Tue 25 Dec 19:27:56 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vlu-3.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlu-3.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlu-3.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-3.0-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-3.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-3.0-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:10 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/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-3.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlu-3.0-parrot-hancs/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-hancs.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-hancs.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 8325 atoms. Observations/parameters ratio is 0.90 ------------------------------------------------------ Starting model: R = 0.3553 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2501 (Rfree = 0.000) for 8325 atoms. Found 66 (89 requested) and removed 135 (44 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.97 2.38 Search for helices and strands: 0 residues in 0 chains, 8439 seeds are put forward NCS extension: 0 residues added, 8439 seeds are put forward Round 1: 540 peptides, 77 chains. Longest chain 39 peptides. Score 0.456 Round 2: 593 peptides, 66 chains. Longest chain 28 peptides. Score 0.557 Round 3: 616 peptides, 57 chains. Longest chain 45 peptides. Score 0.614 Round 4: 625 peptides, 61 chains. Longest chain 30 peptides. Score 0.606 Round 5: 614 peptides, 62 chains. Longest chain 38 peptides. Score 0.592 Taking the results from Round 3 Chains 72, Residues 559, Estimated correctness of the model 54.9 % 15 chains (218 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 12388 restraints for refining 6868 atoms. 9408 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2898 (Rfree = 0.000) for 6868 atoms. Found 74 (74 requested) and removed 83 (37 requested) atoms. Cycle 2: After refmac, R = 0.2709 (Rfree = 0.000) for 6749 atoms. Found 73 (73 requested) and removed 52 (36 requested) atoms. Cycle 3: After refmac, R = 0.2562 (Rfree = 0.000) for 6714 atoms. Found 59 (73 requested) and removed 42 (36 requested) atoms. Cycle 4: After refmac, R = 0.2498 (Rfree = 0.000) for 6689 atoms. Found 44 (72 requested) and removed 40 (36 requested) atoms. Cycle 5: After refmac, R = 0.2450 (Rfree = 0.000) for 6675 atoms. Found 37 (72 requested) and removed 39 (36 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.96 2.37 Search for helices and strands: 0 residues in 0 chains, 6913 seeds are put forward NCS extension: 39 residues added (13 deleted due to clashes), 6952 seeds are put forward Round 1: 567 peptides, 63 chains. Longest chain 41 peptides. Score 0.546 Round 2: 601 peptides, 56 chains. Longest chain 46 peptides. Score 0.606 Round 3: 622 peptides, 56 chains. Longest chain 41 peptides. Score 0.623 Round 4: 606 peptides, 53 chains. Longest chain 37 peptides. Score 0.622 Round 5: 593 peptides, 53 chains. Longest chain 50 peptides. Score 0.611 Taking the results from Round 3 Chains 60, Residues 566, Estimated correctness of the model 56.8 % 13 chains (236 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 11996 restraints for refining 6766 atoms. 8922 conditional restraints added. Observations/parameters ratio is 1.10 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2713 (Rfree = 0.000) for 6766 atoms. Found 73 (73 requested) and removed 76 (36 requested) atoms. Cycle 7: After refmac, R = 0.2507 (Rfree = 0.000) for 6713 atoms. Found 58 (72 requested) and removed 54 (36 requested) atoms. Cycle 8: After refmac, R = 0.2536 (Rfree = 0.000) for 6690 atoms. Found 65 (72 requested) and removed 56 (36 requested) atoms. Cycle 9: After refmac, R = 0.2290 (Rfree = 0.000) for 6671 atoms. Found 33 (72 requested) and removed 47 (36 requested) atoms. Cycle 10: After refmac, R = 0.2183 (Rfree = 0.000) for 6638 atoms. Found 19 (71 requested) and removed 43 (35 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.97 2.38 Search for helices and strands: 0 residues in 0 chains, 6848 seeds are put forward NCS extension: 27 residues added (13 deleted due to clashes), 6875 seeds are put forward Round 1: 593 peptides, 60 chains. Longest chain 38 peptides. Score 0.583 Round 2: 617 peptides, 53 chains. Longest chain 39 peptides. Score 0.631 Round 3: 616 peptides, 56 chains. Longest chain 29 peptides. Score 0.618 Round 4: 611 peptides, 53 chains. Longest chain 38 peptides. Score 0.626 Round 5: 626 peptides, 53 chains. Longest chain 50 peptides. Score 0.638 Taking the results from Round 5 Chains 57, Residues 573, Estimated correctness of the model 59.9 % 16 chains (310 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 29835 reflections ( 99.91 % complete ) and 11280 restraints for refining 6871 atoms. 7896 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2583 (Rfree = 0.000) for 6871 atoms. Found 74 (74 requested) and removed 99 (37 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2372 (Rfree = 0.000) for 6807 atoms. Found 45 (73 requested) and removed 62 (36 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2271 (Rfree = 0.000) for 6766 atoms. Found 28 (73 requested) and removed 45 (36 requested) atoms. Cycle 14: After refmac, R = 0.2227 (Rfree = 0.000) for 6738 atoms. Found 26 (72 requested) and removed 39 (36 requested) atoms. Cycle 15: After refmac, R = 0.2202 (Rfree = 0.000) for 6713 atoms. Found 28 (72 requested) and removed 43 (36 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.98 2.39 Search for helices and strands: 0 residues in 0 chains, 6889 seeds are put forward NCS extension: 25 residues added (16 deleted due to clashes), 6914 seeds are put forward Round 1: 578 peptides, 50 chains. Longest chain 63 peptides. Score 0.611 Round 2: 623 peptides, 53 chains. Longest chain 41 peptides. Score 0.635 Round 3: 631 peptides, 48 chains. Longest chain 51 peptides. Score 0.660 Round 4: 631 peptides, 56 chains. Longest chain 34 peptides. Score 0.630 Round 5: 615 peptides, 50 chains. Longest chain 47 peptides. Score 0.641 Taking the results from Round 3 Chains 55, Residues 583, Estimated correctness of the model 64.3 % 16 chains (327 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 11313 restraints for refining 6872 atoms. 7828 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2453 (Rfree = 0.000) for 6872 atoms. Found 74 (74 requested) and removed 74 (37 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2281 (Rfree = 0.000) for 6844 atoms. Found 39 (74 requested) and removed 53 (37 requested) atoms. Cycle 18: After refmac, R = 0.2202 (Rfree = 0.000) for 6815 atoms. Found 29 (73 requested) and removed 43 (36 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2136 (Rfree = 0.000) for 6791 atoms. Found 27 (73 requested) and removed 44 (36 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2145 (Rfree = 0.000) for 6768 atoms. Found 42 (73 requested) and removed 42 (36 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.97 2.38 Search for helices and strands: 0 residues in 0 chains, 6977 seeds are put forward NCS extension: 11 residues added (13 deleted due to clashes), 6988 seeds are put forward Round 1: 619 peptides, 54 chains. Longest chain 51 peptides. Score 0.628 Round 2: 648 peptides, 47 chains. Longest chain 48 peptides. Score 0.676 Round 3: 649 peptides, 44 chains. Longest chain 63 peptides. Score 0.688 Round 4: 638 peptides, 58 chains. Longest chain 39 peptides. Score 0.628 Round 5: 636 peptides, 53 chains. Longest chain 51 peptides. Score 0.645 Taking the results from Round 3 Chains 50, Residues 605, Estimated correctness of the model 69.5 % 15 chains (345 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 10868 restraints for refining 6873 atoms. 7186 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2415 (Rfree = 0.000) for 6873 atoms. Found 74 (74 requested) and removed 100 (37 requested) atoms. Cycle 22: After refmac, R = 0.2262 (Rfree = 0.000) for 6826 atoms. Found 47 (73 requested) and removed 57 (36 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 23: After refmac, R = 0.2226 (Rfree = 0.000) for 6801 atoms. Found 46 (73 requested) and removed 52 (36 requested) atoms. Cycle 24: After refmac, R = 0.2195 (Rfree = 0.000) for 6784 atoms. Found 35 (73 requested) and removed 46 (36 requested) atoms. Cycle 25: After refmac, R = 0.2174 (Rfree = 0.000) for 6762 atoms. Found 63 (73 requested) and removed 48 (36 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.99 2.40 Search for helices and strands: 0 residues in 0 chains, 6996 seeds are put forward NCS extension: 7 residues added (29 deleted due to clashes), 7003 seeds are put forward Round 1: 611 peptides, 54 chains. Longest chain 44 peptides. Score 0.622 Round 2: 645 peptides, 51 chains. Longest chain 35 peptides. Score 0.660 Round 3: 629 peptides, 52 chains. Longest chain 35 peptides. Score 0.644 Round 4: 646 peptides, 53 chains. Longest chain 46 peptides. Score 0.653 Round 5: 643 peptides, 48 chains. Longest chain 51 peptides. Score 0.669 Taking the results from Round 5 Chains 51, Residues 595, Estimated correctness of the model 66.0 % 11 chains (282 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 11540 restraints for refining 6873 atoms. 8160 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2373 (Rfree = 0.000) for 6873 atoms. Found 66 (74 requested) and removed 60 (37 requested) atoms. Cycle 27: After refmac, R = 0.2292 (Rfree = 0.000) for 6854 atoms. Found 69 (74 requested) and removed 57 (37 requested) atoms. Cycle 28: After refmac, R = 0.2240 (Rfree = 0.000) for 6852 atoms. Found 50 (74 requested) and removed 45 (37 requested) atoms. Cycle 29: After refmac, R = 0.2205 (Rfree = 0.000) for 6829 atoms. Found 49 (73 requested) and removed 45 (36 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2218 (Rfree = 0.000) for 6830 atoms. Found 51 (73 requested) and removed 44 (36 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.00 2.41 Search for helices and strands: 0 residues in 0 chains, 7046 seeds are put forward NCS extension: 26 residues added (48 deleted due to clashes), 7072 seeds are put forward Round 1: 623 peptides, 54 chains. Longest chain 45 peptides. Score 0.631 Round 2: 655 peptides, 49 chains. Longest chain 47 peptides. Score 0.674 Round 3: 644 peptides, 52 chains. Longest chain 42 peptides. Score 0.655 Round 4: 649 peptides, 50 chains. Longest chain 45 peptides. Score 0.666 Round 5: 652 peptides, 55 chains. Longest chain 47 peptides. Score 0.650 Taking the results from Round 2 Chains 53, Residues 606, Estimated correctness of the model 66.9 % 15 chains (357 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 10859 restraints for refining 6872 atoms. 7140 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2301 (Rfree = 0.000) for 6872 atoms. Found 74 (74 requested) and removed 80 (37 requested) atoms. Cycle 32: After refmac, R = 0.2170 (Rfree = 0.000) for 6837 atoms. Found 41 (74 requested) and removed 54 (37 requested) atoms. Cycle 33: After refmac, R = 0.2188 (Rfree = 0.000) for 6800 atoms. Found 52 (73 requested) and removed 52 (36 requested) atoms. Cycle 34: After refmac, R = 0.1929 (Rfree = 0.000) for 6780 atoms. Found 28 (73 requested) and removed 40 (36 requested) atoms. Cycle 35: After refmac, R = 0.1886 (Rfree = 0.000) for 6756 atoms. Found 14 (72 requested) and removed 37 (36 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.97 2.38 Search for helices and strands: 0 residues in 0 chains, 6946 seeds are put forward NCS extension: 19 residues added (35 deleted due to clashes), 6965 seeds are put forward Round 1: 617 peptides, 52 chains. Longest chain 43 peptides. Score 0.634 Round 2: 655 peptides, 43 chains. Longest chain 58 peptides. Score 0.695 Round 3: 643 peptides, 43 chains. Longest chain 57 peptides. Score 0.687 Round 4: 639 peptides, 52 chains. Longest chain 47 peptides. Score 0.651 Round 5: 648 peptides, 47 chains. Longest chain 47 peptides. Score 0.676 Taking the results from Round 2 Chains 47, Residues 612, Estimated correctness of the model 70.7 % 15 chains (404 residues) have been docked in sequence ------------------------------------------------------ 29835 reflections ( 99.91 % complete ) and 10249 restraints for refining 6872 atoms. 6344 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2227 (Rfree = 0.000) for 6872 atoms. Found 57 (74 requested) and removed 78 (37 requested) atoms. Cycle 37: After refmac, R = 0.2126 (Rfree = 0.000) for 6832 atoms. Found 64 (73 requested) and removed 51 (36 requested) atoms. Cycle 38: After refmac, R = 0.2123 (Rfree = 0.000) for 6830 atoms. Found 52 (73 requested) and removed 54 (36 requested) atoms. Cycle 39: After refmac, R = 0.2059 (Rfree = 0.000) for 6814 atoms. Found 47 (73 requested) and removed 47 (36 requested) atoms. Cycle 40: After refmac, R = 0.2014 (Rfree = 0.000) for 6804 atoms. Found 43 (73 requested) and removed 46 (36 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.99 2.40 Search for helices and strands: 0 residues in 0 chains, 7002 seeds are put forward NCS extension: 18 residues added (15 deleted due to clashes), 7020 seeds are put forward Round 1: 602 peptides, 45 chains. Longest chain 47 peptides. Score 0.650 Round 2: 624 peptides, 47 chains. Longest chain 54 peptides. Score 0.659 Round 3: 628 peptides, 46 chains. Longest chain 45 peptides. Score 0.665 Round 4: 639 peptides, 50 chains. Longest chain 51 peptides. Score 0.659 Round 5: 639 peptides, 47 chains. Longest chain 47 peptides. Score 0.670 Taking the results from Round 5 Chains 52, Residues 592, Estimated correctness of the model 66.2 % 18 chains (361 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 29835 reflections ( 99.91 % complete ) and 10929 restraints for refining 6873 atoms. 7240 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2352 (Rfree = 0.000) for 6873 atoms. Found 74 (74 requested) and removed 90 (37 requested) atoms. Cycle 42: After refmac, R = 0.2214 (Rfree = 0.000) for 6828 atoms. Found 66 (73 requested) and removed 54 (36 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2126 (Rfree = 0.000) for 6829 atoms. Found 58 (73 requested) and removed 49 (36 requested) atoms. Cycle 44: After refmac, R = 0.2110 (Rfree = 0.000) for 6822 atoms. Found 70 (73 requested) and removed 52 (36 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1876 (Rfree = 0.000) for 6826 atoms. Found 35 (73 requested) and removed 49 (36 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.97 2.38 Search for helices and strands: 0 residues in 0 chains, 7023 seeds are put forward NCS extension: 18 residues added (30 deleted due to clashes), 7041 seeds are put forward Round 1: 637 peptides, 49 chains. Longest chain 54 peptides. Score 0.661 Round 2: 652 peptides, 45 chains. Longest chain 49 peptides. Score 0.686 Round 3: 642 peptides, 45 chains. Longest chain 54 peptides. Score 0.679 Round 4: 649 peptides, 49 chains. Longest chain 48 peptides. Score 0.670 Round 5: 651 peptides, 49 chains. Longest chain 41 peptides. Score 0.671 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 607, Estimated correctness of the model 69.1 % 19 chains (386 residues) have been docked in sequence Sequence coverage is 63 % Consider running further cycles of model building using 1vlu-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 375 A and 378 A Built loop between residues 31 B and 38 B Built loop between residues 137 B and 140 B Built loop between residues 341 B and 355 B Built loop between residues 375 B and 378 B 42 chains (626 residues) following loop building 14 chains (411 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB ---> Final restrained refinement block. No atom update. 29835 reflections ( 99.91 % complete ) and 10234 restraints for refining 6873 atoms. 6259 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2312 (Rfree = 0.000) for 6873 atoms. Found 0 (74 requested) and removed 26 (37 requested) atoms. Cycle 47: After refmac, R = 0.2167 (Rfree = 0.000) for 6828 atoms. Found 0 (73 requested) and removed 17 (36 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2112 (Rfree = 0.000) for 6803 atoms. Found 0 (73 requested) and removed 22 (36 requested) atoms. Cycle 49: After refmac, R = 0.1905 (Rfree = 0.000) for 6773 atoms. Found 0 (73 requested) and removed 5 (36 requested) atoms. Writing output files ... TimeTaking 135.85