Mon 24 Dec 00:30:54 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-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2itb-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2itb-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-3.8-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-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-3.8-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 00:30:59 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/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2itb-3.8-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 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-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-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3296 target number of atoms Had to go as low as 0.65 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 3663 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3589 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3920 (Rfree = 0.000) for 3663 atoms. Found 9 (20 requested) and removed 33 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.97 4.67 Search for helices and strands: 0 residues in 0 chains, 3736 seeds are put forward NCS extension: 0 residues added, 3736 seeds are put forward Round 1: 41 peptides, 9 chains. Longest chain 8 peptides. Score 0.207 Round 2: 59 peptides, 12 chains. Longest chain 8 peptides. Score 0.241 Round 3: 81 peptides, 17 chains. Longest chain 9 peptides. Score 0.245 Round 4: 101 peptides, 20 chains. Longest chain 9 peptides. Score 0.284 Round 5: 102 peptides, 20 chains. Longest chain 9 peptides. Score 0.289 Taking the results from Round 5 Chains 20, Residues 82, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 7311 restraints for refining 2887 atoms. 7003 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3611 (Rfree = 0.000) for 2887 atoms. Found 7 (15 requested) and removed 25 (7 requested) atoms. Cycle 2: After refmac, R = 0.3447 (Rfree = 0.000) for 2823 atoms. Found 4 (15 requested) and removed 19 (7 requested) atoms. Cycle 3: After refmac, R = 0.3623 (Rfree = 0.000) for 2767 atoms. Found 1 (15 requested) and removed 24 (7 requested) atoms. Cycle 4: After refmac, R = 0.3626 (Rfree = 0.000) for 2716 atoms. Found 5 (15 requested) and removed 22 (7 requested) atoms. Cycle 5: After refmac, R = 0.3577 (Rfree = 0.000) for 2670 atoms. Found 5 (14 requested) and removed 19 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.90 4.59 Search for helices and strands: 0 residues in 0 chains, 2791 seeds are put forward NCS extension: 0 residues added, 2791 seeds are put forward Round 1: 70 peptides, 16 chains. Longest chain 9 peptides. Score 0.205 Round 2: 94 peptides, 19 chains. Longest chain 15 peptides. Score 0.270 Round 3: 112 peptides, 22 chains. Longest chain 9 peptides. Score 0.297 Round 4: 124 peptides, 22 chains. Longest chain 15 peptides. Score 0.355 Round 5: 131 peptides, 24 chains. Longest chain 15 peptides. Score 0.348 Taking the results from Round 4 Chains 22, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 4830 restraints for refining 2193 atoms. 4444 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3594 (Rfree = 0.000) for 2193 atoms. Found 5 (12 requested) and removed 18 (6 requested) atoms. Cycle 7: After refmac, R = 0.3519 (Rfree = 0.000) for 2155 atoms. Found 10 (11 requested) and removed 9 (5 requested) atoms. Cycle 8: After refmac, R = 0.3609 (Rfree = 0.000) for 2132 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 9: After refmac, R = 0.3391 (Rfree = 0.000) for 2110 atoms. Found 10 (11 requested) and removed 11 (5 requested) atoms. Cycle 10: After refmac, R = 0.3566 (Rfree = 0.000) for 2086 atoms. Found 7 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.93 4.63 Search for helices and strands: 0 residues in 0 chains, 2203 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 2214 seeds are put forward Round 1: 103 peptides, 23 chains. Longest chain 7 peptides. Score 0.228 Round 2: 133 peptides, 22 chains. Longest chain 14 peptides. Score 0.397 Round 3: 136 peptides, 24 chains. Longest chain 14 peptides. Score 0.371 Round 4: 142 peptides, 23 chains. Longest chain 17 peptides. Score 0.418 Round 5: 146 peptides, 22 chains. Longest chain 19 peptides. Score 0.454 Taking the results from Round 5 Chains 22, Residues 124, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 4049 restraints for refining 1974 atoms. 3575 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3593 (Rfree = 0.000) for 1974 atoms. Found 10 (10 requested) and removed 25 (5 requested) atoms. Cycle 12: After refmac, R = 0.3507 (Rfree = 0.000) for 1937 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 13: After refmac, R = 0.3475 (Rfree = 0.000) for 1917 atoms. Found 8 (10 requested) and removed 15 (5 requested) atoms. Cycle 14: After refmac, R = 0.3405 (Rfree = 0.000) for 1897 atoms. Found 4 (10 requested) and removed 10 (5 requested) atoms. Cycle 15: After refmac, R = 0.3479 (Rfree = 0.000) for 1871 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.94 4.64 Search for helices and strands: 0 residues in 0 chains, 1976 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 1998 seeds are put forward Round 1: 129 peptides, 25 chains. Longest chain 9 peptides. Score 0.318 Round 2: 141 peptides, 24 chains. Longest chain 12 peptides. Score 0.394 Round 3: 155 peptides, 25 chains. Longest chain 11 peptides. Score 0.436 Round 4: 150 peptides, 22 chains. Longest chain 24 peptides. Score 0.470 Round 5: 150 peptides, 21 chains. Longest chain 30 peptides. Score 0.489 Taking the results from Round 5 Chains 21, Residues 129, Estimated correctness of the model 0.0 % 1 chains (29 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 3962 restraints for refining 2095 atoms. 3329 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3572 (Rfree = 0.000) for 2095 atoms. Found 11 (11 requested) and removed 33 (5 requested) atoms. Cycle 17: After refmac, R = 0.3480 (Rfree = 0.000) for 2041 atoms. Found 11 (11 requested) and removed 22 (5 requested) atoms. Cycle 18: After refmac, R = 0.3330 (Rfree = 0.000) for 2006 atoms. Found 8 (11 requested) and removed 14 (5 requested) atoms. Cycle 19: After refmac, R = 0.3328 (Rfree = 0.000) for 1985 atoms. Found 5 (10 requested) and removed 12 (5 requested) atoms. Cycle 20: After refmac, R = 0.3291 (Rfree = 0.000) for 1963 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 4.24 4.99 Search for helices and strands: 0 residues in 0 chains, 2070 seeds are put forward NCS extension: 43 residues added (1 deleted due to clashes), 2113 seeds are put forward Round 1: 104 peptides, 19 chains. Longest chain 12 peptides. Score 0.321 Round 2: 119 peptides, 20 chains. Longest chain 12 peptides. Score 0.373 Round 3: 125 peptides, 20 chains. Longest chain 15 peptides. Score 0.401 Round 4: 133 peptides, 20 chains. Longest chain 24 peptides. Score 0.436 Round 5: 138 peptides, 20 chains. Longest chain 16 peptides. Score 0.458 Taking the results from Round 5 Chains 20, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 4439 restraints for refining 2098 atoms. 3987 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3770 (Rfree = 0.000) for 2098 atoms. Found 11 (11 requested) and removed 25 (5 requested) atoms. Cycle 22: After refmac, R = 0.3340 (Rfree = 0.000) for 2071 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 23: After refmac, R = 0.3470 (Rfree = 0.000) for 2053 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 24: After refmac, R = 0.3446 (Rfree = 0.000) for 2026 atoms. Found 11 (11 requested) and removed 26 (5 requested) atoms. Cycle 25: After refmac, R = 0.3405 (Rfree = 0.000) for 1999 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.92 4.61 Search for helices and strands: 0 residues in 0 chains, 2102 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2120 seeds are put forward Round 1: 103 peptides, 21 chains. Longest chain 9 peptides. Score 0.272 Round 2: 118 peptides, 21 chains. Longest chain 13 peptides. Score 0.347 Round 3: 123 peptides, 20 chains. Longest chain 17 peptides. Score 0.391 Round 4: 124 peptides, 20 chains. Longest chain 19 peptides. Score 0.396 Round 5: 122 peptides, 22 chains. Longest chain 12 peptides. Score 0.346 Taking the results from Round 4 Chains 22, Residues 104, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 4203 restraints for refining 2090 atoms. 3743 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3560 (Rfree = 0.000) for 2090 atoms. Found 11 (11 requested) and removed 32 (5 requested) atoms. Cycle 27: After refmac, R = 0.3631 (Rfree = 0.000) for 2047 atoms. Found 11 (11 requested) and removed 32 (5 requested) atoms. Cycle 28: After refmac, R = 0.3511 (Rfree = 0.000) for 2010 atoms. Found 11 (11 requested) and removed 22 (5 requested) atoms. Cycle 29: After refmac, R = 0.3469 (Rfree = 0.000) for 1986 atoms. Found 8 (10 requested) and removed 18 (5 requested) atoms. Cycle 30: After refmac, R = 0.3410 (Rfree = 0.000) for 1959 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 4.01 4.72 Search for helices and strands: 0 residues in 0 chains, 2058 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 2081 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 7 peptides. Score 0.264 Round 2: 108 peptides, 20 chains. Longest chain 11 peptides. Score 0.320 Round 3: 110 peptides, 19 chains. Longest chain 8 peptides. Score 0.351 Round 4: 111 peptides, 18 chains. Longest chain 13 peptides. Score 0.377 Round 5: 102 peptides, 16 chains. Longest chain 14 peptides. Score 0.377 Taking the results from Round 5 Chains 16, Residues 86, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 4485 restraints for refining 2087 atoms. 4157 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3635 (Rfree = 0.000) for 2087 atoms. Found 11 (11 requested) and removed 32 (5 requested) atoms. Cycle 32: After refmac, R = 0.3484 (Rfree = 0.000) for 2046 atoms. Found 10 (11 requested) and removed 18 (5 requested) atoms. Cycle 33: After refmac, R = 0.3447 (Rfree = 0.000) for 2026 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 34: After refmac, R = 0.3332 (Rfree = 0.000) for 2015 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 35: After refmac, R = 0.3278 (Rfree = 0.000) for 1995 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 4.06 4.78 Search for helices and strands: 0 residues in 0 chains, 2083 seeds are put forward NCS extension: 0 residues added, 2083 seeds are put forward Round 1: 92 peptides, 19 chains. Longest chain 9 peptides. Score 0.259 Round 2: 105 peptides, 20 chains. Longest chain 10 peptides. Score 0.305 Round 3: 113 peptides, 21 chains. Longest chain 11 peptides. Score 0.323 Round 4: 115 peptides, 20 chains. Longest chain 10 peptides. Score 0.354 Round 5: 123 peptides, 20 chains. Longest chain 13 peptides. Score 0.391 Taking the results from Round 5 Chains 20, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 4362 restraints for refining 2094 atoms. 3970 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3557 (Rfree = 0.000) for 2094 atoms. Found 11 (11 requested) and removed 31 (5 requested) atoms. Cycle 37: After refmac, R = 0.3415 (Rfree = 0.000) for 2057 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. Cycle 38: After refmac, R = 0.3412 (Rfree = 0.000) for 2023 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 39: After refmac, R = 0.3482 (Rfree = 0.000) for 1993 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 40: After refmac, R = 0.3212 (Rfree = 0.000) for 1980 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 4.04 4.76 Search for helices and strands: 0 residues in 0 chains, 2062 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2082 seeds are put forward Round 1: 86 peptides, 20 chains. Longest chain 6 peptides. Score 0.202 Round 2: 101 peptides, 21 chains. Longest chain 8 peptides. Score 0.262 Round 3: 98 peptides, 18 chains. Longest chain 12 peptides. Score 0.313 Round 4: 106 peptides, 21 chains. Longest chain 9 peptides. Score 0.288 Round 5: 103 peptides, 21 chains. Longest chain 8 peptides. Score 0.272 Taking the results from Round 3 Chains 18, Residues 80, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 4214 restraints for refining 1937 atoms. 3912 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3746 (Rfree = 0.000) for 1937 atoms. Found 10 (10 requested) and removed 29 (5 requested) atoms. Cycle 42: After refmac, R = 0.3621 (Rfree = 0.000) for 1902 atoms. Found 10 (10 requested) and removed 22 (5 requested) atoms. Cycle 43: After refmac, R = 0.3480 (Rfree = 0.000) for 1870 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 44: After refmac, R = 0.3109 (Rfree = 0.000) for 1861 atoms. Found 8 (10 requested) and removed 9 (5 requested) atoms. Cycle 45: After refmac, R = 0.3481 (Rfree = 0.000) for 1849 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 4.09 4.81 Search for helices and strands: 0 residues in 0 chains, 1948 seeds are put forward NCS extension: 0 residues added, 1948 seeds are put forward Round 1: 68 peptides, 15 chains. Longest chain 7 peptides. Score 0.218 Round 2: 92 peptides, 20 chains. Longest chain 7 peptides. Score 0.236 Round 3: 107 peptides, 20 chains. Longest chain 13 peptides. Score 0.315 Round 4: 103 peptides, 17 chains. Longest chain 19 peptides. Score 0.360 Round 5: 106 peptides, 18 chains. Longest chain 13 peptides. Score 0.353 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 86, 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. 3834 reflections ( 99.61 % complete ) and 3796 restraints for refining 1819 atoms. 3469 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3805 (Rfree = 0.000) for 1819 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.3577 (Rfree = 0.000) for 1793 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.3337 (Rfree = 0.000) for 1780 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.3605 (Rfree = 0.000) for 1771 atoms. TimeTaking 31.28