Mon 24 Dec 08:05:05 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vlu-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vlu-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vlu-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.4-parrot-noncs ############### 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 08:05:10 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/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.4-parrot-noncs/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 1001 and 0 Target number of residues in the AU: 1001 Target solvent content: 0.6314 Checking the provided sequence file Detected sequence length: 468 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 936 Adjusted target solvent content: 0.66 Input MTZ file: 1vlu-3.4-parrot-noncs.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: 20 Cell parameters: 123.109 190.784 125.153 90.000 90.000 90.000 Input sequence file: 1vlu-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 7488 target number of atoms Had to go as low as 0.90 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: 44.569 3.400 Wilson plot Bfac: 67.14 20628 reflections ( 99.87 % complete ) and 0 restraints for refining 8293 atoms. Observations/parameters ratio is 0.62 ------------------------------------------------------ Starting model: R = 0.3405 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3049 (Rfree = 0.000) for 8293 atoms. Found 62 (62 requested) and removed 79 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.31 2.65 Search for helices and strands: 0 residues in 0 chains, 8490 seeds are put forward NCS extension: 0 residues added, 8490 seeds are put forward Round 1: 468 peptides, 72 chains. Longest chain 20 peptides. Score 0.402 Round 2: 543 peptides, 63 chains. Longest chain 23 peptides. Score 0.524 Round 3: 560 peptides, 59 chains. Longest chain 29 peptides. Score 0.557 Round 4: 555 peptides, 60 chains. Longest chain 41 peptides. Score 0.548 Round 5: 559 peptides, 59 chains. Longest chain 27 peptides. Score 0.557 Taking the results from Round 5 Chains 67, Residues 500, Estimated correctness of the model 14.0 % 8 chains (99 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 14217 restraints for refining 6807 atoms. 11958 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2607 (Rfree = 0.000) for 6807 atoms. Found 51 (51 requested) and removed 69 (25 requested) atoms. Cycle 2: After refmac, R = 0.2414 (Rfree = 0.000) for 6676 atoms. Found 51 (51 requested) and removed 49 (25 requested) atoms. Cycle 3: After refmac, R = 0.2315 (Rfree = 0.000) for 6626 atoms. Found 38 (50 requested) and removed 43 (25 requested) atoms. Cycle 4: After refmac, R = 0.2232 (Rfree = 0.000) for 6593 atoms. Found 29 (49 requested) and removed 34 (24 requested) atoms. Cycle 5: After refmac, R = 0.2204 (Rfree = 0.000) for 6564 atoms. Found 30 (49 requested) and removed 36 (24 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 2.64 Search for helices and strands: 0 residues in 0 chains, 6879 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 6895 seeds are put forward Round 1: 568 peptides, 66 chains. Longest chain 22 peptides. Score 0.534 Round 2: 578 peptides, 69 chains. Longest chain 34 peptides. Score 0.531 Round 3: 593 peptides, 58 chains. Longest chain 30 peptides. Score 0.591 Round 4: 587 peptides, 56 chains. Longest chain 48 peptides. Score 0.594 Round 5: 591 peptides, 55 chains. Longest chain 50 peptides. Score 0.601 Taking the results from Round 5 Chains 62, Residues 536, Estimated correctness of the model 29.0 % 8 chains (139 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 13473 restraints for refining 6808 atoms. 10901 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2691 (Rfree = 0.000) for 6808 atoms. Found 51 (51 requested) and removed 73 (25 requested) atoms. Cycle 7: After refmac, R = 0.2541 (Rfree = 0.000) for 6726 atoms. Found 47 (51 requested) and removed 45 (25 requested) atoms. Cycle 8: After refmac, R = 0.2453 (Rfree = 0.000) for 6701 atoms. Found 25 (50 requested) and removed 42 (25 requested) atoms. Cycle 9: After refmac, R = 0.2428 (Rfree = 0.000) for 6659 atoms. Found 28 (50 requested) and removed 40 (25 requested) atoms. Cycle 10: After refmac, R = 0.2372 (Rfree = 0.000) for 6629 atoms. Found 21 (50 requested) and removed 31 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 2.65 Search for helices and strands: 0 residues in 0 chains, 6874 seeds are put forward NCS extension: 55 residues added (18 deleted due to clashes), 6929 seeds are put forward Round 1: 551 peptides, 67 chains. Longest chain 29 peptides. Score 0.514 Round 2: 591 peptides, 57 chains. Longest chain 29 peptides. Score 0.593 Round 3: 579 peptides, 59 chains. Longest chain 30 peptides. Score 0.574 Round 4: 586 peptides, 63 chains. Longest chain 25 peptides. Score 0.564 Round 5: 611 peptides, 59 chains. Longest chain 46 peptides. Score 0.602 Taking the results from Round 5 Chains 65, Residues 552, Estimated correctness of the model 29.3 % 6 chains (107 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 13782 restraints for refining 6808 atoms. 11227 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2689 (Rfree = 0.000) for 6808 atoms. Found 51 (51 requested) and removed 61 (25 requested) atoms. Cycle 12: After refmac, R = 0.2521 (Rfree = 0.000) for 6752 atoms. Found 47 (51 requested) and removed 42 (25 requested) atoms. Cycle 13: After refmac, R = 0.2435 (Rfree = 0.000) for 6728 atoms. Found 31 (51 requested) and removed 36 (25 requested) atoms. Cycle 14: After refmac, R = 0.2375 (Rfree = 0.000) for 6699 atoms. Found 18 (50 requested) and removed 31 (25 requested) atoms. Cycle 15: After refmac, R = 0.2336 (Rfree = 0.000) for 6669 atoms. Found 19 (50 requested) and removed 34 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 2.64 Search for helices and strands: 0 residues in 0 chains, 6882 seeds are put forward NCS extension: 30 residues added (7 deleted due to clashes), 6912 seeds are put forward Round 1: 565 peptides, 65 chains. Longest chain 29 peptides. Score 0.536 Round 2: 595 peptides, 61 chains. Longest chain 29 peptides. Score 0.580 Round 3: 595 peptides, 66 chains. Longest chain 30 peptides. Score 0.559 Round 4: 594 peptides, 59 chains. Longest chain 31 peptides. Score 0.588 Round 5: 585 peptides, 64 chains. Longest chain 28 peptides. Score 0.559 Taking the results from Round 4 Chains 66, Residues 535, Estimated correctness of the model 24.7 % 10 chains (105 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 13867 restraints for refining 6808 atoms. 11426 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2738 (Rfree = 0.000) for 6808 atoms. Found 51 (51 requested) and removed 50 (25 requested) atoms. Cycle 17: After refmac, R = 0.2566 (Rfree = 0.000) for 6769 atoms. Found 26 (51 requested) and removed 35 (25 requested) atoms. Cycle 18: After refmac, R = 0.2533 (Rfree = 0.000) for 6740 atoms. Found 19 (51 requested) and removed 33 (25 requested) atoms. Cycle 19: After refmac, R = 0.2474 (Rfree = 0.000) for 6708 atoms. Found 18 (50 requested) and removed 27 (25 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2423 (Rfree = 0.000) for 6684 atoms. Found 23 (50 requested) and removed 31 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 2.63 Search for helices and strands: 0 residues in 0 chains, 6931 seeds are put forward NCS extension: 25 residues added (5 deleted due to clashes), 6956 seeds are put forward Round 1: 518 peptides, 67 chains. Longest chain 24 peptides. Score 0.481 Round 2: 581 peptides, 64 chains. Longest chain 22 peptides. Score 0.555 Round 3: 583 peptides, 63 chains. Longest chain 28 peptides. Score 0.561 Round 4: 575 peptides, 65 chains. Longest chain 23 peptides. Score 0.545 Round 5: 548 peptides, 59 chains. Longest chain 36 peptides. Score 0.546 Taking the results from Round 3 Chains 64, Residues 520, Estimated correctness of the model 15.4 % 3 chains (47 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 14507 restraints for refining 6808 atoms. 12316 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2620 (Rfree = 0.000) for 6808 atoms. Found 51 (51 requested) and removed 46 (25 requested) atoms. Cycle 22: After refmac, R = 0.2459 (Rfree = 0.000) for 6774 atoms. Found 29 (51 requested) and removed 34 (25 requested) atoms. Cycle 23: After refmac, R = 0.2441 (Rfree = 0.000) for 6756 atoms. Found 21 (51 requested) and removed 32 (25 requested) atoms. Cycle 24: After refmac, R = 0.2367 (Rfree = 0.000) for 6738 atoms. Found 18 (50 requested) and removed 33 (25 requested) atoms. Cycle 25: After refmac, R = 0.2374 (Rfree = 0.000) for 6713 atoms. Found 15 (50 requested) and removed 32 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 2.64 Search for helices and strands: 0 residues in 0 chains, 6961 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 6974 seeds are put forward Round 1: 501 peptides, 63 chains. Longest chain 33 peptides. Score 0.482 Round 2: 556 peptides, 58 chains. Longest chain 27 peptides. Score 0.558 Round 3: 564 peptides, 65 chains. Longest chain 29 peptides. Score 0.535 Round 4: 571 peptides, 58 chains. Longest chain 36 peptides. Score 0.572 Round 5: 583 peptides, 64 chains. Longest chain 27 peptides. Score 0.557 Taking the results from Round 4 Chains 65, Residues 513, Estimated correctness of the model 19.3 % 12 chains (151 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 13543 restraints for refining 6808 atoms. 11006 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2722 (Rfree = 0.000) for 6808 atoms. Found 51 (51 requested) and removed 51 (25 requested) atoms. Cycle 27: After refmac, R = 0.2591 (Rfree = 0.000) for 6753 atoms. Found 29 (51 requested) and removed 42 (25 requested) atoms. Cycle 28: After refmac, R = 0.2561 (Rfree = 0.000) for 6724 atoms. Found 27 (50 requested) and removed 39 (25 requested) atoms. Cycle 29: After refmac, R = 0.2476 (Rfree = 0.000) for 6702 atoms. Found 26 (50 requested) and removed 28 (25 requested) atoms. Cycle 30: After refmac, R = 0.2371 (Rfree = 0.000) for 6688 atoms. Found 24 (50 requested) and removed 30 (25 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 2.64 Search for helices and strands: 0 residues in 0 chains, 6931 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 6943 seeds are put forward Round 1: 526 peptides, 73 chains. Longest chain 21 peptides. Score 0.461 Round 2: 539 peptides, 60 chains. Longest chain 34 peptides. Score 0.533 Round 3: 550 peptides, 65 chains. Longest chain 27 peptides. Score 0.522 Round 4: 560 peptides, 63 chains. Longest chain 42 peptides. Score 0.540 Round 5: 567 peptides, 60 chains. Longest chain 29 peptides. Score 0.559 Taking the results from Round 5 Chains 61, Residues 507, Estimated correctness of the model 14.7 % 4 chains (69 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 14563 restraints for refining 6808 atoms. 12338 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2621 (Rfree = 0.000) for 6808 atoms. Found 51 (51 requested) and removed 48 (25 requested) atoms. Cycle 32: After refmac, R = 0.2466 (Rfree = 0.000) for 6777 atoms. Found 31 (51 requested) and removed 37 (25 requested) atoms. Cycle 33: After refmac, R = 0.2404 (Rfree = 0.000) for 6758 atoms. Found 17 (51 requested) and removed 28 (25 requested) atoms. Cycle 34: After refmac, R = 0.2383 (Rfree = 0.000) for 6742 atoms. Found 23 (50 requested) and removed 26 (25 requested) atoms. Cycle 35: After refmac, R = 0.2358 (Rfree = 0.000) for 6730 atoms. Found 18 (50 requested) and removed 30 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 2.66 Search for helices and strands: 0 residues in 0 chains, 6953 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 6972 seeds are put forward Round 1: 493 peptides, 70 chains. Longest chain 18 peptides. Score 0.440 Round 2: 522 peptides, 66 chains. Longest chain 32 peptides. Score 0.489 Round 3: 526 peptides, 63 chains. Longest chain 25 peptides. Score 0.507 Round 4: 534 peptides, 64 chains. Longest chain 20 peptides. Score 0.511 Round 5: 541 peptides, 63 chains. Longest chain 24 peptides. Score 0.522 Taking the results from Round 5 Chains 67, Residues 478, Estimated correctness of the model 1.2 % 6 chains (83 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 14503 restraints for refining 6808 atoms. 12367 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2685 (Rfree = 0.000) for 6808 atoms. Found 48 (51 requested) and removed 42 (25 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2536 (Rfree = 0.000) for 6782 atoms. Found 24 (51 requested) and removed 32 (25 requested) atoms. Cycle 38: After refmac, R = 0.2533 (Rfree = 0.000) for 6746 atoms. Found 28 (51 requested) and removed 27 (25 requested) atoms. Cycle 39: After refmac, R = 0.2433 (Rfree = 0.000) for 6738 atoms. Found 22 (50 requested) and removed 29 (25 requested) atoms. Cycle 40: After refmac, R = 0.2430 (Rfree = 0.000) for 6717 atoms. Found 25 (50 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 2.65 Search for helices and strands: 0 residues in 0 chains, 6971 seeds are put forward NCS extension: 19 residues added (10 deleted due to clashes), 6990 seeds are put forward Round 1: 498 peptides, 70 chains. Longest chain 21 peptides. Score 0.445 Round 2: 538 peptides, 68 chains. Longest chain 33 peptides. Score 0.496 Round 3: 528 peptides, 61 chains. Longest chain 22 peptides. Score 0.518 Round 4: 514 peptides, 63 chains. Longest chain 28 peptides. Score 0.495 Round 5: 520 peptides, 68 chains. Longest chain 24 peptides. Score 0.478 Taking the results from Round 3 Chains 65, Residues 467, Estimated correctness of the model 0.0 % 4 chains (39 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 14822 restraints for refining 6809 atoms. 12901 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2576 (Rfree = 0.000) for 6809 atoms. Found 51 (51 requested) and removed 38 (25 requested) atoms. Cycle 42: After refmac, R = 0.2448 (Rfree = 0.000) for 6801 atoms. Found 26 (51 requested) and removed 31 (25 requested) atoms. Cycle 43: After refmac, R = 0.2409 (Rfree = 0.000) for 6773 atoms. Found 32 (51 requested) and removed 33 (25 requested) atoms. Cycle 44: After refmac, R = 0.2320 (Rfree = 0.000) for 6756 atoms. Found 20 (51 requested) and removed 28 (25 requested) atoms. Cycle 45: After refmac, R = 0.2284 (Rfree = 0.000) for 6736 atoms. Found 15 (50 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 2.65 Search for helices and strands: 0 residues in 0 chains, 6956 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 6976 seeds are put forward Round 1: 470 peptides, 76 chains. Longest chain 19 peptides. Score 0.384 Round 2: 498 peptides, 64 chains. Longest chain 24 peptides. Score 0.474 Round 3: 507 peptides, 64 chains. Longest chain 22 peptides. Score 0.484 Round 4: 500 peptides, 71 chains. Longest chain 18 peptides. Score 0.443 Round 5: 506 peptides, 65 chains. Longest chain 30 peptides. Score 0.478 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 66, Residues 443, Estimated correctness of the model 0.0 % 3 chains (36 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 1vlu-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 111 A and 118 A 63 chains (444 residues) following loop building 2 chains (42 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20628 reflections ( 99.87 % complete ) and 14957 restraints for refining 6809 atoms. 13098 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2508 (Rfree = 0.000) for 6809 atoms. Found 0 (51 requested) and removed 22 (25 requested) atoms. Cycle 47: After refmac, R = 0.2479 (Rfree = 0.000) for 6755 atoms. Found 0 (51 requested) and removed 4 (25 requested) atoms. Cycle 48: After refmac, R = 0.2417 (Rfree = 0.000) for 6739 atoms. Found 0 (50 requested) and removed 8 (25 requested) atoms. Cycle 49: After refmac, R = 0.2360 (Rfree = 0.000) for 6723 atoms. TimeTaking 78.52