Sun 23 Dec 22:22:59 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2itb-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2itb-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2itb-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2itb-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-3.8-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:23:07 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/hancs/ArpWArp/wArpResults/WorkingDir/2itb-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2itb-3.8-parrot-hancs/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 230 and 0 Target number of residues in the AU: 230 Target solvent content: 0.6561 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-3.8-parrot-hancs.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-3.8-parrot-hancs.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 3.801 Wilson plot Bfac: 82.18 3834 reflections ( 99.61 % complete ) and 0 restraints for refining 3656 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3598 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4066 (Rfree = 0.000) for 3656 atoms. Found 11 (20 requested) and removed 31 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.01 4.72 Search for helices and strands: 0 residues in 0 chains, 3755 seeds are put forward NCS extension: 0 residues added, 3755 seeds are put forward Round 1: 85 peptides, 19 chains. Longest chain 8 peptides. Score 0.220 Round 2: 99 peptides, 18 chains. Longest chain 16 peptides. Score 0.318 Round 3: 108 peptides, 18 chains. Longest chain 12 peptides. Score 0.363 Round 4: 115 peptides, 19 chains. Longest chain 12 peptides. Score 0.375 Round 5: 130 peptides, 20 chains. Longest chain 17 peptides. Score 0.423 Taking the results from Round 5 Chains 20, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 6875 restraints for refining 2792 atoms. 6455 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3798 (Rfree = 0.000) for 2792 atoms. Found 10 (15 requested) and removed 28 (7 requested) atoms. Cycle 2: After refmac, R = 0.3778 (Rfree = 0.000) for 2712 atoms. Found 12 (15 requested) and removed 22 (7 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.3706 (Rfree = 0.000) for 2671 atoms. Found 4 (14 requested) and removed 20 (7 requested) atoms. Cycle 4: After refmac, R = 0.3541 (Rfree = 0.000) for 2593 atoms. Found 5 (14 requested) and removed 21 (7 requested) atoms. Cycle 5: After refmac, R = 0.3675 (Rfree = 0.000) for 2549 atoms. Found 3 (14 requested) and removed 30 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.91 4.60 Search for helices and strands: 0 residues in 0 chains, 2670 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2690 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 9 peptides. Score 0.240 Round 2: 130 peptides, 23 chains. Longest chain 13 peptides. Score 0.363 Round 3: 124 peptides, 20 chains. Longest chain 13 peptides. Score 0.396 Round 4: 139 peptides, 21 chains. Longest chain 14 peptides. Score 0.443 Round 5: 141 peptides, 20 chains. Longest chain 14 peptides. Score 0.470 Taking the results from Round 5 Chains 21, Residues 121, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 4916 restraints for refining 2340 atoms. 4393 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3565 (Rfree = 0.000) for 2340 atoms. Found 12 (12 requested) and removed 36 (6 requested) atoms. Cycle 7: After refmac, R = 0.3527 (Rfree = 0.000) for 2282 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Cycle 8: After refmac, R = 0.3336 (Rfree = 0.000) for 2235 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 9: After refmac, R = 0.3258 (Rfree = 0.000) for 2206 atoms. Found 11 (12 requested) and removed 14 (6 requested) atoms. Cycle 10: After refmac, R = 0.3220 (Rfree = 0.000) for 2184 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.97 4.67 Search for helices and strands: 0 residues in 0 chains, 2309 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2328 seeds are put forward Round 1: 89 peptides, 17 chains. Longest chain 9 peptides. Score 0.289 Round 2: 128 peptides, 20 chains. Longest chain 15 peptides. Score 0.414 Round 3: 122 peptides, 19 chains. Longest chain 16 peptides. Score 0.407 Round 4: 117 peptides, 17 chains. Longest chain 17 peptides. Score 0.425 Round 5: 125 peptides, 19 chains. Longest chain 13 peptides. Score 0.421 Taking the results from Round 4 Chains 17, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 4656 restraints for refining 2127 atoms. 4273 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3697 (Rfree = 0.000) for 2127 atoms. Found 11 (11 requested) and removed 24 (5 requested) atoms. Cycle 12: After refmac, R = 0.3699 (Rfree = 0.000) for 2096 atoms. Found 11 (11 requested) and removed 23 (5 requested) atoms. Cycle 13: After refmac, R = 0.3614 (Rfree = 0.000) for 2058 atoms. Found 6 (11 requested) and removed 20 (5 requested) atoms. Cycle 14: After refmac, R = 0.3285 (Rfree = 0.000) for 2029 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 15: After refmac, R = 0.3401 (Rfree = 0.000) for 2014 atoms. Found 9 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 4.01 4.72 Search for helices and strands: 0 residues in 0 chains, 2125 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 2152 seeds are put forward Round 1: 101 peptides, 19 chains. Longest chain 12 peptides. Score 0.306 Round 2: 116 peptides, 20 chains. Longest chain 11 peptides. Score 0.359 Round 3: 126 peptides, 20 chains. Longest chain 14 peptides. Score 0.405 Round 4: 123 peptides, 20 chains. Longest chain 10 peptides. Score 0.391 Round 5: 125 peptides, 20 chains. Longest chain 12 peptides. Score 0.401 Taking the results from Round 3 Chains 20, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 4115 restraints for refining 2012 atoms. 3711 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3673 (Rfree = 0.000) for 2012 atoms. Found 11 (11 requested) and removed 32 (5 requested) atoms. Cycle 17: After refmac, R = 0.3569 (Rfree = 0.000) for 1973 atoms. Found 10 (10 requested) and removed 26 (5 requested) atoms. Cycle 18: After refmac, R = 0.3511 (Rfree = 0.000) for 1942 atoms. Found 10 (10 requested) and removed 21 (5 requested) atoms. Cycle 19: After refmac, R = 0.3637 (Rfree = 0.000) for 1919 atoms. Found 10 (10 requested) and removed 22 (5 requested) atoms. Cycle 20: After refmac, R = 0.3528 (Rfree = 0.000) for 1890 atoms. Found 7 (10 requested) and removed 18 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.10 4.83 Search for helices and strands: 0 residues in 0 chains, 1976 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 1995 seeds are put forward Round 1: 98 peptides, 20 chains. Longest chain 8 peptides. Score 0.268 Round 2: 114 peptides, 21 chains. Longest chain 10 peptides. Score 0.328 Round 3: 122 peptides, 19 chains. Longest chain 12 peptides. Score 0.407 Round 4: 123 peptides, 21 chains. Longest chain 9 peptides. Score 0.371 Round 5: 125 peptides, 21 chains. Longest chain 13 peptides. Score 0.380 Taking the results from Round 3 Chains 19, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 3882 restraints for refining 1963 atoms. 3489 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3503 (Rfree = 0.000) for 1963 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 22: After refmac, R = 0.3608 (Rfree = 0.000) for 1944 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. Cycle 23: After refmac, R = 0.3434 (Rfree = 0.000) for 1923 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. Cycle 24: After refmac, R = 0.3432 (Rfree = 0.000) for 1900 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 25: After refmac, R = 0.3486 (Rfree = 0.000) for 1885 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 4.06 4.78 Search for helices and strands: 0 residues in 0 chains, 1962 seeds are put forward NCS extension: 4 residues added (0 deleted due to clashes), 1966 seeds are put forward Round 1: 95 peptides, 20 chains. Longest chain 8 peptides. Score 0.252 Round 2: 122 peptides, 19 chains. Longest chain 11 peptides. Score 0.407 Round 3: 123 peptides, 21 chains. Longest chain 9 peptides. Score 0.371 Round 4: 120 peptides, 20 chains. Longest chain 11 peptides. Score 0.378 Round 5: 131 peptides, 21 chains. Longest chain 16 peptides. Score 0.408 Taking the results from Round 5 Chains 21, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 4316 restraints for refining 2075 atoms. 3897 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3649 (Rfree = 0.000) for 2075 atoms. Found 11 (11 requested) and removed 26 (5 requested) atoms. Cycle 27: After refmac, R = 0.3304 (Rfree = 0.000) for 2038 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 28: After refmac, R = 0.3225 (Rfree = 0.000) for 2020 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 29: After refmac, R = 0.3373 (Rfree = 0.000) for 2003 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 30: After refmac, R = 0.2714 (Rfree = 0.000) for 1984 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.86 4.54 Search for helices and strands: 0 residues in 0 chains, 2056 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 2079 seeds are put forward Round 1: 100 peptides, 20 chains. Longest chain 9 peptides. Score 0.279 Round 2: 117 peptides, 22 chains. Longest chain 12 peptides. Score 0.322 Round 3: 120 peptides, 20 chains. Longest chain 13 peptides. Score 0.378 Round 4: 111 peptides, 20 chains. Longest chain 12 peptides. Score 0.334 Round 5: 121 peptides, 21 chains. Longest chain 10 peptides. Score 0.362 Taking the results from Round 3 Chains 20, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 4075 restraints for refining 1967 atoms. 3695 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3349 (Rfree = 0.000) for 1967 atoms. Found 10 (10 requested) and removed 29 (5 requested) atoms. Cycle 32: After refmac, R = 0.3212 (Rfree = 0.000) for 1921 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 33: After refmac, R = 0.3410 (Rfree = 0.000) for 1907 atoms. Found 7 (10 requested) and removed 22 (5 requested) atoms. Cycle 34: After refmac, R = 0.2920 (Rfree = 0.000) for 1872 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.3255 (Rfree = 0.000) for 1866 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.88 4.57 Search for helices and strands: 0 residues in 0 chains, 1982 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 1996 seeds are put forward Round 1: 80 peptides, 17 chains. Longest chain 7 peptides. Score 0.239 Round 2: 102 peptides, 18 chains. Longest chain 11 peptides. Score 0.333 Round 3: 95 peptides, 17 chains. Longest chain 13 peptides. Score 0.320 Round 4: 102 peptides, 20 chains. Longest chain 9 peptides. Score 0.289 Round 5: 107 peptides, 20 chains. Longest chain 15 peptides. Score 0.315 Taking the results from Round 2 Chains 18, Residues 84, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 3509 restraints for refining 1725 atoms. 3191 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3441 (Rfree = 0.000) for 1725 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 37: After refmac, R = 0.3437 (Rfree = 0.000) for 1712 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 38: After refmac, R = 0.3002 (Rfree = 0.000) for 1701 atoms. Found 6 (9 requested) and removed 5 (4 requested) atoms. Cycle 39: After refmac, R = 0.3307 (Rfree = 0.000) for 1695 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 40: After refmac, R = 0.3196 (Rfree = 0.000) for 1694 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 4.32 5.08 Search for helices and strands: 0 residues in 0 chains, 1798 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 1801 seeds are put forward Round 1: 73 peptides, 15 chains. Longest chain 7 peptides. Score 0.248 Round 2: 97 peptides, 18 chains. Longest chain 9 peptides. Score 0.308 Round 3: 98 peptides, 15 chains. Longest chain 15 peptides. Score 0.379 Round 4: 102 peptides, 17 chains. Longest chain 11 peptides. Score 0.355 Round 5: 91 peptides, 17 chains. Longest chain 11 peptides. Score 0.299 Taking the results from Round 3 Chains 15, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 3565 restraints for refining 1753 atoms. 3248 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3489 (Rfree = 0.000) for 1753 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 42: After refmac, R = 0.3415 (Rfree = 0.000) for 1737 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. Cycle 43: After refmac, R = 0.2998 (Rfree = 0.000) for 1712 atoms. Found 6 (9 requested) and removed 8 (4 requested) atoms. Cycle 44: After refmac, R = 0.3246 (Rfree = 0.000) for 1706 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 45: After refmac, R = 0.3351 (Rfree = 0.000) for 1697 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.88 4.57 Search for helices and strands: 0 residues in 0 chains, 1780 seeds are put forward NCS extension: 0 residues added, 1780 seeds are put forward Round 1: 86 peptides, 16 chains. Longest chain 14 peptides. Score 0.296 Round 2: 86 peptides, 16 chains. Longest chain 11 peptides. Score 0.296 Round 3: 92 peptides, 17 chains. Longest chain 10 peptides. Score 0.304 Round 4: 94 peptides, 17 chains. Longest chain 13 peptides. Score 0.315 Round 5: 105 peptides, 18 chains. Longest chain 14 peptides. Score 0.348 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 87, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2itb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3834 reflections ( 99.61 % complete ) and 3564 restraints for refining 1757 atoms. 3210 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3585 (Rfree = 0.000) for 1757 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.3452 (Rfree = 0.000) for 1741 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.3427 (Rfree = 0.000) for 1729 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.3338 (Rfree = 0.000) for 1711 atoms. TimeTaking 33.78