Mon 24 Dec 00:03:41 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2itb-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2itb-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2itb-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-3.6-parrot-mrncs ############### 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 00:03:46 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/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-3.6-parrot-mrncs/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-mrncs.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-mrncs.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 3662 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3529 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3761 (Rfree = 0.000) for 3662 atoms. Found 15 (23 requested) and removed 51 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 4.18 Search for helices and strands: 0 residues in 0 chains, 3746 seeds are put forward NCS extension: 0 residues added, 3746 seeds are put forward Round 1: 86 peptides, 19 chains. Longest chain 7 peptides. Score 0.226 Round 2: 130 peptides, 25 chains. Longest chain 9 peptides. Score 0.323 Round 3: 130 peptides, 24 chains. Longest chain 9 peptides. Score 0.343 Round 4: 153 peptides, 27 chains. Longest chain 9 peptides. Score 0.390 Round 5: 152 peptides, 26 chains. Longest chain 10 peptides. Score 0.404 Taking the results from Round 5 Chains 26, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 6972 restraints for refining 2869 atoms. 6494 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3540 (Rfree = 0.000) for 2869 atoms. Found 10 (18 requested) and removed 22 (9 requested) atoms. Cycle 2: After refmac, R = 0.3714 (Rfree = 0.000) for 2797 atoms. Found 7 (18 requested) and removed 32 (9 requested) atoms. Cycle 3: After refmac, R = 0.3504 (Rfree = 0.000) for 2725 atoms. Found 13 (17 requested) and removed 21 (8 requested) atoms. Cycle 4: After refmac, R = 0.3276 (Rfree = 0.000) for 2676 atoms. Found 11 (17 requested) and removed 16 (8 requested) atoms. Cycle 5: After refmac, R = 0.3454 (Rfree = 0.000) for 2645 atoms. Found 6 (17 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 4.16 Search for helices and strands: 0 residues in 0 chains, 2757 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2768 seeds are put forward Round 1: 98 peptides, 21 chains. Longest chain 7 peptides. Score 0.246 Round 2: 132 peptides, 24 chains. Longest chain 11 peptides. Score 0.352 Round 3: 135 peptides, 23 chains. Longest chain 11 peptides. Score 0.386 Round 4: 139 peptides, 23 chains. Longest chain 13 peptides. Score 0.404 Round 5: 140 peptides, 22 chains. Longest chain 11 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 5271 restraints for refining 2348 atoms. 4821 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3580 (Rfree = 0.000) for 2348 atoms. Found 14 (15 requested) and removed 45 (7 requested) atoms. Cycle 7: After refmac, R = 0.3425 (Rfree = 0.000) for 2296 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Cycle 8: After refmac, R = 0.3578 (Rfree = 0.000) for 2259 atoms. Found 12 (14 requested) and removed 20 (7 requested) atoms. Cycle 9: After refmac, R = 0.3622 (Rfree = 0.000) for 2238 atoms. Found 14 (14 requested) and removed 30 (7 requested) atoms. Cycle 10: After refmac, R = 0.3570 (Rfree = 0.000) for 2203 atoms. Found 13 (14 requested) and removed 18 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.47 4.08 Search for helices and strands: 0 residues in 0 chains, 2358 seeds are put forward NCS extension: 0 residues added, 2358 seeds are put forward Round 1: 123 peptides, 25 chains. Longest chain 8 peptides. Score 0.288 Round 2: 142 peptides, 26 chains. Longest chain 11 peptides. Score 0.359 Round 3: 145 peptides, 24 chains. Longest chain 12 peptides. Score 0.412 Round 4: 150 peptides, 24 chains. Longest chain 13 peptides. Score 0.433 Round 5: 147 peptides, 23 chains. Longest chain 16 peptides. Score 0.439 Taking the results from Round 5 Chains 23, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 4828 restraints for refining 2264 atoms. 4355 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3704 (Rfree = 0.000) for 2264 atoms. Found 13 (14 requested) and removed 27 (7 requested) atoms. Cycle 12: After refmac, R = 0.3706 (Rfree = 0.000) for 2220 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 13: After refmac, R = 0.3821 (Rfree = 0.000) for 2202 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 14: After refmac, R = 0.3570 (Rfree = 0.000) for 2175 atoms. Found 11 (14 requested) and removed 18 (7 requested) atoms. Cycle 15: After refmac, R = 0.3570 (Rfree = 0.000) for 2149 atoms. Found 11 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.47 4.08 Search for helices and strands: 0 residues in 0 chains, 2295 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2311 seeds are put forward Round 1: 107 peptides, 22 chains. Longest chain 10 peptides. Score 0.271 Round 2: 131 peptides, 23 chains. Longest chain 13 peptides. Score 0.368 Round 3: 146 peptides, 26 chains. Longest chain 11 peptides. Score 0.377 Round 4: 147 peptides, 25 chains. Longest chain 11 peptides. Score 0.401 Round 5: 148 peptides, 24 chains. Longest chain 13 peptides. Score 0.425 Taking the results from Round 5 Chains 24, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 4416 restraints for refining 2132 atoms. 3944 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3721 (Rfree = 0.000) for 2132 atoms. Found 13 (13 requested) and removed 31 (6 requested) atoms. Cycle 17: After refmac, R = 0.3786 (Rfree = 0.000) for 2093 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 18: After refmac, R = 0.3813 (Rfree = 0.000) for 2066 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 19: After refmac, R = 0.3639 (Rfree = 0.000) for 2035 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 20: After refmac, R = 0.3618 (Rfree = 0.000) for 2030 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 4.01 Search for helices and strands: 0 residues in 0 chains, 2134 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2148 seeds are put forward Round 1: 108 peptides, 23 chains. Longest chain 8 peptides. Score 0.255 Round 2: 126 peptides, 22 chains. Longest chain 13 peptides. Score 0.365 Round 3: 130 peptides, 22 chains. Longest chain 10 peptides. Score 0.383 Round 4: 130 peptides, 22 chains. Longest chain 11 peptides. Score 0.383 Round 5: 132 peptides, 22 chains. Longest chain 13 peptides. Score 0.392 Taking the results from Round 5 Chains 22, Residues 110, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 4104 restraints for refining 2026 atoms. 3665 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3828 (Rfree = 0.000) for 2026 atoms. Found 12 (12 requested) and removed 31 (6 requested) atoms. Cycle 22: After refmac, R = 0.3798 (Rfree = 0.000) for 1999 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 23: After refmac, R = 0.3820 (Rfree = 0.000) for 1975 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 24: After refmac, R = 0.3721 (Rfree = 0.000) for 1960 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 25: After refmac, R = 0.3745 (Rfree = 0.000) for 1942 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.47 4.08 Search for helices and strands: 0 residues in 0 chains, 2035 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2050 seeds are put forward Round 1: 119 peptides, 25 chains. Longest chain 8 peptides. Score 0.268 Round 2: 133 peptides, 24 chains. Longest chain 7 peptides. Score 0.357 Round 3: 140 peptides, 24 chains. Longest chain 9 peptides. Score 0.389 Round 4: 146 peptides, 24 chains. Longest chain 15 peptides. Score 0.416 Round 5: 151 peptides, 25 chains. Longest chain 9 peptides. Score 0.419 Taking the results from Round 5 Chains 25, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 4264 restraints for refining 2103 atoms. 3785 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3754 (Rfree = 0.000) for 2103 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 27: After refmac, R = 0.3689 (Rfree = 0.000) for 2054 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 28: After refmac, R = 0.3711 (Rfree = 0.000) for 2026 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 29: After refmac, R = 0.3596 (Rfree = 0.000) for 2001 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 30: After refmac, R = 0.3611 (Rfree = 0.000) for 1985 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 4.14 Search for helices and strands: 0 residues in 0 chains, 2078 seeds are put forward NCS extension: 0 residues added, 2078 seeds are put forward Round 1: 84 peptides, 19 chains. Longest chain 7 peptides. Score 0.214 Round 2: 118 peptides, 22 chains. Longest chain 8 peptides. Score 0.327 Round 3: 121 peptides, 22 chains. Longest chain 10 peptides. Score 0.341 Round 4: 120 peptides, 22 chains. Longest chain 11 peptides. Score 0.336 Round 5: 130 peptides, 22 chains. Longest chain 11 peptides. Score 0.383 Taking the results from Round 5 Chains 22, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 4309 restraints for refining 2027 atoms. 3899 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3866 (Rfree = 0.000) for 2027 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 32: After refmac, R = 0.3646 (Rfree = 0.000) for 1996 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 33: After refmac, R = 0.3731 (Rfree = 0.000) for 1974 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 34: After refmac, R = 0.3732 (Rfree = 0.000) for 1961 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 35: After refmac, R = 0.3632 (Rfree = 0.000) for 1944 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.51 4.13 Search for helices and strands: 0 residues in 0 chains, 2030 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2045 seeds are put forward Round 1: 89 peptides, 18 chains. Longest chain 9 peptides. Score 0.266 Round 2: 104 peptides, 20 chains. Longest chain 10 peptides. Score 0.299 Round 3: 96 peptides, 17 chains. Longest chain 8 peptides. Score 0.325 Round 4: 103 peptides, 17 chains. Longest chain 15 peptides. Score 0.360 Round 5: 115 peptides, 20 chains. Longest chain 10 peptides. Score 0.354 Taking the results from Round 4 Chains 17, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 3889 restraints for refining 1878 atoms. 3562 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3897 (Rfree = 0.000) for 1878 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 37: After refmac, R = 0.3873 (Rfree = 0.000) for 1859 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 38: After refmac, R = 0.3843 (Rfree = 0.000) for 1844 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 39: After refmac, R = 0.3838 (Rfree = 0.000) for 1840 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 40: After refmac, R = 0.3657 (Rfree = 0.000) for 1828 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 4.21 Search for helices and strands: 0 residues in 0 chains, 1907 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 1927 seeds are put forward Round 1: 84 peptides, 18 chains. Longest chain 7 peptides. Score 0.238 Round 2: 119 peptides, 23 chains. Longest chain 10 peptides. Score 0.310 Round 3: 109 peptides, 21 chains. Longest chain 9 peptides. Score 0.303 Round 4: 112 peptides, 21 chains. Longest chain 10 peptides. Score 0.318 Round 5: 109 peptides, 22 chains. Longest chain 10 peptides. Score 0.281 Taking the results from Round 4 Chains 21, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4499 reflections ( 99.67 % complete ) and 3689 restraints for refining 1778 atoms. 3346 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3951 (Rfree = 0.000) for 1778 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 42: After refmac, R = 0.3919 (Rfree = 0.000) for 1762 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 43: After refmac, R = 0.3837 (Rfree = 0.000) for 1754 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 44: After refmac, R = 0.3978 (Rfree = 0.000) for 1743 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 45: After refmac, R = 0.3891 (Rfree = 0.000) for 1733 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 4.10 Search for helices and strands: 0 residues in 0 chains, 1834 seeds are put forward NCS extension: 0 residues added, 1834 seeds are put forward Round 1: 77 peptides, 17 chains. Longest chain 7 peptides. Score 0.222 Round 2: 83 peptides, 18 chains. Longest chain 6 peptides. Score 0.232 Round 3: 93 peptides, 19 chains. Longest chain 6 peptides. Score 0.264 Round 4: 88 peptides, 16 chains. Longest chain 10 peptides. Score 0.306 Round 5: 99 peptides, 16 chains. Longest chain 11 peptides. Score 0.362 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 83, 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 3553 restraints for refining 1747 atoms. 3237 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3983 (Rfree = 0.000) for 1747 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.3874 (Rfree = 0.000) for 1732 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.3891 (Rfree = 0.000) for 1721 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.3891 (Rfree = 0.000) for 1708 atoms. TimeTaking 31.7