Mon 24 Dec 07:28:55 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-3.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vlu-3.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vlu-3.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.0-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-3.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.0-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 07:29:00 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-3.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vlu-3.0-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 1068 and 0 Target number of residues in the AU: 1068 Target solvent content: 0.6067 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-3.0-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-3.0-parrot-noncs.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 3.000 Wilson plot Bfac: 55.41 29835 reflections ( 99.91 % complete ) and 0 restraints for refining 8250 atoms. Observations/parameters ratio is 0.90 ------------------------------------------------------ Starting model: R = 0.3574 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3122 (Rfree = 0.000) for 8250 atoms. Found 88 (88 requested) and removed 128 (44 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.02 2.42 Search for helices and strands: 0 residues in 0 chains, 8406 seeds are put forward NCS extension: 0 residues added, 8406 seeds are put forward Round 1: 516 peptides, 76 chains. Longest chain 29 peptides. Score 0.436 Round 2: 574 peptides, 63 chains. Longest chain 28 peptides. Score 0.553 Round 3: 584 peptides, 63 chains. Longest chain 34 peptides. Score 0.562 Round 4: 608 peptides, 66 chains. Longest chain 28 peptides. Score 0.571 Round 5: 589 peptides, 55 chains. Longest chain 33 peptides. Score 0.600 Taking the results from Round 5 Chains 58, Residues 534, Estimated correctness of the model 51.9 % 13 chains (207 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 12850 restraints for refining 6871 atoms. 10040 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3000 (Rfree = 0.000) for 6871 atoms. Found 74 (74 requested) and removed 123 (37 requested) atoms. Cycle 2: After refmac, R = 0.2796 (Rfree = 0.000) for 6701 atoms. Found 73 (73 requested) and removed 87 (36 requested) atoms. Cycle 3: After refmac, R = 0.2730 (Rfree = 0.000) for 6630 atoms. Found 72 (72 requested) and removed 78 (36 requested) atoms. Cycle 4: After refmac, R = 0.2387 (Rfree = 0.000) for 6584 atoms. Found 58 (71 requested) and removed 52 (35 requested) atoms. Cycle 5: After refmac, R = 0.2261 (Rfree = 0.000) for 6578 atoms. Found 27 (71 requested) and removed 39 (35 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.00 2.41 Search for helices and strands: 0 residues in 0 chains, 6815 seeds are put forward NCS extension: 16 residues added (35 deleted due to clashes), 6831 seeds are put forward Round 1: 588 peptides, 61 chains. Longest chain 34 peptides. Score 0.574 Round 2: 616 peptides, 55 chains. Longest chain 36 peptides. Score 0.622 Round 3: 606 peptides, 56 chains. Longest chain 35 peptides. Score 0.610 Round 4: 618 peptides, 55 chains. Longest chain 39 peptides. Score 0.624 Round 5: 623 peptides, 55 chains. Longest chain 46 peptides. Score 0.628 Taking the results from Round 5 Chains 62, Residues 568, Estimated correctness of the model 57.9 % 13 chains (234 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 12216 restraints for refining 6870 atoms. 9122 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2709 (Rfree = 0.000) for 6870 atoms. Found 74 (74 requested) and removed 83 (37 requested) atoms. Cycle 7: After refmac, R = 0.2366 (Rfree = 0.000) for 6794 atoms. Found 58 (73 requested) and removed 62 (36 requested) atoms. Cycle 8: After refmac, R = 0.2455 (Rfree = 0.000) for 6765 atoms. Found 66 (73 requested) and removed 55 (36 requested) atoms. Cycle 9: After refmac, R = 0.2397 (Rfree = 0.000) for 6746 atoms. Found 57 (73 requested) and removed 54 (36 requested) atoms. Cycle 10: After refmac, R = 0.2355 (Rfree = 0.000) for 6723 atoms. Found 64 (72 requested) and removed 57 (36 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.96 2.37 Search for helices and strands: 0 residues in 0 chains, 6988 seeds are put forward NCS extension: 30 residues added (4 deleted due to clashes), 7018 seeds are put forward Round 1: 617 peptides, 58 chains. Longest chain 49 peptides. Score 0.611 Round 2: 645 peptides, 59 chains. Longest chain 46 peptides. Score 0.630 Round 3: 647 peptides, 50 chains. Longest chain 66 peptides. Score 0.665 Round 4: 643 peptides, 58 chains. Longest chain 51 peptides. Score 0.632 Round 5: 640 peptides, 58 chains. Longest chain 35 peptides. Score 0.630 Taking the results from Round 3 Chains 57, Residues 597, Estimated correctness of the model 65.2 % 13 chains (341 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 10818 restraints for refining 6872 atoms. 7188 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2436 (Rfree = 0.000) for 6872 atoms. Found 68 (74 requested) and removed 71 (37 requested) atoms. Cycle 12: After refmac, R = 0.2377 (Rfree = 0.000) for 6813 atoms. Found 65 (74 requested) and removed 51 (37 requested) atoms. Cycle 13: After refmac, R = 0.2302 (Rfree = 0.000) for 6798 atoms. Found 53 (73 requested) and removed 51 (36 requested) atoms. Cycle 14: After refmac, R = 0.2282 (Rfree = 0.000) for 6772 atoms. Found 61 (73 requested) and removed 55 (36 requested) atoms. Cycle 15: After refmac, R = 0.2150 (Rfree = 0.000) for 6756 atoms. Found 59 (73 requested) and removed 40 (36 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.97 2.38 Search for helices and strands: 0 residues in 0 chains, 6984 seeds are put forward NCS extension: 35 residues added (20 deleted due to clashes), 7019 seeds are put forward Round 1: 628 peptides, 58 chains. Longest chain 46 peptides. Score 0.620 Round 2: 650 peptides, 50 chains. Longest chain 55 peptides. Score 0.667 Round 3: 660 peptides, 49 chains. Longest chain 71 peptides. Score 0.678 Round 4: 646 peptides, 47 chains. Longest chain 51 peptides. Score 0.675 Round 5: 643 peptides, 54 chains. Longest chain 38 peptides. Score 0.647 Taking the results from Round 3 Chains 54, Residues 611, Estimated correctness of the model 67.7 % 13 chains (299 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 11522 restraints for refining 6872 atoms. 8014 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2427 (Rfree = 0.000) for 6872 atoms. Found 74 (74 requested) and removed 80 (37 requested) atoms. Cycle 17: After refmac, R = 0.2249 (Rfree = 0.000) for 6843 atoms. Found 67 (74 requested) and removed 52 (37 requested) atoms. Cycle 18: After refmac, R = 0.2188 (Rfree = 0.000) for 6841 atoms. Found 61 (73 requested) and removed 57 (36 requested) atoms. Cycle 19: After refmac, R = 0.2140 (Rfree = 0.000) for 6815 atoms. Found 51 (73 requested) and removed 47 (36 requested) atoms. Cycle 20: After refmac, R = 0.2153 (Rfree = 0.000) for 6798 atoms. Found 58 (73 requested) and removed 53 (36 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.97 2.38 Search for helices and strands: 0 residues in 0 chains, 7060 seeds are put forward NCS extension: 48 residues added (8 deleted due to clashes), 7108 seeds are put forward Round 1: 619 peptides, 57 chains. Longest chain 69 peptides. Score 0.617 Round 2: 642 peptides, 47 chains. Longest chain 51 peptides. Score 0.672 Round 3: 641 peptides, 48 chains. Longest chain 45 peptides. Score 0.668 Round 4: 642 peptides, 50 chains. Longest chain 37 peptides. Score 0.661 Round 5: 654 peptides, 48 chains. Longest chain 54 peptides. Score 0.677 Taking the results from Round 5 Chains 49, Residues 606, Estimated correctness of the model 67.5 % 16 chains (376 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 10743 restraints for refining 6872 atoms. 6966 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2376 (Rfree = 0.000) for 6872 atoms. Found 71 (74 requested) and removed 79 (37 requested) atoms. Cycle 22: After refmac, R = 0.2282 (Rfree = 0.000) for 6839 atoms. Found 58 (74 requested) and removed 59 (37 requested) atoms. Cycle 23: After refmac, R = 0.2202 (Rfree = 0.000) for 6817 atoms. Found 62 (73 requested) and removed 59 (36 requested) atoms. Cycle 24: After refmac, R = 0.2136 (Rfree = 0.000) for 6813 atoms. Found 50 (73 requested) and removed 58 (36 requested) atoms. Cycle 25: After refmac, R = 0.2117 (Rfree = 0.000) for 6796 atoms. Found 54 (73 requested) and removed 52 (36 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.96 2.37 Search for helices and strands: 0 residues in 0 chains, 7001 seeds are put forward NCS extension: 15 residues added (16 deleted due to clashes), 7016 seeds are put forward Round 1: 639 peptides, 58 chains. Longest chain 36 peptides. Score 0.629 Round 2: 665 peptides, 45 chains. Longest chain 58 peptides. Score 0.695 Round 3: 664 peptides, 47 chains. Longest chain 45 peptides. Score 0.688 Round 4: 665 peptides, 52 chains. Longest chain 59 peptides. Score 0.671 Round 5: 661 peptides, 53 chains. Longest chain 56 peptides. Score 0.664 Taking the results from Round 2 Chains 53, Residues 620, Estimated correctness of the model 70.7 % 15 chains (380 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 10580 restraints for refining 6872 atoms. 6728 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2391 (Rfree = 0.000) for 6872 atoms. Found 72 (74 requested) and removed 100 (37 requested) atoms. Cycle 27: After refmac, R = 0.2217 (Rfree = 0.000) for 6820 atoms. Found 73 (73 requested) and removed 69 (36 requested) atoms. Cycle 28: After refmac, R = 0.2139 (Rfree = 0.000) for 6809 atoms. Found 54 (73 requested) and removed 50 (36 requested) atoms. Cycle 29: After refmac, R = 0.2095 (Rfree = 0.000) for 6796 atoms. Found 70 (73 requested) and removed 53 (36 requested) atoms. Cycle 30: After refmac, R = 0.2044 (Rfree = 0.000) for 6805 atoms. Found 60 (73 requested) and removed 49 (36 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.95 2.37 Search for helices and strands: 0 residues in 0 chains, 7044 seeds are put forward NCS extension: 41 residues added (9 deleted due to clashes), 7085 seeds are put forward Round 1: 648 peptides, 46 chains. Longest chain 94 peptides. Score 0.680 Round 2: 664 peptides, 45 chains. Longest chain 69 peptides. Score 0.695 Round 3: 661 peptides, 49 chains. Longest chain 52 peptides. Score 0.678 Round 4: 655 peptides, 47 chains. Longest chain 61 peptides. Score 0.681 Round 5: 659 peptides, 54 chains. Longest chain 50 peptides. Score 0.659 Taking the results from Round 2 Chains 51, Residues 619, Estimated correctness of the model 70.7 % 17 chains (414 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 10240 restraints for refining 6873 atoms. 6248 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2283 (Rfree = 0.000) for 6873 atoms. Found 74 (74 requested) and removed 80 (37 requested) atoms. Cycle 32: After refmac, R = 0.2195 (Rfree = 0.000) for 6834 atoms. Found 67 (74 requested) and removed 51 (37 requested) atoms. Cycle 33: After refmac, R = 0.2095 (Rfree = 0.000) for 6830 atoms. Found 47 (73 requested) and removed 54 (36 requested) atoms. Cycle 34: After refmac, R = 0.1854 (Rfree = 0.000) for 6808 atoms. Found 35 (73 requested) and removed 43 (36 requested) atoms. Cycle 35: After refmac, R = 0.1794 (Rfree = 0.000) for 6788 atoms. Found 25 (73 requested) and removed 44 (36 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.97 2.38 Search for helices and strands: 0 residues in 0 chains, 6985 seeds are put forward NCS extension: 49 residues added (43 deleted due to clashes), 7034 seeds are put forward Round 1: 620 peptides, 42 chains. Longest chain 93 peptides. Score 0.674 Round 2: 657 peptides, 41 chains. Longest chain 60 peptides. Score 0.704 Round 3: 660 peptides, 51 chains. Longest chain 45 peptides. Score 0.671 Round 4: 667 peptides, 43 chains. Longest chain 72 peptides. Score 0.703 Round 5: 646 peptides, 54 chains. Longest chain 58 peptides. Score 0.649 Taking the results from Round 2 Chains 47, Residues 616, Estimated correctness of the model 72.3 % 15 chains (413 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 131 A and 137 A Built loop between residues 195 A and 202 A Built loop between residues 132 B and 136 B Built loop between residues 176 B and 180 B 42 chains (631 residues) following loop building 11 chains (430 residues) in sequence following loop building ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 9991 restraints for refining 6872 atoms. 5979 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2224 (Rfree = 0.000) for 6872 atoms. Found 74 (74 requested) and removed 82 (37 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2153 (Rfree = 0.000) for 6839 atoms. Found 73 (73 requested) and removed 74 (37 requested) atoms. Cycle 38: After refmac, R = 0.2032 (Rfree = 0.000) for 6831 atoms. Found 53 (70 requested) and removed 56 (36 requested) atoms. Cycle 39: After refmac, R = 0.1978 (Rfree = 0.000) for 6811 atoms. Found 60 (69 requested) and removed 61 (36 requested) atoms. Cycle 40: After refmac, R = 0.1770 (Rfree = 0.000) for 6800 atoms. Found 39 (67 requested) and removed 47 (36 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.97 2.38 Search for helices and strands: 0 residues in 0 chains, 6989 seeds are put forward NCS extension: 32 residues added (36 deleted due to clashes), 7021 seeds are put forward Round 1: 635 peptides, 46 chains. Longest chain 59 peptides. Score 0.671 Round 2: 649 peptides, 40 chains. Longest chain 70 peptides. Score 0.702 Round 3: 651 peptides, 48 chains. Longest chain 44 peptides. Score 0.675 Round 4: 632 peptides, 51 chains. Longest chain 38 peptides. Score 0.650 Round 5: 659 peptides, 42 chains. Longest chain 52 peptides. Score 0.701 Taking the results from Round 2 Chains 41, Residues 609, Estimated correctness of the model 71.9 % 14 chains (418 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 126 A and 129 A Built loop between residues 197 A and 202 A 39 chains (615 residues) following loop building 12 chains (424 residues) in sequence following loop building ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 10019 restraints for refining 6873 atoms. 6064 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2185 (Rfree = 0.000) for 6873 atoms. Found 61 (67 requested) and removed 75 (37 requested) atoms. Cycle 42: After refmac, R = 0.2065 (Rfree = 0.000) for 6845 atoms. Found 56 (64 requested) and removed 60 (36 requested) atoms. Cycle 43: After refmac, R = 0.2047 (Rfree = 0.000) for 6827 atoms. Found 52 (63 requested) and removed 52 (36 requested) atoms. Cycle 44: After refmac, R = 0.2011 (Rfree = 0.000) for 6822 atoms. Found 50 (61 requested) and removed 51 (36 requested) atoms. Cycle 45: After refmac, R = 0.1964 (Rfree = 0.000) for 6813 atoms. Found 50 (60 requested) and removed 51 (36 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.96 2.37 Search for helices and strands: 0 residues in 0 chains, 7022 seeds are put forward NCS extension: 162 residues added (61 deleted due to clashes), 7184 seeds are put forward Round 1: 634 peptides, 44 chains. Longest chain 54 peptides. Score 0.677 Round 2: 647 peptides, 38 chains. Longest chain 85 peptides. Score 0.707 Round 3: 651 peptides, 41 chains. Longest chain 58 peptides. Score 0.699 Round 4: 637 peptides, 42 chains. Longest chain 56 peptides. Score 0.686 Round 5: 638 peptides, 43 chains. Longest chain 68 peptides. Score 0.684 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 41, Residues 609, Estimated correctness of the model 72.8 % 13 chains (406 residues) have been docked in sequence Sequence coverage is 66 % Consider running further cycles of model building using 1vlu-3_warpNtrace.pdb as input Building loops using Loopy2018 41 chains (609 residues) following loop building 13 chains (406 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 29835 reflections ( 99.91 % complete ) and 10211 restraints for refining 6873 atoms. 6296 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2148 (Rfree = 0.000) for 6873 atoms. Found 0 (59 requested) and removed 18 (37 requested) atoms. Cycle 47: After refmac, R = 0.2102 (Rfree = 0.000) for 6843 atoms. Found 0 (57 requested) and removed 19 (36 requested) atoms. Cycle 48: After refmac, R = 0.2043 (Rfree = 0.000) for 6814 atoms. Found 0 (55 requested) and removed 19 (36 requested) atoms. Cycle 49: After refmac, R = 0.2042 (Rfree = 0.000) for 6788 atoms. TimeTaking 93.92