Mon 24 Dec 07:37:19 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-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2itb-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2itb-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2itb-3.8-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-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2itb-3.8-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 07:37:23 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-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2itb-3.8-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 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-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-3.8-parrot-noncs.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 3627 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3717 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3924 (Rfree = 0.000) for 3627 atoms. Found 16 (19 requested) and removed 45 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.00 4.71 Search for helices and strands: 0 residues in 0 chains, 3712 seeds are put forward NCS extension: 0 residues added, 3712 seeds are put forward Round 1: 64 peptides, 15 chains. Longest chain 5 peptides. Score 0.193 Round 2: 92 peptides, 19 chains. Longest chain 8 peptides. Score 0.259 Round 3: 109 peptides, 22 chains. Longest chain 9 peptides. Score 0.281 Round 4: 127 peptides, 20 chains. Longest chain 13 peptides. Score 0.410 Round 5: 121 peptides, 21 chains. Longest chain 13 peptides. Score 0.362 Taking the results from Round 4 Chains 21, Residues 107, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 6523 restraints for refining 2786 atoms. 6079 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3849 (Rfree = 0.000) for 2786 atoms. Found 14 (15 requested) and removed 47 (7 requested) atoms. Cycle 2: After refmac, R = 0.3691 (Rfree = 0.000) for 2686 atoms. Found 9 (15 requested) and removed 25 (7 requested) atoms. Cycle 3: After refmac, R = 0.3642 (Rfree = 0.000) for 2625 atoms. Found 6 (14 requested) and removed 19 (7 requested) atoms. Cycle 4: After refmac, R = 0.3612 (Rfree = 0.000) for 2578 atoms. Found 5 (14 requested) and removed 28 (7 requested) atoms. Cycle 5: After refmac, R = 0.3659 (Rfree = 0.000) for 2528 atoms. Found 6 (14 requested) and removed 30 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 4.13 4.86 Search for helices and strands: 0 residues in 0 chains, 2610 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2628 seeds are put forward Round 1: 77 peptides, 16 chains. Longest chain 7 peptides. Score 0.246 Round 2: 105 peptides, 18 chains. Longest chain 12 peptides. Score 0.348 Round 3: 107 peptides, 20 chains. Longest chain 13 peptides. Score 0.315 Round 4: 109 peptides, 18 chains. Longest chain 11 peptides. Score 0.367 Round 5: 105 peptides, 17 chains. Longest chain 12 peptides. Score 0.369 Taking the results from Round 5 Chains 17, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 5110 restraints for refining 2252 atoms. 4775 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3567 (Rfree = 0.000) for 2252 atoms. Found 9 (12 requested) and removed 22 (6 requested) atoms. Cycle 7: After refmac, R = 0.3509 (Rfree = 0.000) for 2206 atoms. Found 5 (12 requested) and removed 13 (6 requested) atoms. Cycle 8: After refmac, R = 0.3581 (Rfree = 0.000) for 2169 atoms. Found 8 (12 requested) and removed 18 (6 requested) atoms. Cycle 9: After refmac, R = 0.3431 (Rfree = 0.000) for 2137 atoms. Found 5 (11 requested) and removed 13 (5 requested) atoms. Cycle 10: After refmac, R = 0.3501 (Rfree = 0.000) for 2115 atoms. Found 4 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.17 4.91 Search for helices and strands: 0 residues in 0 chains, 2218 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 2235 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 7 peptides. Score 0.240 Round 2: 121 peptides, 19 chains. Longest chain 17 peptides. Score 0.403 Round 3: 118 peptides, 19 chains. Longest chain 14 peptides. Score 0.389 Round 4: 130 peptides, 22 chains. Longest chain 12 peptides. Score 0.383 Round 5: 130 peptides, 18 chains. Longest chain 24 peptides. Score 0.462 Taking the results from Round 5 Chains 20, Residues 112, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 4324 restraints for refining 2107 atoms. 3873 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3590 (Rfree = 0.000) for 2107 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 12: After refmac, R = 0.3202 (Rfree = 0.000) for 2083 atoms. Found 3 (11 requested) and removed 15 (5 requested) atoms. Cycle 13: After refmac, R = 0.3490 (Rfree = 0.000) for 2050 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 14: After refmac, R = 0.3403 (Rfree = 0.000) for 2034 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 15: After refmac, R = 0.3447 (Rfree = 0.000) for 2027 atoms. Found 11 (11 requested) and removed 19 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.90 4.59 Search for helices and strands: 0 residues in 0 chains, 2127 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2148 seeds are put forward Round 1: 113 peptides, 22 chains. Longest chain 11 peptides. Score 0.302 Round 2: 133 peptides, 23 chains. Longest chain 12 peptides. Score 0.377 Round 3: 131 peptides, 22 chains. Longest chain 10 peptides. Score 0.388 Round 4: 132 peptides, 17 chains. Longest chain 16 peptides. Score 0.489 Round 5: 127 peptides, 18 chains. Longest chain 16 peptides. Score 0.449 Taking the results from Round 4 Chains 17, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 4657 restraints for refining 2179 atoms. 4214 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3633 (Rfree = 0.000) for 2179 atoms. Found 11 (11 requested) and removed 26 (5 requested) atoms. Cycle 17: After refmac, R = 0.3457 (Rfree = 0.000) for 2136 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 18: After refmac, R = 0.3550 (Rfree = 0.000) for 2104 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 19: After refmac, R = 0.3378 (Rfree = 0.000) for 2086 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 20: After refmac, R = 0.3442 (Rfree = 0.000) for 2065 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.86 4.54 Search for helices and strands: 0 residues in 0 chains, 2171 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 2196 seeds are put forward Round 1: 102 peptides, 19 chains. Longest chain 9 peptides. Score 0.311 Round 2: 124 peptides, 18 chains. Longest chain 13 peptides. Score 0.436 Round 3: 130 peptides, 18 chains. Longest chain 13 peptides. Score 0.462 Round 4: 120 peptides, 18 chains. Longest chain 11 peptides. Score 0.418 Round 5: 130 peptides, 21 chains. Longest chain 13 peptides. Score 0.403 Taking the results from Round 3 Chains 18, Residues 112, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 4120 restraints for refining 2023 atoms. 3671 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3601 (Rfree = 0.000) for 2023 atoms. Found 11 (11 requested) and removed 23 (5 requested) atoms. Cycle 22: After refmac, R = 0.3241 (Rfree = 0.000) for 1990 atoms. Found 5 (11 requested) and removed 14 (5 requested) atoms. Cycle 23: After refmac, R = 0.3507 (Rfree = 0.000) for 1969 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 24: After refmac, R = 0.3275 (Rfree = 0.000) for 1948 atoms. Found 6 (10 requested) and removed 15 (5 requested) atoms. Cycle 25: After refmac, R = 0.3489 (Rfree = 0.000) for 1926 atoms. Found 8 (10 requested) and removed 19 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 4.01 4.72 Search for helices and strands: 0 residues in 0 chains, 2015 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2029 seeds are put forward Round 1: 90 peptides, 18 chains. Longest chain 9 peptides. Score 0.271 Round 2: 101 peptides, 18 chains. Longest chain 9 peptides. Score 0.328 Round 3: 110 peptides, 17 chains. Longest chain 13 peptides. Score 0.393 Round 4: 104 peptides, 17 chains. Longest chain 10 peptides. Score 0.365 Round 5: 105 peptides, 16 chains. Longest chain 11 peptides. Score 0.391 Taking the results from Round 3 Chains 17, Residues 93, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 3560 restraints for refining 1844 atoms. 3161 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3573 (Rfree = 0.000) for 1844 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 27: After refmac, R = 0.3595 (Rfree = 0.000) for 1820 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 28: After refmac, R = 0.3542 (Rfree = 0.000) for 1803 atoms. Found 8 (9 requested) and removed 6 (4 requested) atoms. Cycle 29: After refmac, R = 0.3421 (Rfree = 0.000) for 1793 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. Cycle 30: After refmac, R = 0.3426 (Rfree = 0.000) for 1783 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 4.13 4.86 Search for helices and strands: 0 residues in 0 chains, 1893 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 1911 seeds are put forward Round 1: 88 peptides, 17 chains. Longest chain 9 peptides. Score 0.283 Round 2: 106 peptides, 21 chains. Longest chain 9 peptides. Score 0.288 Round 3: 107 peptides, 17 chains. Longest chain 11 peptides. Score 0.379 Round 4: 101 peptides, 18 chains. Longest chain 12 peptides. Score 0.328 Round 5: 109 peptides, 20 chains. Longest chain 11 peptides. Score 0.325 Taking the results from Round 3 Chains 17, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 3483 restraints for refining 1734 atoms. 3140 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3707 (Rfree = 0.000) for 1734 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 32: After refmac, R = 0.3675 (Rfree = 0.000) for 1714 atoms. Found 8 (9 requested) and removed 16 (4 requested) atoms. Cycle 33: After refmac, R = 0.3523 (Rfree = 0.000) for 1695 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 34: After refmac, R = 0.3384 (Rfree = 0.000) for 1681 atoms. Found 4 (9 requested) and removed 9 (4 requested) atoms. Cycle 35: After refmac, R = 0.3587 (Rfree = 0.000) for 1671 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 4.26 5.01 Search for helices and strands: 0 residues in 0 chains, 1777 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 1789 seeds are put forward Round 1: 77 peptides, 15 chains. Longest chain 12 peptides. Score 0.270 Round 2: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.282 Round 3: 111 peptides, 21 chains. Longest chain 10 peptides. Score 0.313 Round 4: 122 peptides, 21 chains. Longest chain 14 peptides. Score 0.366 Round 5: 110 peptides, 20 chains. Longest chain 10 peptides. Score 0.330 Taking the results from Round 4 Chains 21, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 3262 restraints for refining 1691 atoms. 2879 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3813 (Rfree = 0.000) for 1691 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 37: After refmac, R = 0.3902 (Rfree = 0.000) for 1660 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. Cycle 38: After refmac, R = 0.3705 (Rfree = 0.000) for 1633 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 39: After refmac, R = 0.3771 (Rfree = 0.000) for 1621 atoms. Found 8 (8 requested) and removed 22 (4 requested) atoms. Cycle 40: After refmac, R = 0.3710 (Rfree = 0.000) for 1602 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 4.17 4.91 Search for helices and strands: 0 residues in 0 chains, 1718 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 1743 seeds are put forward Round 1: 76 peptides, 16 chains. Longest chain 10 peptides. Score 0.240 Round 2: 96 peptides, 17 chains. Longest chain 10 peptides. Score 0.325 Round 3: 80 peptides, 12 chains. Longest chain 11 peptides. Score 0.358 Round 4: 86 peptides, 17 chains. Longest chain 7 peptides. Score 0.273 Round 5: 95 peptides, 15 chains. Longest chain 11 peptides. Score 0.365 Taking the results from Round 5 Chains 15, Residues 80, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3834 reflections ( 99.61 % complete ) and 3474 restraints for refining 1735 atoms. 3124 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3894 (Rfree = 0.000) for 1735 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 42: After refmac, R = 0.3832 (Rfree = 0.000) for 1708 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 43: After refmac, R = 0.3868 (Rfree = 0.000) for 1685 atoms. Found 9 (9 requested) and removed 23 (4 requested) atoms. Cycle 44: After refmac, R = 0.3740 (Rfree = 0.000) for 1654 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 45: After refmac, R = 0.3785 (Rfree = 0.000) for 1635 atoms. Found 9 (9 requested) and removed 22 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.94 4.64 Search for helices and strands: 0 residues in 0 chains, 1684 seeds are put forward NCS extension: 7 residues added (0 deleted due to clashes), 1691 seeds are put forward Round 1: 55 peptides, 10 chains. Longest chain 10 peptides. Score 0.271 Round 2: 67 peptides, 14 chains. Longest chain 9 peptides. Score 0.237 Round 3: 77 peptides, 15 chains. Longest chain 8 peptides. Score 0.270 Round 4: 86 peptides, 16 chains. Longest chain 7 peptides. Score 0.296 Round 5: 74 peptides, 12 chains. Longest chain 9 peptides. Score 0.327 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 62, 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 3507 restraints for refining 1627 atoms. 3271 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.4029 (Rfree = 0.000) for 1627 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.3909 (Rfree = 0.000) for 1611 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.3758 (Rfree = 0.000) for 1592 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.3816 (Rfree = 0.000) for 1574 atoms. TimeTaking 24.03