null Mon 24 Dec 07:39:26 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-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ash-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ash-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ash-3.4-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-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ash-3.4-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 07:39:30 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-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ash-3.4-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 1136 and 0 Target number of residues in the AU: 1136 Target solvent content: 0.6503 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-3.4-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-3.4-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 3.400 Wilson plot Bfac: 78.27 23968 reflections ( 99.79 % complete ) and 0 restraints for refining 13483 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3390 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2947 (Rfree = 0.000) for 13483 atoms. Found 101 (101 requested) and removed 98 (50 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 13785 seeds are put forward NCS extension: 0 residues added, 13785 seeds are put forward Round 1: 623 peptides, 122 chains. Longest chain 11 peptides. Score 0.312 Round 2: 794 peptides, 127 chains. Longest chain 19 peptides. Score 0.451 Round 3: 834 peptides, 126 chains. Longest chain 19 peptides. Score 0.488 Round 4: 835 peptides, 123 chains. Longest chain 18 peptides. Score 0.500 Round 5: 872 peptides, 126 chains. Longest chain 22 peptides. Score 0.518 Taking the results from Round 5 Chains 126, Residues 746, Estimated correctness of the model 0.0 % 6 chains (38 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 25176 restraints for refining 11079 atoms. 22205 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2536 (Rfree = 0.000) for 11079 atoms. Found 51 (83 requested) and removed 62 (41 requested) atoms. Cycle 2: After refmac, R = 0.2329 (Rfree = 0.000) for 10907 atoms. Found 55 (83 requested) and removed 54 (41 requested) atoms. Cycle 3: After refmac, R = 0.2260 (Rfree = 0.000) for 10843 atoms. Found 48 (82 requested) and removed 50 (41 requested) atoms. Cycle 4: After refmac, R = 0.2127 (Rfree = 0.000) for 10800 atoms. Found 46 (81 requested) and removed 49 (40 requested) atoms. Cycle 5: After refmac, R = 0.2064 (Rfree = 0.000) for 10773 atoms. Found 29 (81 requested) and removed 49 (40 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 11195 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 11213 seeds are put forward Round 1: 768 peptides, 134 chains. Longest chain 15 peptides. Score 0.401 Round 2: 845 peptides, 120 chains. Longest chain 23 peptides. Score 0.518 Round 3: 865 peptides, 125 chains. Longest chain 20 peptides. Score 0.516 Round 4: 863 peptides, 121 chains. Longest chain 24 peptides. Score 0.529 Round 5: 866 peptides, 121 chains. Longest chain 27 peptides. Score 0.531 Taking the results from Round 5 Chains 127, Residues 745, Estimated correctness of the model 4.6 % 7 chains (85 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 24738 restraints for refining 11085 atoms. 21551 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2352 (Rfree = 0.000) for 11085 atoms. Found 62 (83 requested) and removed 71 (41 requested) atoms. Cycle 7: After refmac, R = 0.2199 (Rfree = 0.000) for 10993 atoms. Found 26 (83 requested) and removed 51 (41 requested) atoms. Cycle 8: After refmac, R = 0.2145 (Rfree = 0.000) for 10924 atoms. Found 36 (82 requested) and removed 48 (41 requested) atoms. Cycle 9: After refmac, R = 0.2086 (Rfree = 0.000) for 10892 atoms. Found 30 (82 requested) and removed 55 (41 requested) atoms. Cycle 10: After refmac, R = 0.2036 (Rfree = 0.000) for 10842 atoms. Found 23 (82 requested) and removed 50 (41 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 11188 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 11202 seeds are put forward Round 1: 778 peptides, 129 chains. Longest chain 17 peptides. Score 0.429 Round 2: 854 peptides, 126 chains. Longest chain 25 peptides. Score 0.504 Round 3: 866 peptides, 117 chains. Longest chain 21 peptides. Score 0.544 Round 4: 838 peptides, 115 chains. Longest chain 20 peptides. Score 0.530 Round 5: 858 peptides, 114 chains. Longest chain 21 peptides. Score 0.548 Taking the results from Round 5 Chains 116, Residues 744, Estimated correctness of the model 10.8 % 8 chains (61 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 24715 restraints for refining 11084 atoms. 21643 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2229 (Rfree = 0.000) for 11084 atoms. Found 59 (83 requested) and removed 61 (41 requested) atoms. Cycle 12: After refmac, R = 0.2085 (Rfree = 0.000) for 11014 atoms. Found 31 (83 requested) and removed 49 (41 requested) atoms. Cycle 13: After refmac, R = 0.2011 (Rfree = 0.000) for 10969 atoms. Found 22 (83 requested) and removed 47 (41 requested) atoms. Cycle 14: After refmac, R = 0.1969 (Rfree = 0.000) for 10925 atoms. Found 21 (82 requested) and removed 47 (41 requested) atoms. Cycle 15: After refmac, R = 0.1911 (Rfree = 0.000) for 10882 atoms. Found 15 (82 requested) and removed 41 (41 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 11216 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 11236 seeds are put forward Round 1: 770 peptides, 133 chains. Longest chain 17 peptides. Score 0.407 Round 2: 825 peptides, 120 chains. Longest chain 19 peptides. Score 0.502 Round 3: 850 peptides, 117 chains. Longest chain 20 peptides. Score 0.532 Round 4: 866 peptides, 116 chains. Longest chain 29 peptides. Score 0.548 Round 5: 863 peptides, 115 chains. Longest chain 26 peptides. Score 0.549 Taking the results from Round 5 Chains 117, Residues 748, Estimated correctness of the model 11.2 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 25024 restraints for refining 11084 atoms. 22084 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2201 (Rfree = 0.000) for 11084 atoms. Found 67 (83 requested) and removed 51 (41 requested) atoms. Cycle 17: After refmac, R = 0.2064 (Rfree = 0.000) for 11055 atoms. Found 39 (83 requested) and removed 51 (41 requested) atoms. Cycle 18: After refmac, R = 0.1996 (Rfree = 0.000) for 11021 atoms. Found 27 (83 requested) and removed 53 (41 requested) atoms. Cycle 19: After refmac, R = 0.1956 (Rfree = 0.000) for 10980 atoms. Found 35 (83 requested) and removed 45 (41 requested) atoms. Cycle 20: After refmac, R = 0.1886 (Rfree = 0.000) for 10947 atoms. Found 29 (82 requested) and removed 43 (41 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 3.31 Search for helices and strands: 0 residues in 0 chains, 11361 seeds are put forward NCS extension: 42 residues added (2 deleted due to clashes), 11403 seeds are put forward Round 1: 690 peptides, 126 chains. Longest chain 13 peptides. Score 0.361 Round 2: 775 peptides, 125 chains. Longest chain 14 peptides. Score 0.442 Round 3: 812 peptides, 119 chains. Longest chain 15 peptides. Score 0.495 Round 4: 799 peptides, 114 chains. Longest chain 21 peptides. Score 0.503 Round 5: 818 peptides, 118 chains. Longest chain 21 peptides. Score 0.504 Taking the results from Round 5 Chains 121, Residues 700, Estimated correctness of the model 0.0 % 11 chains (69 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 24971 restraints for refining 11085 atoms. 22059 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2174 (Rfree = 0.000) for 11085 atoms. Found 63 (83 requested) and removed 56 (41 requested) atoms. Cycle 22: After refmac, R = 0.2058 (Rfree = 0.000) for 11037 atoms. Found 32 (83 requested) and removed 44 (41 requested) atoms. Cycle 23: After refmac, R = 0.2002 (Rfree = 0.000) for 10996 atoms. Found 37 (83 requested) and removed 45 (41 requested) atoms. Cycle 24: After refmac, R = 0.1960 (Rfree = 0.000) for 10963 atoms. Found 30 (82 requested) and removed 43 (41 requested) atoms. Cycle 25: After refmac, R = 0.1914 (Rfree = 0.000) for 10938 atoms. Found 24 (82 requested) and removed 42 (41 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.31 Search for helices and strands: 0 residues in 0 chains, 11321 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 11339 seeds are put forward Round 1: 691 peptides, 127 chains. Longest chain 16 peptides. Score 0.358 Round 2: 738 peptides, 113 chains. Longest chain 18 peptides. Score 0.455 Round 3: 757 peptides, 112 chains. Longest chain 20 peptides. Score 0.475 Round 4: 754 peptides, 107 chains. Longest chain 20 peptides. Score 0.491 Round 5: 776 peptides, 112 chains. Longest chain 20 peptides. Score 0.491 Taking the results from Round 5 Chains 113, Residues 664, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 25758 restraints for refining 11086 atoms. 23181 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2144 (Rfree = 0.000) for 11086 atoms. Found 58 (83 requested) and removed 43 (41 requested) atoms. Cycle 27: After refmac, R = 0.2003 (Rfree = 0.000) for 11059 atoms. Found 42 (83 requested) and removed 45 (41 requested) atoms. Cycle 28: After refmac, R = 0.1951 (Rfree = 0.000) for 11020 atoms. Found 49 (83 requested) and removed 45 (41 requested) atoms. Cycle 29: After refmac, R = 0.1894 (Rfree = 0.000) for 11006 atoms. Found 42 (83 requested) and removed 45 (41 requested) atoms. Cycle 30: After refmac, R = 0.1840 (Rfree = 0.000) for 10986 atoms. Found 34 (83 requested) and removed 46 (41 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.29 Search for helices and strands: 0 residues in 0 chains, 11374 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 11391 seeds are put forward Round 1: 658 peptides, 124 chains. Longest chain 13 peptides. Score 0.338 Round 2: 716 peptides, 115 chains. Longest chain 18 peptides. Score 0.428 Round 3: 715 peptides, 107 chains. Longest chain 18 peptides. Score 0.458 Round 4: 752 peptides, 110 chains. Longest chain 16 peptides. Score 0.479 Round 5: 771 peptides, 120 chains. Longest chain 17 peptides. Score 0.457 Taking the results from Round 4 Chains 110, Residues 642, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 25667 restraints for refining 11085 atoms. 23190 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2044 (Rfree = 0.000) for 11085 atoms. Found 68 (83 requested) and removed 43 (41 requested) atoms. Cycle 32: After refmac, R = 0.1999 (Rfree = 0.000) for 11081 atoms. Found 54 (83 requested) and removed 45 (41 requested) atoms. Cycle 33: After refmac, R = 0.1898 (Rfree = 0.000) for 11069 atoms. Found 33 (83 requested) and removed 47 (41 requested) atoms. Cycle 34: After refmac, R = 0.1888 (Rfree = 0.000) for 11040 atoms. Found 34 (83 requested) and removed 41 (41 requested) atoms. Cycle 35: After refmac, R = 0.1847 (Rfree = 0.000) for 11018 atoms. Found 27 (83 requested) and removed 41 (41 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 11417 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 11433 seeds are put forward Round 1: 606 peptides, 117 chains. Longest chain 13 peptides. Score 0.316 Round 2: 705 peptides, 119 chains. Longest chain 16 peptides. Score 0.403 Round 3: 707 peptides, 111 chains. Longest chain 16 peptides. Score 0.436 Round 4: 735 peptides, 108 chains. Longest chain 20 peptides. Score 0.472 Round 5: 706 peptides, 106 chains. Longest chain 19 peptides. Score 0.454 Taking the results from Round 4 Chains 109, Residues 627, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 25510 restraints for refining 11084 atoms. 23030 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2098 (Rfree = 0.000) for 11084 atoms. Found 66 (83 requested) and removed 45 (41 requested) atoms. Cycle 37: After refmac, R = 0.1990 (Rfree = 0.000) for 11066 atoms. Found 45 (83 requested) and removed 43 (41 requested) atoms. Cycle 38: After refmac, R = 0.1910 (Rfree = 0.000) for 11048 atoms. Found 34 (83 requested) and removed 43 (41 requested) atoms. Cycle 39: After refmac, R = 0.1862 (Rfree = 0.000) for 11029 atoms. Found 30 (83 requested) and removed 42 (41 requested) atoms. Cycle 40: After refmac, R = 0.1827 (Rfree = 0.000) for 11010 atoms. Found 26 (83 requested) and removed 41 (41 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 3.31 Search for helices and strands: 0 residues in 0 chains, 11369 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 11390 seeds are put forward Round 1: 637 peptides, 124 chains. Longest chain 13 peptides. Score 0.317 Round 2: 698 peptides, 116 chains. Longest chain 16 peptides. Score 0.408 Round 3: 703 peptides, 112 chains. Longest chain 18 peptides. Score 0.429 Round 4: 705 peptides, 110 chains. Longest chain 19 peptides. Score 0.438 Round 5: 701 peptides, 107 chains. Longest chain 22 peptides. Score 0.446 Taking the results from Round 5 Chains 109, Residues 594, Estimated correctness of the model 0.0 % 7 chains (63 residues) have been docked in sequence ------------------------------------------------------ 23968 reflections ( 99.79 % complete ) and 25239 restraints for refining 11084 atoms. 22721 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2056 (Rfree = 0.000) for 11084 atoms. Found 71 (83 requested) and removed 50 (41 requested) atoms. Cycle 42: After refmac, R = 0.1964 (Rfree = 0.000) for 11058 atoms. Found 48 (83 requested) and removed 43 (41 requested) atoms. Cycle 43: After refmac, R = 0.1877 (Rfree = 0.000) for 11040 atoms. Found 36 (83 requested) and removed 44 (41 requested) atoms. Cycle 44: After refmac, R = 0.1865 (Rfree = 0.000) for 11018 atoms. Found 46 (83 requested) and removed 43 (41 requested) atoms. Cycle 45: After refmac, R = 0.1808 (Rfree = 0.000) for 11000 atoms. Found 33 (83 requested) and removed 43 (41 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 3.29 Search for helices and strands: 0 residues in 0 chains, 11381 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 11394 seeds are put forward Round 1: 568 peptides, 117 chains. Longest chain 11 peptides. Score 0.277 Round 2: 622 peptides, 103 chains. Longest chain 15 peptides. Score 0.391 Round 3: 626 peptides, 100 chains. Longest chain 19 peptides. Score 0.407 Round 4: 649 peptides, 106 chains. Longest chain 13 peptides. Score 0.403 Round 5: 644 peptides, 102 chains. Longest chain 17 peptides. Score 0.415 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 105, Residues 542, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2ash-3_warpNtrace.pdb as input Building loops using Loopy2018 105 chains (542 residues) following loop building 2 chains (23 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 23968 reflections ( 99.79 % complete ) and 26122 restraints for refining 11084 atoms. 23980 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1991 (Rfree = 0.000) for 11084 atoms. Found 0 (83 requested) and removed 41 (41 requested) atoms. Cycle 47: After refmac, R = 0.1935 (Rfree = 0.000) for 11003 atoms. Found 0 (83 requested) and removed 41 (41 requested) atoms. Cycle 48: After refmac, R = 0.1891 (Rfree = 0.000) for 10950 atoms. Found 0 (82 requested) and removed 41 (41 requested) atoms. Cycle 49: After refmac, R = 0.1818 (Rfree = 0.000) for 10895 atoms. Found 0 (82 requested) and removed 41 (41 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:37:40 GMT 2018 Job finished. TimeTaking 118.24 Used memory is bytes: 23925888