Mon 24 Dec 07:46:17 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 1ztc-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1ztc-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1ztc-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.2-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/1ztc-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.2-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 07:46:22 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/1ztc-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1ztc-3.2-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 1182 and 0 Target number of residues in the AU: 1182 Target solvent content: 0.6324 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-3.2-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: 19 Cell parameters: 89.783 127.343 152.224 90.000 90.000 90.000 Input sequence file: 1ztc-3.2-parrot-noncs.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 3.200 Wilson plot Bfac: 67.79 29180 reflections ( 98.97 % complete ) and 0 restraints for refining 7956 atoms. Observations/parameters ratio is 0.92 ------------------------------------------------------ Starting model: R = 0.3471 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3108 (Rfree = 0.000) for 7956 atoms. Found 71 (71 requested) and removed 93 (35 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 2.31 Search for helices and strands: 0 residues in 0 chains, 8058 seeds are put forward NCS extension: 0 residues added, 8058 seeds are put forward Round 1: 613 peptides, 83 chains. Longest chain 17 peptides. Score 0.466 Round 2: 686 peptides, 74 chains. Longest chain 30 peptides. Score 0.560 Round 3: 695 peptides, 64 chains. Longest chain 32 peptides. Score 0.602 Round 4: 680 peptides, 60 chains. Longest chain 42 peptides. Score 0.605 Round 5: 715 peptides, 63 chains. Longest chain 41 peptides. Score 0.619 Taking the results from Round 5 Chains 64, Residues 652, Estimated correctness of the model 46.1 % 7 chains (181 residues) have been docked in sequence ------------------------------------------------------ 29180 reflections ( 98.97 % complete ) and 11550 restraints for refining 6509 atoms. 8222 conditional restraints added. Observations/parameters ratio is 1.12 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2882 (Rfree = 0.000) for 6509 atoms. Found 58 (58 requested) and removed 52 (29 requested) atoms. Cycle 2: After refmac, R = 0.2601 (Rfree = 0.000) for 6438 atoms. Found 58 (58 requested) and removed 47 (29 requested) atoms. Cycle 3: After refmac, R = 0.2419 (Rfree = 0.000) for 6413 atoms. Found 45 (57 requested) and removed 45 (28 requested) atoms. Cycle 4: After refmac, R = 0.2320 (Rfree = 0.000) for 6400 atoms. Found 42 (57 requested) and removed 28 (28 requested) atoms. Cycle 5: After refmac, R = 0.2260 (Rfree = 0.000) for 6404 atoms. Found 21 (57 requested) and removed 31 (28 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.23 2.32 Search for helices and strands: 0 residues in 0 chains, 6622 seeds are put forward NCS extension: 14 residues added (39 deleted due to clashes), 6636 seeds are put forward Round 1: 693 peptides, 57 chains. Longest chain 34 peptides. Score 0.624 Round 2: 707 peptides, 53 chains. Longest chain 51 peptides. Score 0.647 Round 3: 705 peptides, 50 chains. Longest chain 42 peptides. Score 0.655 Round 4: 703 peptides, 56 chains. Longest chain 33 peptides. Score 0.634 Round 5: 711 peptides, 48 chains. Longest chain 51 peptides. Score 0.665 Taking the results from Round 5 Chains 53, Residues 663, Estimated correctness of the model 57.4 % 8 chains (223 residues) have been docked in sequence ------------------------------------------------------ 29180 reflections ( 98.97 % complete ) and 11090 restraints for refining 6456 atoms. 7545 conditional restraints added. Observations/parameters ratio is 1.13 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2637 (Rfree = 0.000) for 6456 atoms. Found 57 (57 requested) and removed 55 (28 requested) atoms. Cycle 7: After refmac, R = 0.2412 (Rfree = 0.000) for 6423 atoms. Found 47 (57 requested) and removed 42 (28 requested) atoms. Cycle 8: After refmac, R = 0.2319 (Rfree = 0.000) for 6402 atoms. Found 26 (57 requested) and removed 33 (28 requested) atoms. Cycle 9: After refmac, R = 0.2281 (Rfree = 0.000) for 6386 atoms. Found 29 (57 requested) and removed 30 (28 requested) atoms. Cycle 10: After refmac, R = 0.2242 (Rfree = 0.000) for 6382 atoms. Found 19 (57 requested) and removed 33 (28 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.21 2.30 Search for helices and strands: 0 residues in 0 chains, 6558 seeds are put forward NCS extension: 25 residues added (22 deleted due to clashes), 6583 seeds are put forward Round 1: 714 peptides, 55 chains. Longest chain 62 peptides. Score 0.645 Round 2: 736 peptides, 51 chains. Longest chain 46 peptides. Score 0.671 Round 3: 729 peptides, 52 chains. Longest chain 47 peptides. Score 0.664 Round 4: 731 peptides, 52 chains. Longest chain 40 peptides. Score 0.665 Round 5: 698 peptides, 55 chains. Longest chain 43 peptides. Score 0.634 Taking the results from Round 2 Chains 58, Residues 685, Estimated correctness of the model 58.8 % 9 chains (213 residues) have been docked in sequence ------------------------------------------------------ 29180 reflections ( 98.97 % complete ) and 11091 restraints for refining 6454 atoms. 7466 conditional restraints added. Observations/parameters ratio is 1.13 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2462 (Rfree = 0.000) for 6454 atoms. Found 57 (57 requested) and removed 63 (28 requested) atoms. Cycle 12: After refmac, R = 0.2221 (Rfree = 0.000) for 6418 atoms. Found 36 (57 requested) and removed 41 (28 requested) atoms. Cycle 13: After refmac, R = 0.2128 (Rfree = 0.000) for 6395 atoms. Found 34 (57 requested) and removed 31 (28 requested) atoms. Cycle 14: After refmac, R = 0.2084 (Rfree = 0.000) for 6388 atoms. Found 36 (57 requested) and removed 35 (28 requested) atoms. Cycle 15: After refmac, R = 0.2030 (Rfree = 0.000) for 6386 atoms. Found 28 (57 requested) and removed 33 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 2.28 Search for helices and strands: 0 residues in 0 chains, 6579 seeds are put forward NCS extension: 15 residues added (39 deleted due to clashes), 6594 seeds are put forward Round 1: 706 peptides, 55 chains. Longest chain 46 peptides. Score 0.640 Round 2: 716 peptides, 42 chains. Longest chain 49 peptides. Score 0.687 Round 3: 722 peptides, 49 chains. Longest chain 61 peptides. Score 0.669 Round 4: 732 peptides, 45 chains. Longest chain 45 peptides. Score 0.688 Round 5: 727 peptides, 52 chains. Longest chain 48 peptides. Score 0.663 Taking the results from Round 4 Chains 54, Residues 687, Estimated correctness of the model 62.6 % 15 chains (371 residues) have been docked in sequence ------------------------------------------------------ 29180 reflections ( 98.97 % complete ) and 9990 restraints for refining 6652 atoms. 5606 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2497 (Rfree = 0.000) for 6652 atoms. Found 59 (59 requested) and removed 66 (29 requested) atoms. Cycle 17: After refmac, R = 0.2430 (Rfree = 0.000) for 6604 atoms. Found 59 (59 requested) and removed 46 (29 requested) atoms. Cycle 18: After refmac, R = 0.2183 (Rfree = 0.000) for 6595 atoms. Found 58 (59 requested) and removed 35 (29 requested) atoms. Cycle 19: After refmac, R = 0.2106 (Rfree = 0.000) for 6605 atoms. Found 36 (59 requested) and removed 38 (29 requested) atoms. Cycle 20: After refmac, R = 0.2064 (Rfree = 0.000) for 6589 atoms. Found 28 (59 requested) and removed 33 (29 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.21 2.30 Search for helices and strands: 0 residues in 0 chains, 6789 seeds are put forward NCS extension: 16 residues added (31 deleted due to clashes), 6805 seeds are put forward Round 1: 713 peptides, 54 chains. Longest chain 47 peptides. Score 0.647 Round 2: 711 peptides, 50 chains. Longest chain 49 peptides. Score 0.659 Round 3: 713 peptides, 50 chains. Longest chain 50 peptides. Score 0.660 Round 4: 695 peptides, 49 chains. Longest chain 50 peptides. Score 0.652 Round 5: 695 peptides, 55 chains. Longest chain 50 peptides. Score 0.632 Taking the results from Round 3 Chains 56, Residues 663, Estimated correctness of the model 56.2 % 15 chains (366 residues) have been docked in sequence ------------------------------------------------------ 29180 reflections ( 98.97 % complete ) and 10743 restraints for refining 6772 atoms. 6495 conditional restraints added. Observations/parameters ratio is 1.08 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2456 (Rfree = 0.000) for 6772 atoms. Found 60 (60 requested) and removed 79 (30 requested) atoms. Cycle 22: After refmac, R = 0.2415 (Rfree = 0.000) for 6727 atoms. Found 60 (60 requested) and removed 47 (30 requested) atoms. Cycle 23: After refmac, R = 0.2178 (Rfree = 0.000) for 6716 atoms. Found 45 (60 requested) and removed 35 (30 requested) atoms. Cycle 24: After refmac, R = 0.2115 (Rfree = 0.000) for 6707 atoms. Found 23 (60 requested) and removed 33 (30 requested) atoms. Cycle 25: After refmac, R = 0.2106 (Rfree = 0.000) for 6690 atoms. Found 17 (60 requested) and removed 30 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 2.30 Search for helices and strands: 0 residues in 0 chains, 6857 seeds are put forward NCS extension: 6 residues added (35 deleted due to clashes), 6863 seeds are put forward Round 1: 711 peptides, 56 chains. Longest chain 40 peptides. Score 0.640 Round 2: 708 peptides, 51 chains. Longest chain 53 peptides. Score 0.654 Round 3: 726 peptides, 49 chains. Longest chain 42 peptides. Score 0.672 Round 4: 723 peptides, 47 chains. Longest chain 42 peptides. Score 0.676 Round 5: 718 peptides, 54 chains. Longest chain 42 peptides. Score 0.651 Taking the results from Round 4 Chains 55, Residues 676, Estimated correctness of the model 59.9 % 17 chains (387 residues) have been docked in sequence ------------------------------------------------------ 29180 reflections ( 98.97 % complete ) and 10345 restraints for refining 6708 atoms. 5977 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2414 (Rfree = 0.000) for 6708 atoms. Found 60 (60 requested) and removed 57 (30 requested) atoms. Cycle 27: After refmac, R = 0.2378 (Rfree = 0.000) for 6659 atoms. Found 60 (60 requested) and removed 40 (30 requested) atoms. Cycle 28: After refmac, R = 0.2463 (Rfree = 0.000) for 6652 atoms. Found 59 (59 requested) and removed 37 (29 requested) atoms. Cycle 29: After refmac, R = 0.2134 (Rfree = 0.000) for 6646 atoms. Found 58 (59 requested) and removed 35 (29 requested) atoms. Cycle 30: After refmac, R = 0.2047 (Rfree = 0.000) for 6646 atoms. Found 27 (59 requested) and removed 34 (29 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.21 2.30 Search for helices and strands: 0 residues in 0 chains, 6846 seeds are put forward NCS extension: 4 residues added (18 deleted due to clashes), 6850 seeds are put forward Round 1: 706 peptides, 52 chains. Longest chain 45 peptides. Score 0.649 Round 2: 704 peptides, 48 chains. Longest chain 42 peptides. Score 0.661 Round 3: 721 peptides, 43 chains. Longest chain 52 peptides. Score 0.687 Round 4: 712 peptides, 48 chains. Longest chain 52 peptides. Score 0.666 Round 5: 703 peptides, 46 chains. Longest chain 48 peptides. Score 0.667 Taking the results from Round 3 Chains 53, Residues 678, Estimated correctness of the model 62.4 % 16 chains (395 residues) have been docked in sequence ------------------------------------------------------ 29180 reflections ( 98.97 % complete ) and 10353 restraints for refining 6699 atoms. 5948 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2438 (Rfree = 0.000) for 6699 atoms. Found 60 (60 requested) and removed 76 (30 requested) atoms. Cycle 32: After refmac, R = 0.2409 (Rfree = 0.000) for 6642 atoms. Found 59 (59 requested) and removed 54 (29 requested) atoms. Cycle 33: After refmac, R = 0.2350 (Rfree = 0.000) for 6619 atoms. Found 59 (59 requested) and removed 57 (29 requested) atoms. Cycle 34: After refmac, R = 0.2308 (Rfree = 0.000) for 6609 atoms. Found 59 (59 requested) and removed 47 (29 requested) atoms. Cycle 35: After refmac, R = 0.2285 (Rfree = 0.000) for 6609 atoms. Found 59 (59 requested) and removed 40 (29 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 2.28 Search for helices and strands: 0 residues in 0 chains, 6799 seeds are put forward NCS extension: 8 residues added (24 deleted due to clashes), 6807 seeds are put forward Round 1: 727 peptides, 45 chains. Longest chain 54 peptides. Score 0.685 Round 2: 746 peptides, 44 chains. Longest chain 66 peptides. Score 0.699 Round 3: 744 peptides, 41 chains. Longest chain 51 peptides. Score 0.706 Round 4: 729 peptides, 43 chains. Longest chain 42 peptides. Score 0.692 Round 5: 726 peptides, 47 chains. Longest chain 41 peptides. Score 0.678 Taking the results from Round 3 Chains 45, Residues 703, Estimated correctness of the model 66.4 % 17 chains (487 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 108 C and 118 C Built loop between residues 186 C and 197 C Built loop between residues 84 B and 87 B 40 chains (717 residues) following loop building 14 chains (508 residues) in sequence following loop building ------------------------------------------------------ 29180 reflections ( 98.97 % complete ) and 9510 restraints for refining 6861 atoms. 4478 conditional restraints added. Observations/parameters ratio is 1.06 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2405 (Rfree = 0.000) for 6861 atoms. Found 61 (61 requested) and removed 57 (30 requested) atoms. Cycle 37: After refmac, R = 0.2386 (Rfree = 0.000) for 6820 atoms. Found 60 (60 requested) and removed 39 (30 requested) atoms. Cycle 38: After refmac, R = 0.2300 (Rfree = 0.000) for 6816 atoms. Found 59 (59 requested) and removed 36 (30 requested) atoms. Cycle 39: After refmac, R = 0.2289 (Rfree = 0.000) for 6813 atoms. Found 57 (57 requested) and removed 44 (30 requested) atoms. Cycle 40: After refmac, R = 0.2015 (Rfree = 0.000) for 6806 atoms. Found 45 (56 requested) and removed 37 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.20 2.30 Search for helices and strands: 0 residues in 0 chains, 7020 seeds are put forward NCS extension: 19 residues added (34 deleted due to clashes), 7039 seeds are put forward Round 1: 704 peptides, 52 chains. Longest chain 54 peptides. Score 0.648 Round 2: 729 peptides, 47 chains. Longest chain 51 peptides. Score 0.680 Round 3: 741 peptides, 47 chains. Longest chain 46 peptides. Score 0.687 Round 4: 721 peptides, 46 chains. Longest chain 54 peptides. Score 0.678 Round 5: 732 peptides, 52 chains. Longest chain 40 peptides. Score 0.666 Taking the results from Round 3 Chains 57, Residues 694, Estimated correctness of the model 62.4 % 17 chains (387 residues) have been docked in sequence ------------------------------------------------------ 29180 reflections ( 98.97 % complete ) and 10454 restraints for refining 6703 atoms. 6044 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2392 (Rfree = 0.000) for 6703 atoms. Found 54 (54 requested) and removed 43 (30 requested) atoms. Cycle 42: After refmac, R = 0.2380 (Rfree = 0.000) for 6683 atoms. Found 54 (54 requested) and removed 41 (30 requested) atoms. Cycle 43: After refmac, R = 0.2326 (Rfree = 0.000) for 6661 atoms. Found 54 (54 requested) and removed 46 (30 requested) atoms. Cycle 44: After refmac, R = 0.2240 (Rfree = 0.000) for 6654 atoms. Found 53 (53 requested) and removed 50 (29 requested) atoms. Cycle 45: After refmac, R = 0.2272 (Rfree = 0.000) for 6618 atoms. Found 53 (53 requested) and removed 52 (29 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 2.30 Search for helices and strands: 0 residues in 0 chains, 6815 seeds are put forward NCS extension: 7 residues added (26 deleted due to clashes), 6822 seeds are put forward Round 1: 711 peptides, 51 chains. Longest chain 44 peptides. Score 0.656 Round 2: 721 peptides, 43 chains. Longest chain 56 peptides. Score 0.687 Round 3: 726 peptides, 47 chains. Longest chain 44 peptides. Score 0.678 Round 4: 731 peptides, 45 chains. Longest chain 63 peptides. Score 0.687 Round 5: 721 peptides, 49 chains. Longest chain 54 peptides. Score 0.668 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 50, Residues 686, Estimated correctness of the model 62.4 % 16 chains (422 residues) have been docked in sequence Sequence coverage is 61 % Consider running further cycles of model building using 1ztc-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 48 C and 60 C Built loop between residues 73 D and 76 D 47 chains (691 residues) following loop building 14 chains (435 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 29180 reflections ( 98.97 % complete ) and 9922 restraints for refining 6626 atoms. 5324 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2462 (Rfree = 0.000) for 6626 atoms. Found 0 (53 requested) and removed 29 (29 requested) atoms. Cycle 47: After refmac, R = 0.2443 (Rfree = 0.000) for 6561 atoms. Found 0 (53 requested) and removed 29 (29 requested) atoms. Cycle 48: After refmac, R = 0.2389 (Rfree = 0.000) for 6507 atoms. Found 0 (52 requested) and removed 29 (29 requested) atoms. Cycle 49: After refmac, R = 0.2334 (Rfree = 0.000) for 6465 atoms. TimeTaking 88.17