Mon 24 Dec 07:55:46 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 2itb-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2itb-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2itb-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2itb-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/2itb-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2itb-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 07:55:50 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/2itb-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2itb-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 236 and 0 Target number of residues in the AU: 236 Target solvent content: 0.6471 Checking the provided sequence file Detected sequence length: 206 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 412 Adjusted target solvent content: 0.38 Input MTZ file: 2itb-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: 19 Cell parameters: 61.232 70.168 84.235 90.000 90.000 90.000 Input sequence file: 2itb-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 3296 target number of atoms Had to go as low as 0.60 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: 53.913 3.600 Wilson plot Bfac: 76.14 4499 reflections ( 99.67 % complete ) and 0 restraints for refining 3660 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3682 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4079 (Rfree = 0.000) for 3660 atoms. Found 18 (23 requested) and removed 59 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.63 4.27 Search for helices and strands: 0 residues in 0 chains, 3733 seeds are put forward NCS extension: 0 residues added, 3733 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 11 peptides. Score 0.269 Round 2: 105 peptides, 17 chains. Longest chain 11 peptides. Score 0.369 Round 3: 120 peptides, 19 chains. Longest chain 10 peptides. Score 0.398 Round 4: 117 peptides, 17 chains. Longest chain 11 peptides. Score 0.425 Round 5: 128 peptides, 18 chains. Longest chain 14 peptides. Score 0.453 Taking the results from Round 5 Chains 18, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 6432 restraints for refining 2749 atoms. 6010 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3943 (Rfree = 0.000) for 2749 atoms. Found 13 (17 requested) and removed 31 (8 requested) atoms. Cycle 2: After refmac, R = 0.3802 (Rfree = 0.000) for 2667 atoms. Found 10 (17 requested) and removed 21 (8 requested) atoms. Cycle 3: After refmac, R = 0.3814 (Rfree = 0.000) for 2592 atoms. Found 12 (17 requested) and removed 26 (8 requested) atoms. Cycle 4: After refmac, R = 0.3766 (Rfree = 0.000) for 2523 atoms. Found 14 (16 requested) and removed 28 (8 requested) atoms. Cycle 5: After refmac, R = 0.3683 (Rfree = 0.000) for 2462 atoms. Found 6 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 4.11 Search for helices and strands: 0 residues in 0 chains, 2575 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2590 seeds are put forward Round 1: 96 peptides, 19 chains. Longest chain 7 peptides. Score 0.280 Round 2: 137 peptides, 22 chains. Longest chain 22 peptides. Score 0.415 Round 3: 136 peptides, 20 chains. Longest chain 11 peptides. Score 0.449 Round 4: 136 peptides, 20 chains. Longest chain 16 peptides. Score 0.449 Round 5: 146 peptides, 18 chains. Longest chain 14 peptides. Score 0.526 Taking the results from Round 5 Chains 19, Residues 128, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 4677 restraints for refining 2278 atoms. 4151 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3775 (Rfree = 0.000) for 2278 atoms. Found 14 (14 requested) and removed 34 (7 requested) atoms. Cycle 7: After refmac, R = 0.3741 (Rfree = 0.000) for 2213 atoms. Found 14 (14 requested) and removed 25 (7 requested) atoms. Cycle 8: After refmac, R = 0.3742 (Rfree = 0.000) for 2183 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Cycle 9: After refmac, R = 0.3601 (Rfree = 0.000) for 2144 atoms. Found 12 (13 requested) and removed 12 (6 requested) atoms. Cycle 10: After refmac, R = 0.3579 (Rfree = 0.000) for 2117 atoms. Found 9 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.61 4.25 Search for helices and strands: 0 residues in 0 chains, 2232 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2245 seeds are put forward Round 1: 110 peptides, 21 chains. Longest chain 11 peptides. Score 0.308 Round 2: 140 peptides, 22 chains. Longest chain 13 peptides. Score 0.428 Round 3: 138 peptides, 22 chains. Longest chain 12 peptides. Score 0.419 Round 4: 140 peptides, 22 chains. Longest chain 15 peptides. Score 0.428 Round 5: 138 peptides, 21 chains. Longest chain 13 peptides. Score 0.439 Taking the results from Round 5 Chains 21, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 4345 restraints for refining 2105 atoms. 3898 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3719 (Rfree = 0.000) for 2105 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 12: After refmac, R = 0.3627 (Rfree = 0.000) for 2072 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 13: After refmac, R = 0.3622 (Rfree = 0.000) for 2035 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 14: After refmac, R = 0.3458 (Rfree = 0.000) for 2013 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 15: After refmac, R = 0.3347 (Rfree = 0.000) for 1999 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.56 4.19 Search for helices and strands: 0 residues in 0 chains, 2117 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2135 seeds are put forward Round 1: 110 peptides, 22 chains. Longest chain 8 peptides. Score 0.287 Round 2: 129 peptides, 22 chains. Longest chain 11 peptides. Score 0.379 Round 3: 123 peptides, 21 chains. Longest chain 11 peptides. Score 0.371 Round 4: 130 peptides, 22 chains. Longest chain 11 peptides. Score 0.383 Round 5: 139 peptides, 23 chains. Longest chain 10 peptides. Score 0.404 Taking the results from Round 5 Chains 23, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 4378 restraints for refining 2071 atoms. 3937 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3652 (Rfree = 0.000) for 2071 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 17: After refmac, R = 0.3685 (Rfree = 0.000) for 2053 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 18: After refmac, R = 0.3656 (Rfree = 0.000) for 2028 atoms. Found 13 (13 requested) and removed 24 (6 requested) atoms. Cycle 19: After refmac, R = 0.3569 (Rfree = 0.000) for 1993 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 20: After refmac, R = 0.3633 (Rfree = 0.000) for 1979 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.53 4.16 Search for helices and strands: 0 residues in 0 chains, 2073 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2084 seeds are put forward Round 1: 117 peptides, 22 chains. Longest chain 13 peptides. Score 0.322 Round 2: 140 peptides, 24 chains. Longest chain 12 peptides. Score 0.389 Round 3: 148 peptides, 23 chains. Longest chain 13 peptides. Score 0.443 Round 4: 157 peptides, 23 chains. Longest chain 13 peptides. Score 0.481 Round 5: 159 peptides, 23 chains. Longest chain 15 peptides. Score 0.489 Taking the results from Round 5 Chains 23, Residues 136, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 4282 restraints for refining 2112 atoms. 3707 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3951 (Rfree = 0.000) for 2112 atoms. Found 13 (13 requested) and removed 41 (6 requested) atoms. Cycle 22: After refmac, R = 0.3680 (Rfree = 0.000) for 2060 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 23: After refmac, R = 0.3489 (Rfree = 0.000) for 2023 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 24: After refmac, R = 0.3531 (Rfree = 0.000) for 2009 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 25: After refmac, R = 0.3480 (Rfree = 0.000) for 1991 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 4.18 Search for helices and strands: 0 residues in 0 chains, 2097 seeds are put forward NCS extension: 10 residues added (3 deleted due to clashes), 2107 seeds are put forward Round 1: 117 peptides, 24 chains. Longest chain 11 peptides. Score 0.279 Round 2: 134 peptides, 24 chains. Longest chain 11 peptides. Score 0.362 Round 3: 134 peptides, 26 chains. Longest chain 8 peptides. Score 0.321 Round 4: 138 peptides, 24 chains. Longest chain 14 peptides. Score 0.380 Round 5: 140 peptides, 22 chains. Longest chain 9 peptides. Score 0.428 Taking the results from Round 5 Chains 22, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 4527 restraints for refining 2092 atoms. 4077 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3819 (Rfree = 0.000) for 2092 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 27: After refmac, R = 0.3745 (Rfree = 0.000) for 2061 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 28: After refmac, R = 0.3740 (Rfree = 0.000) for 2036 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 29: After refmac, R = 0.3653 (Rfree = 0.000) for 2018 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 30: After refmac, R = 0.3719 (Rfree = 0.000) for 2005 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 4.21 Search for helices and strands: 0 residues in 0 chains, 2084 seeds are put forward NCS extension: 0 residues added, 2084 seeds are put forward Round 1: 103 peptides, 22 chains. Longest chain 12 peptides. Score 0.250 Round 2: 130 peptides, 23 chains. Longest chain 13 peptides. Score 0.363 Round 3: 134 peptides, 24 chains. Longest chain 13 peptides. Score 0.362 Round 4: 132 peptides, 19 chains. Longest chain 14 peptides. Score 0.451 Round 5: 128 peptides, 22 chains. Longest chain 13 peptides. Score 0.374 Taking the results from Round 4 Chains 19, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 4347 restraints for refining 2030 atoms. 3914 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3862 (Rfree = 0.000) for 2030 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 32: After refmac, R = 0.3900 (Rfree = 0.000) for 2002 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 33: After refmac, R = 0.3824 (Rfree = 0.000) for 1976 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 34: After refmac, R = 0.3719 (Rfree = 0.000) for 1954 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 35: After refmac, R = 0.3698 (Rfree = 0.000) for 1942 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 4.11 Search for helices and strands: 0 residues in 0 chains, 2025 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 2040 seeds are put forward Round 1: 86 peptides, 19 chains. Longest chain 6 peptides. Score 0.226 Round 2: 105 peptides, 21 chains. Longest chain 8 peptides. Score 0.283 Round 3: 102 peptides, 18 chains. Longest chain 8 peptides. Score 0.333 Round 4: 105 peptides, 18 chains. Longest chain 8 peptides. Score 0.348 Round 5: 107 peptides, 19 chains. Longest chain 12 peptides. Score 0.336 Taking the results from Round 4 Chains 18, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 3974 restraints for refining 1907 atoms. 3644 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3919 (Rfree = 0.000) for 1907 atoms. Found 12 (12 requested) and removed 30 (6 requested) atoms. Cycle 37: After refmac, R = 0.3765 (Rfree = 0.000) for 1874 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 38: After refmac, R = 0.3743 (Rfree = 0.000) for 1851 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.3723 (Rfree = 0.000) for 1849 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.3705 (Rfree = 0.000) for 1849 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.49 4.11 Search for helices and strands: 0 residues in 0 chains, 1934 seeds are put forward NCS extension: 0 residues added, 1934 seeds are put forward Round 1: 81 peptides, 16 chains. Longest chain 11 peptides. Score 0.269 Round 2: 103 peptides, 19 chains. Longest chain 11 peptides. Score 0.316 Round 3: 105 peptides, 18 chains. Longest chain 12 peptides. Score 0.348 Round 4: 110 peptides, 18 chains. Longest chain 12 peptides. Score 0.372 Round 5: 103 peptides, 15 chains. Longest chain 16 peptides. Score 0.403 Taking the results from Round 5 Chains 16, Residues 88, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 3690 restraints for refining 1837 atoms. 3310 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3772 (Rfree = 0.000) for 1837 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 42: After refmac, R = 0.3732 (Rfree = 0.000) for 1821 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 43: After refmac, R = 0.3715 (Rfree = 0.000) for 1812 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 44: After refmac, R = 0.3668 (Rfree = 0.000) for 1798 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 45: After refmac, R = 0.3655 (Rfree = 0.000) for 1791 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 4.21 Search for helices and strands: 0 residues in 0 chains, 1880 seeds are put forward NCS extension: 0 residues added, 1880 seeds are put forward Round 1: 96 peptides, 19 chains. Longest chain 11 peptides. Score 0.280 Round 2: 105 peptides, 17 chains. Longest chain 17 peptides. Score 0.369 Round 3: 113 peptides, 19 chains. Longest chain 9 peptides. Score 0.365 Round 4: 107 peptides, 18 chains. Longest chain 11 peptides. Score 0.358 Round 5: 111 peptides, 18 chains. Longest chain 14 peptides. Score 0.377 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2itb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4499 reflections ( 99.67 % complete ) and 3775 restraints for refining 1830 atoms. 3421 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3863 (Rfree = 0.000) for 1830 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.3707 (Rfree = 0.000) for 1811 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.3702 (Rfree = 0.000) for 1797 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.3683 (Rfree = 0.000) for 1782 atoms. TimeTaking 28.6