Mon 24 Dec 00:15:55 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 1vlu-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vlu-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vlu-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.4-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/1vlu-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.4-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 00:15:59 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/1vlu-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.4-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 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-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: 20 Cell parameters: 123.109 190.784 125.153 90.000 90.000 90.000 Input sequence file: 1vlu-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7488 target number of atoms Had to go as low as 0.85 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 8334 atoms. Observations/parameters ratio is 0.62 ------------------------------------------------------ Starting model: R = 0.3315 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3144 (Rfree = 0.000) for 8334 atoms. Found 62 (62 requested) and removed 80 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 2.67 Search for helices and strands: 0 residues in 0 chains, 8525 seeds are put forward NCS extension: 0 residues added, 8525 seeds are put forward Round 1: 468 peptides, 71 chains. Longest chain 18 peptides. Score 0.407 Round 2: 518 peptides, 63 chains. Longest chain 24 peptides. Score 0.499 Round 3: 547 peptides, 56 chains. Longest chain 34 peptides. Score 0.559 Round 4: 550 peptides, 50 chains. Longest chain 39 peptides. Score 0.587 Round 5: 549 peptides, 59 chains. Longest chain 37 peptides. Score 0.547 Taking the results from Round 4 Chains 55, Residues 500, Estimated correctness of the model 24.4 % 7 chains (122 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 13887 restraints for refining 6804 atoms. 11491 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2618 (Rfree = 0.000) for 6804 atoms. Found 51 (51 requested) and removed 60 (25 requested) atoms. Cycle 2: After refmac, R = 0.2478 (Rfree = 0.000) for 6651 atoms. Found 51 (51 requested) and removed 51 (25 requested) atoms. Cycle 3: After refmac, R = 0.2391 (Rfree = 0.000) for 6610 atoms. Found 39 (50 requested) and removed 43 (25 requested) atoms. Cycle 4: After refmac, R = 0.2325 (Rfree = 0.000) for 6581 atoms. Found 18 (49 requested) and removed 41 (24 requested) atoms. Cycle 5: After refmac, R = 0.2301 (Rfree = 0.000) for 6537 atoms. Found 24 (49 requested) and removed 31 (24 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 2.65 Search for helices and strands: 0 residues in 0 chains, 6837 seeds are put forward NCS extension: 58 residues added (13 deleted due to clashes), 6895 seeds are put forward Round 1: 529 peptides, 68 chains. Longest chain 34 peptides. Score 0.487 Round 2: 540 peptides, 63 chains. Longest chain 24 peptides. Score 0.521 Round 3: 548 peptides, 54 chains. Longest chain 27 peptides. Score 0.568 Round 4: 553 peptides, 61 chains. Longest chain 29 peptides. Score 0.542 Round 5: 546 peptides, 62 chains. Longest chain 34 peptides. Score 0.531 Taking the results from Round 3 Chains 60, Residues 494, Estimated correctness of the model 17.9 % 12 chains (161 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 13576 restraints for refining 6808 atoms. 11095 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2615 (Rfree = 0.000) for 6808 atoms. Found 51 (51 requested) and removed 52 (25 requested) atoms. Cycle 7: After refmac, R = 0.2445 (Rfree = 0.000) for 6732 atoms. Found 49 (51 requested) and removed 51 (25 requested) atoms. Cycle 8: After refmac, R = 0.2362 (Rfree = 0.000) for 6683 atoms. Found 41 (50 requested) and removed 50 (25 requested) atoms. Cycle 9: After refmac, R = 0.2267 (Rfree = 0.000) for 6632 atoms. Found 32 (50 requested) and removed 41 (25 requested) atoms. Cycle 10: After refmac, R = 0.2249 (Rfree = 0.000) for 6594 atoms. Found 24 (50 requested) and removed 36 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.29 2.64 Search for helices and strands: 0 residues in 0 chains, 6842 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 6865 seeds are put forward Round 1: 539 peptides, 73 chains. Longest chain 20 peptides. Score 0.474 Round 2: 561 peptides, 61 chains. Longest chain 32 peptides. Score 0.550 Round 3: 574 peptides, 62 chains. Longest chain 33 peptides. Score 0.557 Round 4: 554 peptides, 58 chains. Longest chain 35 peptides. Score 0.556 Round 5: 553 peptides, 60 chains. Longest chain 31 peptides. Score 0.547 Taking the results from Round 3 Chains 70, Residues 512, Estimated correctness of the model 14.0 % 7 chains (90 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 14014 restraints for refining 6807 atoms. 11716 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2596 (Rfree = 0.000) for 6807 atoms. Found 51 (51 requested) and removed 67 (25 requested) atoms. Cycle 12: After refmac, R = 0.2459 (Rfree = 0.000) for 6741 atoms. Found 41 (51 requested) and removed 41 (25 requested) atoms. Cycle 13: After refmac, R = 0.2409 (Rfree = 0.000) for 6713 atoms. Found 33 (50 requested) and removed 41 (25 requested) atoms. Cycle 14: After refmac, R = 0.2373 (Rfree = 0.000) for 6679 atoms. Found 31 (50 requested) and removed 32 (25 requested) atoms. Cycle 15: After refmac, R = 0.2359 (Rfree = 0.000) for 6662 atoms. Found 27 (50 requested) and removed 32 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 2.64 Search for helices and strands: 0 residues in 0 chains, 6903 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 6924 seeds are put forward Round 1: 532 peptides, 69 chains. Longest chain 30 peptides. Score 0.486 Round 2: 548 peptides, 58 chains. Longest chain 29 peptides. Score 0.551 Round 3: 568 peptides, 50 chains. Longest chain 40 peptides. Score 0.603 Round 4: 562 peptides, 64 chains. Longest chain 28 peptides. Score 0.537 Round 5: 567 peptides, 59 chains. Longest chain 25 peptides. Score 0.564 Taking the results from Round 3 Chains 56, Residues 518, Estimated correctness of the model 29.7 % 10 chains (130 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 13674 restraints for refining 6809 atoms. 11212 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2651 (Rfree = 0.000) for 6809 atoms. Found 51 (51 requested) and removed 53 (25 requested) atoms. Cycle 17: After refmac, R = 0.2546 (Rfree = 0.000) for 6754 atoms. Found 42 (51 requested) and removed 40 (25 requested) atoms. Cycle 18: After refmac, R = 0.2462 (Rfree = 0.000) for 6724 atoms. Found 50 (51 requested) and removed 33 (25 requested) atoms. Cycle 19: After refmac, R = 0.2402 (Rfree = 0.000) for 6722 atoms. Found 40 (50 requested) and removed 36 (25 requested) atoms. Cycle 20: After refmac, R = 0.2368 (Rfree = 0.000) for 6709 atoms. Found 24 (50 requested) and removed 29 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 2.65 Search for helices and strands: 0 residues in 0 chains, 6909 seeds are put forward NCS extension: 47 residues added (9 deleted due to clashes), 6956 seeds are put forward Round 1: 546 peptides, 65 chains. Longest chain 26 peptides. Score 0.518 Round 2: 553 peptides, 57 chains. Longest chain 30 peptides. Score 0.560 Round 3: 559 peptides, 59 chains. Longest chain 31 peptides. Score 0.557 Round 4: 569 peptides, 64 chains. Longest chain 25 peptides. Score 0.544 Round 5: 572 peptides, 57 chains. Longest chain 28 peptides. Score 0.577 Taking the results from Round 5 Chains 59, Residues 515, Estimated correctness of the model 21.0 % 7 chains (81 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 14117 restraints for refining 6806 atoms. 11835 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2670 (Rfree = 0.000) for 6806 atoms. Found 51 (51 requested) and removed 52 (25 requested) atoms. Cycle 22: After refmac, R = 0.2516 (Rfree = 0.000) for 6763 atoms. Found 26 (51 requested) and removed 34 (25 requested) atoms. Cycle 23: After refmac, R = 0.2469 (Rfree = 0.000) for 6731 atoms. Found 33 (50 requested) and removed 36 (25 requested) atoms. Cycle 24: After refmac, R = 0.2435 (Rfree = 0.000) for 6716 atoms. Found 23 (50 requested) and removed 37 (25 requested) atoms. Cycle 25: After refmac, R = 0.2414 (Rfree = 0.000) for 6690 atoms. Found 23 (50 requested) and removed 29 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 2.67 Search for helices and strands: 0 residues in 0 chains, 6952 seeds are put forward NCS extension: 28 residues added (14 deleted due to clashes), 6980 seeds are put forward Round 1: 517 peptides, 71 chains. Longest chain 26 peptides. Score 0.461 Round 2: 563 peptides, 67 chains. Longest chain 26 peptides. Score 0.525 Round 3: 581 peptides, 67 chains. Longest chain 27 peptides. Score 0.542 Round 4: 577 peptides, 66 chains. Longest chain 27 peptides. Score 0.543 Round 5: 586 peptides, 66 chains. Longest chain 51 peptides. Score 0.551 Taking the results from Round 5 Chains 69, Residues 520, Estimated correctness of the model 11.9 % 8 chains (124 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 13692 restraints for refining 6807 atoms. 11234 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2702 (Rfree = 0.000) for 6807 atoms. Found 50 (51 requested) and removed 47 (25 requested) atoms. Cycle 27: After refmac, R = 0.2498 (Rfree = 0.000) for 6758 atoms. Found 25 (51 requested) and removed 36 (25 requested) atoms. Cycle 28: After refmac, R = 0.2428 (Rfree = 0.000) for 6722 atoms. Found 20 (50 requested) and removed 35 (25 requested) atoms. Cycle 29: After refmac, R = 0.2357 (Rfree = 0.000) for 6690 atoms. Found 21 (50 requested) and removed 30 (25 requested) atoms. Cycle 30: After refmac, R = 0.2289 (Rfree = 0.000) for 6670 atoms. Found 17 (50 requested) and removed 29 (25 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 2.66 Search for helices and strands: 0 residues in 0 chains, 6956 seeds are put forward NCS extension: 35 residues added (3 deleted due to clashes), 6991 seeds are put forward Round 1: 506 peptides, 68 chains. Longest chain 23 peptides. Score 0.463 Round 2: 578 peptides, 65 chains. Longest chain 44 peptides. Score 0.548 Round 3: 556 peptides, 65 chains. Longest chain 35 peptides. Score 0.527 Round 4: 564 peptides, 62 chains. Longest chain 29 peptides. Score 0.548 Round 5: 568 peptides, 63 chains. Longest chain 28 peptides. Score 0.547 Taking the results from Round 4 Chains 68, Residues 502, Estimated correctness of the model 10.8 % 9 chains (132 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 13825 restraints for refining 6809 atoms. 11417 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2618 (Rfree = 0.000) for 6809 atoms. Found 51 (51 requested) and removed 50 (25 requested) atoms. Cycle 32: After refmac, R = 0.2444 (Rfree = 0.000) for 6782 atoms. Found 18 (51 requested) and removed 40 (25 requested) atoms. Cycle 33: After refmac, R = 0.2414 (Rfree = 0.000) for 6745 atoms. Found 16 (51 requested) and removed 30 (25 requested) atoms. Cycle 34: After refmac, R = 0.2321 (Rfree = 0.000) for 6724 atoms. Found 13 (50 requested) and removed 33 (25 requested) atoms. Cycle 35: After refmac, R = 0.2299 (Rfree = 0.000) for 6690 atoms. Found 13 (50 requested) and removed 32 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 2.64 Search for helices and strands: 0 residues in 0 chains, 6938 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 6972 seeds are put forward Round 1: 513 peptides, 66 chains. Longest chain 35 peptides. Score 0.480 Round 2: 564 peptides, 66 chains. Longest chain 31 peptides. Score 0.530 Round 3: 573 peptides, 70 chains. Longest chain 33 peptides. Score 0.521 Round 4: 577 peptides, 60 chains. Longest chain 30 peptides. Score 0.568 Round 5: 588 peptides, 61 chains. Longest chain 39 peptides. Score 0.574 Taking the results from Round 5 Chains 66, Residues 527, Estimated correctness of the model 20.0 % 7 chains (75 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 14250 restraints for refining 6809 atoms. 11968 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2637 (Rfree = 0.000) for 6809 atoms. Found 51 (51 requested) and removed 48 (25 requested) atoms. Cycle 37: After refmac, R = 0.2441 (Rfree = 0.000) for 6781 atoms. Found 35 (51 requested) and removed 30 (25 requested) atoms. Cycle 38: After refmac, R = 0.2374 (Rfree = 0.000) for 6763 atoms. Found 18 (51 requested) and removed 34 (25 requested) atoms. Cycle 39: After refmac, R = 0.2305 (Rfree = 0.000) for 6736 atoms. Found 15 (50 requested) and removed 28 (25 requested) atoms. Cycle 40: After refmac, R = 0.2266 (Rfree = 0.000) for 6715 atoms. Found 14 (50 requested) and removed 26 (25 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 2.65 Search for helices and strands: 0 residues in 0 chains, 6926 seeds are put forward NCS extension: 48 residues added (13 deleted due to clashes), 6974 seeds are put forward Round 1: 506 peptides, 70 chains. Longest chain 25 peptides. Score 0.454 Round 2: 526 peptides, 64 chains. Longest chain 24 peptides. Score 0.503 Round 3: 542 peptides, 66 chains. Longest chain 34 peptides. Score 0.509 Round 4: 554 peptides, 61 chains. Longest chain 26 peptides. Score 0.543 Round 5: 567 peptides, 61 chains. Longest chain 33 peptides. Score 0.555 Taking the results from Round 5 Chains 63, Residues 506, Estimated correctness of the model 13.3 % 6 chains (68 residues) have been docked in sequence ------------------------------------------------------ 20628 reflections ( 99.87 % complete ) and 14404 restraints for refining 6807 atoms. 12215 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2621 (Rfree = 0.000) for 6807 atoms. Found 51 (51 requested) and removed 42 (25 requested) atoms. Cycle 42: After refmac, R = 0.2468 (Rfree = 0.000) for 6787 atoms. Found 34 (51 requested) and removed 33 (25 requested) atoms. Cycle 43: After refmac, R = 0.2434 (Rfree = 0.000) for 6772 atoms. Found 31 (51 requested) and removed 36 (25 requested) atoms. Cycle 44: After refmac, R = 0.2366 (Rfree = 0.000) for 6760 atoms. Found 32 (51 requested) and removed 30 (25 requested) atoms. Cycle 45: After refmac, R = 0.2301 (Rfree = 0.000) for 6753 atoms. Found 17 (51 requested) and removed 26 (25 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 2.64 Search for helices and strands: 0 residues in 0 chains, 6999 seeds are put forward NCS extension: 15 residues added (11 deleted due to clashes), 7014 seeds are put forward Round 1: 494 peptides, 77 chains. Longest chain 16 peptides. Score 0.407 Round 2: 527 peptides, 70 chains. Longest chain 20 peptides. Score 0.476 Round 3: 541 peptides, 63 chains. Longest chain 20 peptides. Score 0.522 Round 4: 543 peptides, 68 chains. Longest chain 20 peptides. Score 0.501 Round 5: 557 peptides, 66 chains. Longest chain 37 peptides. Score 0.524 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 66, Residues 491, Estimated correctness of the model 1.9 % 3 chains (53 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 1vlu-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 396 A and 406 A 65 chains (500 residues) following loop building 2 chains (62 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20628 reflections ( 99.87 % complete ) and 14401 restraints for refining 6809 atoms. 12219 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2637 (Rfree = 0.000) for 6809 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Cycle 47: After refmac, R = 0.2508 (Rfree = 0.000) for 6754 atoms. Found 0 (51 requested) and removed 8 (25 requested) atoms. Cycle 48: After refmac, R = 0.2454 (Rfree = 0.000) for 6740 atoms. Found 0 (50 requested) and removed 10 (25 requested) atoms. Cycle 49: After refmac, R = 0.2428 (Rfree = 0.000) for 6722 atoms. TimeTaking 78.3