null Mon 24 Dec 07:31:13 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 2ash-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ash-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ash-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ash-3.6-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/2ash-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ash-3.6-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 07:31:17 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/2ash-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ash-3.6-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 1112 and 0 Target number of residues in the AU: 1112 Target solvent content: 0.6577 Checking the provided sequence file Detected sequence length: 381 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1524 Adjusted target solvent content: 0.53 Input MTZ file: 2ash-3.6-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: 5 Cell parameters: 170.109 99.745 124.866 90.000 123.929 90.000 Input sequence file: 2ash-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 12192 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: 103.605 3.600 Wilson plot Bfac: 83.27 20233 reflections ( 99.76 % complete ) and 0 restraints for refining 13480 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3415 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2970 (Rfree = 0.000) for 13480 atoms. Found 86 (86 requested) and removed 75 (43 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.44 Search for helices and strands: 0 residues in 0 chains, 13758 seeds are put forward NCS extension: 0 residues added, 13758 seeds are put forward Round 1: 562 peptides, 108 chains. Longest chain 12 peptides. Score 0.310 Round 2: 737 peptides, 124 chains. Longest chain 12 peptides. Score 0.412 Round 3: 785 peptides, 114 chains. Longest chain 21 peptides. Score 0.491 Round 4: 821 peptides, 114 chains. Longest chain 22 peptides. Score 0.520 Round 5: 822 peptides, 116 chains. Longest chain 16 peptides. Score 0.514 Taking the results from Round 4 Chains 114, Residues 707, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 25538 restraints for refining 11046 atoms. 22804 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2331 (Rfree = 0.000) for 11046 atoms. Found 55 (70 requested) and removed 55 (35 requested) atoms. Cycle 2: After refmac, R = 0.2146 (Rfree = 0.000) for 10878 atoms. Found 21 (70 requested) and removed 48 (35 requested) atoms. Cycle 3: After refmac, R = 0.2093 (Rfree = 0.000) for 10807 atoms. Found 13 (69 requested) and removed 36 (34 requested) atoms. Cycle 4: After refmac, R = 0.2069 (Rfree = 0.000) for 10763 atoms. Found 9 (69 requested) and removed 36 (34 requested) atoms. Cycle 5: After refmac, R = 0.2060 (Rfree = 0.000) for 10727 atoms. Found 13 (68 requested) and removed 36 (34 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.43 Search for helices and strands: 0 residues in 0 chains, 11075 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 11094 seeds are put forward Round 1: 708 peptides, 121 chains. Longest chain 15 peptides. Score 0.398 Round 2: 788 peptides, 122 chains. Longest chain 21 peptides. Score 0.464 Round 3: 784 peptides, 118 chains. Longest chain 17 peptides. Score 0.476 Round 4: 804 peptides, 111 chains. Longest chain 21 peptides. Score 0.517 Round 5: 820 peptides, 115 chains. Longest chain 21 peptides. Score 0.516 Taking the results from Round 4 Chains 114, Residues 693, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 25243 restraints for refining 11009 atoms. 22502 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2240 (Rfree = 0.000) for 11009 atoms. Found 67 (70 requested) and removed 62 (35 requested) atoms. Cycle 7: After refmac, R = 0.2122 (Rfree = 0.000) for 10952 atoms. Found 26 (70 requested) and removed 45 (35 requested) atoms. Cycle 8: After refmac, R = 0.2087 (Rfree = 0.000) for 10912 atoms. Found 19 (70 requested) and removed 41 (35 requested) atoms. Cycle 9: After refmac, R = 0.2066 (Rfree = 0.000) for 10885 atoms. Found 8 (69 requested) and removed 39 (34 requested) atoms. Cycle 10: After refmac, R = 0.2055 (Rfree = 0.000) for 10850 atoms. Found 2 (69 requested) and removed 38 (34 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 3.41 Search for helices and strands: 0 residues in 0 chains, 11179 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 11194 seeds are put forward Round 1: 756 peptides, 135 chains. Longest chain 20 peptides. Score 0.386 Round 2: 822 peptides, 124 chains. Longest chain 21 peptides. Score 0.485 Round 3: 820 peptides, 113 chains. Longest chain 22 peptides. Score 0.523 Round 4: 827 peptides, 115 chains. Longest chain 18 peptides. Score 0.521 Round 5: 822 peptides, 111 chains. Longest chain 21 peptides. Score 0.531 Taking the results from Round 5 Chains 111, Residues 711, Estimated correctness of the model 0.0 % 6 chains (59 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 25158 restraints for refining 11050 atoms. 22222 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2213 (Rfree = 0.000) for 11050 atoms. Found 56 (70 requested) and removed 59 (35 requested) atoms. Cycle 12: After refmac, R = 0.2062 (Rfree = 0.000) for 10974 atoms. Found 29 (70 requested) and removed 39 (35 requested) atoms. Cycle 13: After refmac, R = 0.2019 (Rfree = 0.000) for 10948 atoms. Found 20 (70 requested) and removed 41 (35 requested) atoms. Cycle 14: After refmac, R = 0.1994 (Rfree = 0.000) for 10920 atoms. Found 15 (70 requested) and removed 35 (35 requested) atoms. Cycle 15: After refmac, R = 0.1980 (Rfree = 0.000) for 10898 atoms. Found 7 (69 requested) and removed 34 (34 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.43 Search for helices and strands: 0 residues in 0 chains, 11222 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 11236 seeds are put forward Round 1: 724 peptides, 128 chains. Longest chain 18 peptides. Score 0.385 Round 2: 784 peptides, 113 chains. Longest chain 20 peptides. Score 0.494 Round 3: 790 peptides, 119 chains. Longest chain 20 peptides. Score 0.477 Round 4: 789 peptides, 116 chains. Longest chain 20 peptides. Score 0.487 Round 5: 805 peptides, 116 chains. Longest chain 21 peptides. Score 0.500 Taking the results from Round 5 Chains 117, Residues 689, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 25630 restraints for refining 11050 atoms. 22922 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2125 (Rfree = 0.000) for 11050 atoms. Found 55 (70 requested) and removed 57 (35 requested) atoms. Cycle 17: After refmac, R = 0.1948 (Rfree = 0.000) for 10993 atoms. Found 26 (70 requested) and removed 44 (35 requested) atoms. Cycle 18: After refmac, R = 0.1887 (Rfree = 0.000) for 10956 atoms. Found 8 (70 requested) and removed 38 (35 requested) atoms. Cycle 19: After refmac, R = 0.1869 (Rfree = 0.000) for 10914 atoms. Found 17 (70 requested) and removed 35 (35 requested) atoms. Cycle 20: After refmac, R = 0.1840 (Rfree = 0.000) for 10894 atoms. Found 8 (69 requested) and removed 37 (34 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 11244 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 11257 seeds are put forward Round 1: 669 peptides, 122 chains. Longest chain 14 peptides. Score 0.357 Round 2: 724 peptides, 114 chains. Longest chain 14 peptides. Score 0.439 Round 3: 738 peptides, 112 chains. Longest chain 15 peptides. Score 0.459 Round 4: 752 peptides, 109 chains. Longest chain 16 peptides. Score 0.482 Round 5: 741 peptides, 109 chains. Longest chain 19 peptides. Score 0.473 Taking the results from Round 4 Chains 112, Residues 643, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 25896 restraints for refining 11052 atoms. 23369 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2074 (Rfree = 0.000) for 11052 atoms. Found 57 (70 requested) and removed 45 (35 requested) atoms. Cycle 22: After refmac, R = 0.1926 (Rfree = 0.000) for 11022 atoms. Found 27 (70 requested) and removed 41 (35 requested) atoms. Cycle 23: After refmac, R = 0.1885 (Rfree = 0.000) for 10995 atoms. Found 16 (70 requested) and removed 37 (35 requested) atoms. Cycle 24: After refmac, R = 0.1864 (Rfree = 0.000) for 10969 atoms. Found 13 (70 requested) and removed 42 (35 requested) atoms. Cycle 25: After refmac, R = 0.1854 (Rfree = 0.000) for 10938 atoms. Found 8 (70 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.44 Search for helices and strands: 0 residues in 0 chains, 11269 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 11284 seeds are put forward Round 1: 640 peptides, 115 chains. Longest chain 16 peptides. Score 0.358 Round 2: 737 peptides, 116 chains. Longest chain 17 peptides. Score 0.443 Round 3: 751 peptides, 110 chains. Longest chain 19 peptides. Score 0.478 Round 4: 752 peptides, 109 chains. Longest chain 20 peptides. Score 0.482 Round 5: 751 peptides, 111 chains. Longest chain 19 peptides. Score 0.474 Taking the results from Round 4 Chains 109, Residues 643, Estimated correctness of the model 0.0 % 5 chains (33 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 25482 restraints for refining 11049 atoms. 22916 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2023 (Rfree = 0.000) for 11049 atoms. Found 46 (70 requested) and removed 43 (35 requested) atoms. Cycle 27: After refmac, R = 0.1876 (Rfree = 0.000) for 11016 atoms. Found 23 (70 requested) and removed 38 (35 requested) atoms. Cycle 28: After refmac, R = 0.1841 (Rfree = 0.000) for 10992 atoms. Found 13 (70 requested) and removed 36 (35 requested) atoms. Cycle 29: After refmac, R = 0.1825 (Rfree = 0.000) for 10964 atoms. Found 7 (70 requested) and removed 36 (35 requested) atoms. Cycle 30: After refmac, R = 0.1821 (Rfree = 0.000) for 10931 atoms. Found 5 (70 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 11259 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 11279 seeds are put forward Round 1: 672 peptides, 125 chains. Longest chain 15 peptides. Score 0.348 Round 2: 712 peptides, 110 chains. Longest chain 27 peptides. Score 0.444 Round 3: 731 peptides, 117 chains. Longest chain 18 peptides. Score 0.434 Round 4: 739 peptides, 110 chains. Longest chain 24 peptides. Score 0.468 Round 5: 729 peptides, 111 chains. Longest chain 22 peptides. Score 0.455 Taking the results from Round 4 Chains 112, Residues 629, Estimated correctness of the model 0.0 % 6 chains (48 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 25348 restraints for refining 11052 atoms. 22772 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2043 (Rfree = 0.000) for 11052 atoms. Found 63 (70 requested) and removed 44 (35 requested) atoms. Cycle 32: After refmac, R = 0.1897 (Rfree = 0.000) for 11032 atoms. Found 20 (71 requested) and removed 41 (35 requested) atoms. Cycle 33: After refmac, R = 0.1874 (Rfree = 0.000) for 11000 atoms. Found 12 (70 requested) and removed 35 (35 requested) atoms. Cycle 34: After refmac, R = 0.1852 (Rfree = 0.000) for 10971 atoms. Found 5 (70 requested) and removed 35 (35 requested) atoms. Cycle 35: After refmac, R = 0.1839 (Rfree = 0.000) for 10940 atoms. Found 8 (70 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 11263 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 11283 seeds are put forward Round 1: 598 peptides, 114 chains. Longest chain 18 peptides. Score 0.321 Round 2: 677 peptides, 105 chains. Longest chain 23 peptides. Score 0.433 Round 3: 700 peptides, 107 chains. Longest chain 27 peptides. Score 0.445 Round 4: 674 peptides, 97 chains. Longest chain 25 peptides. Score 0.462 Round 5: 690 peptides, 101 chains. Longest chain 24 peptides. Score 0.460 Taking the results from Round 4 Chains 99, Residues 577, Estimated correctness of the model 0.0 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 25758 restraints for refining 11050 atoms. 23403 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2090 (Rfree = 0.000) for 11050 atoms. Found 53 (70 requested) and removed 40 (35 requested) atoms. Cycle 37: After refmac, R = 0.1922 (Rfree = 0.000) for 11036 atoms. Found 20 (70 requested) and removed 35 (35 requested) atoms. Cycle 38: After refmac, R = 0.1910 (Rfree = 0.000) for 11011 atoms. Found 23 (70 requested) and removed 38 (35 requested) atoms. Cycle 39: After refmac, R = 0.1889 (Rfree = 0.000) for 10994 atoms. Found 6 (70 requested) and removed 35 (35 requested) atoms. Cycle 40: After refmac, R = 0.1880 (Rfree = 0.000) for 10960 atoms. Found 8 (70 requested) and removed 35 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 11267 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 11291 seeds are put forward Round 1: 597 peptides, 114 chains. Longest chain 14 peptides. Score 0.320 Round 2: 679 peptides, 109 chains. Longest chain 17 peptides. Score 0.419 Round 3: 680 peptides, 114 chains. Longest chain 15 peptides. Score 0.400 Round 4: 655 peptides, 104 chains. Longest chain 18 peptides. Score 0.417 Round 5: 650 peptides, 101 chains. Longest chain 18 peptides. Score 0.425 Taking the results from Round 5 Chains 102, Residues 549, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 20233 reflections ( 99.76 % complete ) and 26527 restraints for refining 11052 atoms. 24383 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2118 (Rfree = 0.000) for 11052 atoms. Found 64 (70 requested) and removed 38 (35 requested) atoms. Cycle 42: After refmac, R = 0.1949 (Rfree = 0.000) for 11040 atoms. Found 26 (71 requested) and removed 39 (35 requested) atoms. Cycle 43: After refmac, R = 0.1993 (Rfree = 0.000) for 11003 atoms. Found 37 (70 requested) and removed 39 (35 requested) atoms. Cycle 44: After refmac, R = 0.1931 (Rfree = 0.000) for 10985 atoms. Found 39 (70 requested) and removed 39 (35 requested) atoms. Cycle 45: After refmac, R = 0.1844 (Rfree = 0.000) for 10974 atoms. Found 35 (70 requested) and removed 41 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.44 Search for helices and strands: 0 residues in 0 chains, 11336 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 11350 seeds are put forward Round 1: 496 peptides, 98 chains. Longest chain 13 peptides. Score 0.286 Round 2: 575 peptides, 100 chains. Longest chain 16 peptides. Score 0.358 Round 3: 590 peptides, 100 chains. Longest chain 16 peptides. Score 0.373 Round 4: 615 peptides, 99 chains. Longest chain 16 peptides. Score 0.400 Round 5: 609 peptides, 95 chains. Longest chain 22 peptides. Score 0.411 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 95, Residues 514, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 1 % Consider running further cycles of model building using 2ash-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20233 reflections ( 99.76 % complete ) and 26357 restraints for refining 11052 atoms. 24382 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1944 (Rfree = 0.000) for 11052 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 47: After refmac, R = 0.1904 (Rfree = 0.000) for 10997 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 48: After refmac, R = 0.1983 (Rfree = 0.000) for 10944 atoms. Found 0 (70 requested) and removed 35 (35 requested) atoms. Cycle 49: After refmac, R = 0.1938 (Rfree = 0.000) for 10892 atoms. Found 0 (69 requested) and removed 34 (34 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:29:18 GMT 2018 Job finished. TimeTaking 118.1 Used memory is bytes: 19229680