null Mon 24 Dec 07:33:55 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 2ash-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ash-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ash-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ash-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/2ash-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ash-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 07:33:59 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/noncs/ArpWArp/wArpResults/WorkingDir/2ash-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ash-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 1160 and 0 Target number of residues in the AU: 1160 Target solvent content: 0.6429 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-3.2-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: 5 Cell parameters: 170.109 99.745 124.866 90.000 123.929 90.000 Input sequence file: 2ash-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 12192 target number of atoms Had to go as low as 0.80 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 3.200 Wilson plot Bfac: 73.62 28706 reflections ( 99.82 % complete ) and 0 restraints for refining 13655 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3412 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3015 (Rfree = 0.000) for 13655 atoms. Found 122 (122 requested) and removed 119 (61 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 3.13 Search for helices and strands: 0 residues in 0 chains, 13961 seeds are put forward NCS extension: 0 residues added, 13961 seeds are put forward Round 1: 662 peptides, 131 chains. Longest chain 16 peptides. Score 0.313 Round 2: 810 peptides, 134 chains. Longest chain 29 peptides. Score 0.439 Round 3: 849 peptides, 123 chains. Longest chain 17 peptides. Score 0.511 Round 4: 903 peptides, 126 chains. Longest chain 19 peptides. Score 0.542 Round 5: 902 peptides, 125 chains. Longest chain 36 peptides. Score 0.545 Taking the results from Round 5 Chains 128, Residues 777, Estimated correctness of the model 25.4 % 8 chains (45 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 24656 restraints for refining 11121 atoms. 21546 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2614 (Rfree = 0.000) for 11121 atoms. Found 59 (99 requested) and removed 64 (49 requested) atoms. Cycle 2: After refmac, R = 0.2419 (Rfree = 0.000) for 10972 atoms. Found 35 (99 requested) and removed 67 (49 requested) atoms. Cycle 3: After refmac, R = 0.2329 (Rfree = 0.000) for 10881 atoms. Found 30 (98 requested) and removed 58 (49 requested) atoms. Cycle 4: After refmac, R = 0.2296 (Rfree = 0.000) for 10819 atoms. Found 28 (97 requested) and removed 53 (48 requested) atoms. Cycle 5: After refmac, R = 0.2257 (Rfree = 0.000) for 10761 atoms. Found 15 (96 requested) and removed 52 (48 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.13 Search for helices and strands: 0 residues in 0 chains, 11153 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 11182 seeds are put forward Round 1: 832 peptides, 135 chains. Longest chain 20 peptides. Score 0.454 Round 2: 924 peptides, 126 chains. Longest chain 27 peptides. Score 0.558 Round 3: 917 peptides, 114 chains. Longest chain 35 peptides. Score 0.591 Round 4: 947 peptides, 121 chains. Longest chain 32 peptides. Score 0.590 Round 5: 917 peptides, 113 chains. Longest chain 29 peptides. Score 0.594 Taking the results from Round 5 Chains 118, Residues 804, Estimated correctness of the model 39.4 % 8 chains (93 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 24324 restraints for refining 11129 atoms. 20872 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2447 (Rfree = 0.000) for 11129 atoms. Found 88 (99 requested) and removed 64 (49 requested) atoms. Cycle 7: After refmac, R = 0.2239 (Rfree = 0.000) for 11097 atoms. Found 27 (100 requested) and removed 62 (50 requested) atoms. Cycle 8: After refmac, R = 0.2175 (Rfree = 0.000) for 11042 atoms. Found 20 (99 requested) and removed 54 (49 requested) atoms. Cycle 9: After refmac, R = 0.2109 (Rfree = 0.000) for 10988 atoms. Found 22 (98 requested) and removed 49 (49 requested) atoms. Cycle 10: After refmac, R = 0.2051 (Rfree = 0.000) for 10951 atoms. Found 19 (98 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.28 3.15 Search for helices and strands: 0 residues in 0 chains, 11318 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 11335 seeds are put forward Round 1: 814 peptides, 134 chains. Longest chain 17 peptides. Score 0.442 Round 2: 876 peptides, 120 chains. Longest chain 28 peptides. Score 0.542 Round 3: 870 peptides, 122 chains. Longest chain 22 peptides. Score 0.530 Round 4: 870 peptides, 115 chains. Longest chain 22 peptides. Score 0.554 Round 5: 889 peptides, 116 chains. Longest chain 23 peptides. Score 0.565 Taking the results from Round 5 Chains 119, Residues 773, Estimated correctness of the model 31.3 % 8 chains (89 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 24113 restraints for refining 11128 atoms. 20794 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2319 (Rfree = 0.000) for 11128 atoms. Found 71 (99 requested) and removed 62 (49 requested) atoms. Cycle 12: After refmac, R = 0.2162 (Rfree = 0.000) for 11080 atoms. Found 30 (99 requested) and removed 51 (49 requested) atoms. Cycle 13: After refmac, R = 0.2132 (Rfree = 0.000) for 11045 atoms. Found 22 (99 requested) and removed 53 (49 requested) atoms. Cycle 14: After refmac, R = 0.2082 (Rfree = 0.000) for 10998 atoms. Found 26 (98 requested) and removed 51 (49 requested) atoms. Cycle 15: After refmac, R = 0.2053 (Rfree = 0.000) for 10955 atoms. Found 13 (98 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 3.14 Search for helices and strands: 0 residues in 0 chains, 11272 seeds are put forward NCS extension: 31 residues added (0 deleted due to clashes), 11303 seeds are put forward Round 1: 771 peptides, 125 chains. Longest chain 15 peptides. Score 0.439 Round 2: 825 peptides, 112 chains. Longest chain 18 peptides. Score 0.530 Round 3: 849 peptides, 112 chains. Longest chain 24 peptides. Score 0.548 Round 4: 865 peptides, 115 chains. Longest chain 24 peptides. Score 0.550 Round 5: 848 peptides, 105 chains. Longest chain 23 peptides. Score 0.571 Taking the results from Round 5 Chains 106, Residues 743, Estimated correctness of the model 33.0 % 9 chains (77 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 24689 restraints for refining 11129 atoms. 21546 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2325 (Rfree = 0.000) for 11129 atoms. Found 76 (99 requested) and removed 65 (49 requested) atoms. Cycle 17: After refmac, R = 0.2165 (Rfree = 0.000) for 11105 atoms. Found 30 (99 requested) and removed 50 (49 requested) atoms. Cycle 18: After refmac, R = 0.2358 (Rfree = 0.000) for 11063 atoms. Found 62 (99 requested) and removed 53 (49 requested) atoms. Cycle 19: After refmac, R = 0.2053 (Rfree = 0.000) for 11043 atoms. Found 25 (99 requested) and removed 50 (49 requested) atoms. Cycle 20: After refmac, R = 0.2171 (Rfree = 0.000) for 11010 atoms. Found 36 (98 requested) and removed 50 (49 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 3.12 Search for helices and strands: 0 residues in 0 chains, 11390 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 11419 seeds are put forward Round 1: 741 peptides, 127 chains. Longest chain 17 peptides. Score 0.404 Round 2: 849 peptides, 125 chains. Longest chain 25 peptides. Score 0.504 Round 3: 858 peptides, 117 chains. Longest chain 25 peptides. Score 0.538 Round 4: 880 peptides, 116 chains. Longest chain 24 peptides. Score 0.558 Round 5: 904 peptides, 119 chains. Longest chain 25 peptides. Score 0.566 Taking the results from Round 5 Chains 125, Residues 785, Estimated correctness of the model 31.6 % 7 chains (73 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 24465 restraints for refining 11129 atoms. 21176 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2317 (Rfree = 0.000) for 11129 atoms. Found 74 (99 requested) and removed 64 (49 requested) atoms. Cycle 22: After refmac, R = 0.2116 (Rfree = 0.000) for 11113 atoms. Found 31 (99 requested) and removed 54 (49 requested) atoms. Cycle 23: After refmac, R = 0.2081 (Rfree = 0.000) for 11072 atoms. Found 26 (99 requested) and removed 49 (49 requested) atoms. Cycle 24: After refmac, R = 0.2063 (Rfree = 0.000) for 11038 atoms. Found 37 (99 requested) and removed 49 (49 requested) atoms. Cycle 25: After refmac, R = 0.2047 (Rfree = 0.000) for 11016 atoms. Found 29 (98 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 3.13 Search for helices and strands: 0 residues in 0 chains, 11364 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 11390 seeds are put forward Round 1: 765 peptides, 126 chains. Longest chain 18 peptides. Score 0.429 Round 2: 858 peptides, 119 chains. Longest chain 24 peptides. Score 0.532 Round 3: 857 peptides, 118 chains. Longest chain 24 peptides. Score 0.534 Round 4: 811 peptides, 108 chains. Longest chain 19 peptides. Score 0.533 Round 5: 855 peptides, 115 chains. Longest chain 27 peptides. Score 0.543 Taking the results from Round 5 Chains 118, Residues 740, Estimated correctness of the model 24.8 % 8 chains (69 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 24639 restraints for refining 11131 atoms. 21534 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2282 (Rfree = 0.000) for 11131 atoms. Found 70 (99 requested) and removed 55 (49 requested) atoms. Cycle 27: After refmac, R = 0.2116 (Rfree = 0.000) for 11113 atoms. Found 32 (100 requested) and removed 53 (50 requested) atoms. Cycle 28: After refmac, R = 0.2055 (Rfree = 0.000) for 11070 atoms. Found 28 (99 requested) and removed 54 (49 requested) atoms. Cycle 29: After refmac, R = 0.2000 (Rfree = 0.000) for 11028 atoms. Found 27 (99 requested) and removed 49 (49 requested) atoms. Cycle 30: After refmac, R = 0.1953 (Rfree = 0.000) for 10999 atoms. Found 25 (98 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 3.12 Search for helices and strands: 0 residues in 0 chains, 11345 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 11366 seeds are put forward Round 1: 739 peptides, 130 chains. Longest chain 17 peptides. Score 0.391 Round 2: 827 peptides, 121 chains. Longest chain 24 peptides. Score 0.500 Round 3: 819 peptides, 115 chains. Longest chain 27 peptides. Score 0.515 Round 4: 833 peptides, 120 chains. Longest chain 27 peptides. Score 0.509 Round 5: 821 peptides, 115 chains. Longest chain 30 peptides. Score 0.517 Taking the results from Round 5 Chains 116, Residues 706, Estimated correctness of the model 16.8 % 7 chains (42 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 25006 restraints for refining 11130 atoms. 22154 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2179 (Rfree = 0.000) for 11130 atoms. Found 69 (99 requested) and removed 51 (49 requested) atoms. Cycle 32: After refmac, R = 0.2030 (Rfree = 0.000) for 11117 atoms. Found 19 (100 requested) and removed 52 (50 requested) atoms. Cycle 33: After refmac, R = 0.1995 (Rfree = 0.000) for 11059 atoms. Found 38 (99 requested) and removed 49 (49 requested) atoms. Cycle 34: After refmac, R = 0.1961 (Rfree = 0.000) for 11033 atoms. Found 19 (99 requested) and removed 49 (49 requested) atoms. Cycle 35: After refmac, R = 0.1940 (Rfree = 0.000) for 10988 atoms. Found 26 (98 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.14 Search for helices and strands: 0 residues in 0 chains, 11307 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 11336 seeds are put forward Round 1: 687 peptides, 122 chains. Longest chain 22 peptides. Score 0.374 Round 2: 796 peptides, 120 chains. Longest chain 22 peptides. Score 0.478 Round 3: 786 peptides, 117 chains. Longest chain 28 peptides. Score 0.481 Round 4: 790 peptides, 116 chains. Longest chain 21 peptides. Score 0.488 Round 5: 814 peptides, 119 chains. Longest chain 27 peptides. Score 0.497 Taking the results from Round 5 Chains 123, Residues 695, Estimated correctness of the model 10.4 % 9 chains (66 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 24843 restraints for refining 11130 atoms. 21986 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2183 (Rfree = 0.000) for 11130 atoms. Found 86 (99 requested) and removed 58 (49 requested) atoms. Cycle 37: After refmac, R = 0.2044 (Rfree = 0.000) for 11134 atoms. Found 14 (100 requested) and removed 51 (50 requested) atoms. Cycle 38: After refmac, R = 0.2008 (Rfree = 0.000) for 11078 atoms. Found 30 (99 requested) and removed 50 (49 requested) atoms. Cycle 39: After refmac, R = 0.2004 (Rfree = 0.000) for 11034 atoms. Found 54 (99 requested) and removed 50 (49 requested) atoms. Cycle 40: After refmac, R = 0.1977 (Rfree = 0.000) for 11022 atoms. Found 57 (99 requested) and removed 51 (49 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 3.13 Search for helices and strands: 0 residues in 0 chains, 11364 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 11385 seeds are put forward Round 1: 650 peptides, 120 chains. Longest chain 15 peptides. Score 0.347 Round 2: 736 peptides, 114 chains. Longest chain 24 peptides. Score 0.450 Round 3: 781 peptides, 110 chains. Longest chain 24 peptides. Score 0.502 Round 4: 758 peptides, 111 chains. Longest chain 22 peptides. Score 0.480 Round 5: 760 peptides, 108 chains. Longest chain 25 peptides. Score 0.493 Taking the results from Round 3 Chains 119, Residues 671, Estimated correctness of the model 12.0 % 10 chains (91 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 24384 restraints for refining 11131 atoms. 21486 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2087 (Rfree = 0.000) for 11131 atoms. Found 66 (99 requested) and removed 57 (49 requested) atoms. Cycle 42: After refmac, R = 0.1948 (Rfree = 0.000) for 11123 atoms. Found 23 (99 requested) and removed 50 (49 requested) atoms. Cycle 43: After refmac, R = 0.1930 (Rfree = 0.000) for 11078 atoms. Found 25 (99 requested) and removed 51 (49 requested) atoms. Cycle 44: After refmac, R = 0.1991 (Rfree = 0.000) for 11044 atoms. Found 63 (99 requested) and removed 49 (49 requested) atoms. Cycle 45: After refmac, R = 0.1877 (Rfree = 0.000) for 11042 atoms. Found 24 (99 requested) and removed 50 (49 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 3.14 Search for helices and strands: 0 residues in 0 chains, 11374 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 11390 seeds are put forward Round 1: 623 peptides, 113 chains. Longest chain 20 peptides. Score 0.350 Round 2: 716 peptides, 110 chains. Longest chain 17 peptides. Score 0.448 Round 3: 696 peptides, 98 chains. Longest chain 23 peptides. Score 0.477 Round 4: 701 peptides, 108 chains. Longest chain 23 peptides. Score 0.442 Round 5: 714 peptides, 105 chains. Longest chain 25 peptides. Score 0.465 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 100, Residues 598, Estimated correctness of the model 3.7 % 7 chains (76 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2ash-3_warpNtrace.pdb as input Building loops using Loopy2018 100 chains (598 residues) following loop building 7 chains (76 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 28706 reflections ( 99.82 % complete ) and 25115 restraints for refining 11130 atoms. 22548 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2019 (Rfree = 0.000) for 11130 atoms. Found 0 (99 requested) and removed 49 (49 requested) atoms. Cycle 47: After refmac, R = 0.2024 (Rfree = 0.000) for 11056 atoms. Found 0 (99 requested) and removed 49 (49 requested) atoms. Cycle 48: After refmac, R = 0.1946 (Rfree = 0.000) for 10989 atoms. Found 0 (98 requested) and removed 40 (49 requested) atoms. Cycle 49: After refmac, R = 0.2329 (Rfree = 0.000) for 10938 atoms. Found 0 (98 requested) and removed 49 (49 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:38:59 GMT 2018 Job finished. TimeTaking 125.08 Used memory is bytes: 25419120