle 43: After refmac, R = 0.2562 (Rfree = 0.000) for 6372 atoms. Found 35 (35 requested) and removed 19 (17 requested) atoms. Cycle 44: After refmac, R = 0.2496 (Rfree = 0.000) for 6374 atoms. Found 35 (35 requested) and removed 18 (17 requested) atoms. Cycle 45: After refmac, R = 0.2427 (Rfree = 0.000) for 6379 atoms. Found 35 (35 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 2.62 Search for helices and strands: 0 residues in 0 chains, 6610 seeds are put forward NCS extension: 17 residues added (6 deleted due to clashes), 6627 seeds are put forward Round 1: 529 peptides, 74 chains. Longest chain 20 peptides. Score 0.427 Round 2: 595 peptides, 69 chains. Longest chain 31 peptides. Score 0.506 Round 3: 587 peptides, 68 chains. Longest chain 33 peptides. Score 0.503 Round 4: 606 peptides, 63 chains. Longest chain 30 peptides. Score 0.538 Round 5: 591 peptides, 66 chains. Longest chain 23 peptides. Score 0.514 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 64, Residues 543, Estimated correctness of the model 0.0 % 1 chains (27 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1ztc-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17528 reflections ( 98.52 % complete ) and 14041 restraints for refining 6448 atoms. 11811 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2570 (Rfree = 0.000) for 6448 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2469 (Rfree = 0.000) for 6390 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.2404 (Rfree = 0.000) for 6347 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.2373 (Rfree = 0.000) for 6315 atoms. TimeTaking 92.17