Sun 23 Dec 22:22:49 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 2awa-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2awa-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2awa-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2awa-3.6-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/2awa-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2awa-3.6-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 22:22:59 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/hancs/ArpWArp/wArpResults/WorkingDir/2awa-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2awa-3.6-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 1162 and 0 Target number of residues in the AU: 1162 Target solvent content: 0.6530 Checking the provided sequence file Detected sequence length: 390 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1560 Adjusted target solvent content: 0.53 Input MTZ file: 2awa-3.6-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: 4 Cell parameters: 94.281 70.854 135.686 90.000 91.232 90.000 Input sequence file: 2awa-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 12480 target number of atoms Had to go as low as 0.85 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: 135.654 3.600 Wilson plot Bfac: 80.06 Failed to save intermediate PDB 20163 reflections ( 95.48 % complete ) and 0 restraints for refining 13747 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3556 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3116 (Rfree = 0.000) for 13747 atoms. Found 88 (88 requested) and removed 104 (44 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.40 Search for helices and strands: 0 residues in 0 chains, 13905 seeds are put forward NCS extension: 0 residues added, 13905 seeds are put forward Round 1: 503 peptides, 108 chains. Longest chain 13 peptides. Score 0.246 Round 2: 694 peptides, 131 chains. Longest chain 13 peptides. Score 0.340 Round 3: 721 peptides, 128 chains. Longest chain 16 peptides. Score 0.377 Round 4: 767 peptides, 127 chains. Longest chain 16 peptides. Score 0.422 Round 5: 760 peptides, 123 chains. Longest chain 17 peptides. Score 0.431 Taking the results from Round 5 Chains 123, Residues 637, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 20163 reflections ( 95.48 % complete ) and 26604 restraints for refining 11312 atoms. 24179 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2521 (Rfree = 0.000) for 11312 atoms. Found 34 (72 requested) and removed 74 (36 requested) atoms. Cycle 2: After refmac, R = 0.2430 (Rfree = 0.000) for 11092 atoms. Found 42 (72 requested) and removed 64 (36 requested) atoms. Cycle 3: After refmac, R = 0.2287 (Rfree = 0.000) for 10984 atoms. Found 31 (71 requested) and removed 53 (35 requested) atoms. Cycle 4: After refmac, R = 0.2213 (Rfree = 0.000) for 10899 atoms. Found 27 (70 requested) and removed 64 (35 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2151 (Rfree = 0.000) for 10820 atoms. Found 27 (69 requested) and removed 60 (34 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 3.35 Search for helices and strands: 0 residues in 0 chains, 11148 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 11163 seeds are put forward Round 1: 681 peptides, 135 chains. Longest chain 11 peptides. Score 0.312 Round 2: 766 peptides, 128 chains. Longest chain 17 peptides. Score 0.417 Round 3: 766 peptides, 124 chains. Longest chain 17 peptides. Score 0.432 Round 4: 795 peptides, 128 chains. Longest chain 17 peptides. Score 0.442 Round 5: 805 peptides, 129 chains. Longest chain 14 peptides. Score 0.447 Taking the results from Round 5 Chains 129, Residues 676, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 20163 reflections ( 95.48 % complete ) and 25768 restraints for refining 11307 atoms. 23193 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2217 (Rfree = 0.000) for 11307 atoms. Found 48 (72 requested) and removed 91 (36 requested) atoms. Cycle 7: After refmac, R = 0.2173 (Rfree = 0.000) for 11179 atoms. Found 43 (72 requested) and removed 72 (36 requested) atoms. Cycle 8: After refmac, R = 0.2062 (Rfree = 0.000) for 11114 atoms. Found 16 (71 requested) and removed 57 (35 requested) atoms. Cycle 9: After refmac, R = 0.2059 (Rfree = 0.000) for 11035 atoms. Found 26 (71 requested) and removed 50 (35 requested) atoms. Cycle 10: After refmac, R = 0.2030 (Rfree = 0.000) for 10984 atoms. Found 23 (70 requested) and removed 51 (35 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 3.39 Search for helices and strands: 0 residues in 0 chains, 11271 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 11285 seeds are put forward Round 1: 659 peptides, 131 chains. Longest chain 11 peptides. Score 0.307 Round 2: 719 peptides, 119 chains. Longest chain 18 peptides. Score 0.410 Round 3: 724 peptides, 113 chains. Longest chain 21 peptides. Score 0.437 Round 4: 764 peptides, 112 chains. Longest chain 23 peptides. Score 0.474 Round 5: 773 peptides, 114 chains. Longest chain 17 peptides. Score 0.475 Taking the results from Round 5 Chains 114, Residues 659, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 20163 reflections ( 95.48 % complete ) and 25558 restraints for refining 11313 atoms. 23020 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2231 (Rfree = 0.000) for 11313 atoms. Found 34 (72 requested) and removed 56 (36 requested) atoms. Cycle 12: After refmac, R = 0.2233 (Rfree = 0.000) for 11214 atoms. Found 60 (72 requested) and removed 58 (36 requested) atoms. Cycle 13: After refmac, R = 0.2124 (Rfree = 0.000) for 11143 atoms. Found 44 (71 requested) and removed 58 (35 requested) atoms. Cycle 14: After refmac, R = 0.1971 (Rfree = 0.000) for 11079 atoms. Found 28 (71 requested) and removed 41 (35 requested) atoms. Cycle 15: After refmac, R = 0.1683 (Rfree = 0.000) for 11030 atoms. Found 15 (70 requested) and removed 39 (35 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.39 Search for helices and strands: 0 residues in 0 chains, 11254 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 11280 seeds are put forward Round 1: 641 peptides, 123 chains. Longest chain 14 peptides. Score 0.322 Round 2: 750 peptides, 125 chains. Longest chain 20 peptides. Score 0.414 Round 3: 760 peptides, 121 chains. Longest chain 19 peptides. Score 0.438 Round 4: 753 peptides, 115 chains. Longest chain 19 peptides. Score 0.454 Round 5: 756 peptides, 113 chains. Longest chain 19 peptides. Score 0.464 Taking the results from Round 5 Chains 113, Residues 643, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 20163 reflections ( 95.48 % complete ) and 25709 restraints for refining 11310 atoms. 23224 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2058 (Rfree = 0.000) for 11310 atoms. Found 39 (72 requested) and removed 49 (36 requested) atoms. Cycle 17: After refmac, R = 0.1893 (Rfree = 0.000) for 11260 atoms. Found 24 (72 requested) and removed 43 (36 requested) atoms. Cycle 18: After refmac, R = 0.1984 (Rfree = 0.000) for 11217 atoms. Found 30 (72 requested) and removed 43 (36 requested) atoms. Cycle 19: After refmac, R = 0.1908 (Rfree = 0.000) for 11175 atoms. Found 37 (71 requested) and removed 52 (35 requested) atoms. Cycle 20: After refmac, R = 0.1897 (Rfree = 0.000) for 11138 atoms. Found 33 (71 requested) and removed 44 (35 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 3.40 Search for helices and strands: 0 residues in 0 chains, 11352 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 11370 seeds are put forward Round 1: 656 peptides, 126 chains. Longest chain 15 peptides. Score 0.324 Round 2: 713 peptides, 124 chains. Longest chain 14 peptides. Score 0.385 Round 3: 708 peptides, 118 chains. Longest chain 17 peptides. Score 0.404 Round 4: 750 peptides, 120 chains. Longest chain 18 peptides. Score 0.433 Round 5: 755 peptides, 114 chains. Longest chain 16 peptides. Score 0.460 Taking the results from Round 5 Chains 115, Residues 641, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 20163 reflections ( 95.48 % complete ) and 25971 restraints for refining 11313 atoms. 23487 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2102 (Rfree = 0.000) for 11313 atoms. Found 42 (72 requested) and removed 49 (36 requested) atoms. Cycle 22: After refmac, R = 0.2102 (Rfree = 0.000) for 11259 atoms. Found 45 (72 requested) and removed 49 (36 requested) atoms. Cycle 23: After refmac, R = 0.2089 (Rfree = 0.000) for 11214 atoms. Found 29 (72 requested) and removed 43 (36 requested) atoms. Cycle 24: After refmac, R = 0.2019 (Rfree = 0.000) for 11183 atoms. Found 36 (71 requested) and removed 45 (35 requested) atoms. Cycle 25: After refmac, R = 0.2022 (Rfree = 0.000) for 11162 atoms. Found 25 (71 requested) and removed 42 (35 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 3.40 Search for helices and strands: 0 residues in 0 chains, 11394 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 11413 seeds are put forward Round 1: 600 peptides, 111 chains. Longest chain 16 peptides. Score 0.332 Round 2: 658 peptides, 109 chains. Longest chain 17 peptides. Score 0.395 Round 3: 688 peptides, 106 chains. Longest chain 18 peptides. Score 0.433 Round 4: 708 peptides, 112 chains. Longest chain 15 peptides. Score 0.427 Round 5: 715 peptides, 109 chains. Longest chain 20 peptides. Score 0.445 Taking the results from Round 5 Chains 109, Residues 606, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 20163 reflections ( 95.48 % complete ) and 26137 restraints for refining 11313 atoms. 23822 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2002 (Rfree = 0.000) for 11313 atoms. Found 34 (72 requested) and removed 44 (36 requested) atoms. Cycle 27: After refmac, R = 0.1920 (Rfree = 0.000) for 11265 atoms. Found 21 (72 requested) and removed 45 (36 requested) atoms. Cycle 28: After refmac, R = 0.1911 (Rfree = 0.000) for 11219 atoms. Found 25 (72 requested) and removed 41 (36 requested) atoms. Cycle 29: After refmac, R = 0.1863 (Rfree = 0.000) for 11189 atoms. Found 33 (71 requested) and removed 42 (35 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1869 (Rfree = 0.000) for 11164 atoms. Found 26 (71 requested) and removed 44 (35 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 3.38 Search for helices and strands: 0 residues in 0 chains, 11393 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 11418 seeds are put forward Round 1: 601 peptides, 119 chains. Longest chain 12 peptides. Score 0.299 Round 2: 700 peptides, 116 chains. Longest chain 18 peptides. Score 0.405 Round 3: 706 peptides, 118 chains. Longest chain 15 peptides. Score 0.402 Round 4: 703 peptides, 112 chains. Longest chain 14 peptides. Score 0.423 Round 5: 705 peptides, 110 chains. Longest chain 14 peptides. Score 0.432 Taking the results from Round 5 Chains 111, Residues 595, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 20163 reflections ( 95.48 % complete ) and 26008 restraints for refining 11311 atoms. 23680 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1991 (Rfree = 0.000) for 11311 atoms. Found 33 (72 requested) and removed 50 (36 requested) atoms. Cycle 32: After refmac, R = 0.1921 (Rfree = 0.000) for 11238 atoms. Found 39 (72 requested) and removed 43 (36 requested) atoms. Cycle 33: After refmac, R = 0.1880 (Rfree = 0.000) for 11203 atoms. Found 28 (72 requested) and removed 43 (36 requested) atoms. Cycle 34: After refmac, R = 0.1790 (Rfree = 0.000) for 11168 atoms. Found 26 (71 requested) and removed 40 (35 requested) atoms. Cycle 35: After refmac, R = 0.1815 (Rfree = 0.000) for 11140 atoms. Found 30 (71 requested) and removed 37 (35 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 3.38 Search for helices and strands: 0 residues in 0 chains, 11345 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 11363 seeds are put forward Round 1: 563 peptides, 118 chains. Longest chain 10 peptides. Score 0.265 Round 2: 600 peptides, 110 chains. Longest chain 10 peptides. Score 0.336 Round 3: 630 peptides, 101 chains. Longest chain 12 peptides. Score 0.401 Round 4: 642 peptides, 110 chains. Longest chain 12 peptides. Score 0.376 Round 5: 636 peptides, 99 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 5 Chains 99, Residues 537, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 20163 reflections ( 95.48 % complete ) and 26287 restraints for refining 11312 atoms. 24199 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2029 (Rfree = 0.000) for 11312 atoms. Found 39 (72 requested) and removed 47 (36 requested) atoms. Cycle 37: After refmac, R = 0.1934 (Rfree = 0.000) for 11271 atoms. Found 45 (72 requested) and removed 40 (36 requested) atoms. Cycle 38: After refmac, R = 0.1936 (Rfree = 0.000) for 11251 atoms. Found 53 (72 requested) and removed 43 (36 requested) atoms. Cycle 39: After refmac, R = 0.1845 (Rfree = 0.000) for 11237 atoms. Found 48 (72 requested) and removed 41 (36 requested) atoms. Cycle 40: After refmac, R = 0.1817 (Rfree = 0.000) for 11224 atoms. Found 36 (72 requested) and removed 42 (36 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.38 Search for helices and strands: 0 residues in 0 chains, 11441 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 11455 seeds are put forward Round 1: 586 peptides, 122 chains. Longest chain 10 peptides. Score 0.272 Round 2: 657 peptides, 118 chains. Longest chain 10 peptides. Score 0.358 Round 3: 673 peptides, 118 chains. Longest chain 11 peptides. Score 0.372 Round 4: 685 peptides, 116 chains. Longest chain 20 peptides. Score 0.391 Round 5: 705 peptides, 117 chains. Longest chain 14 peptides. Score 0.405 Taking the results from Round 5 Chains 117, Residues 588, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 20163 reflections ( 95.48 % complete ) and 26207 restraints for refining 11312 atoms. 23972 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1975 (Rfree = 0.000) for 11312 atoms. Found 40 (72 requested) and removed 42 (36 requested) atoms. Cycle 42: After refmac, R = 0.1965 (Rfree = 0.000) for 11263 atoms. Found 37 (72 requested) and removed 43 (36 requested) atoms. Cycle 43: After refmac, R = 0.1961 (Rfree = 0.000) for 11231 atoms. Found 45 (72 requested) and removed 39 (36 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1974 (Rfree = 0.000) for 11216 atoms. Found 52 (72 requested) and removed 47 (36 requested) atoms. Cycle 45: After refmac, R = 0.1631 (Rfree = 0.000) for 11199 atoms. Found 9 (71 requested) and removed 38 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.37 Search for helices and strands: 0 residues in 0 chains, 11389 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 11403 seeds are put forward Round 1: 542 peptides, 112 chains. Longest chain 10 peptides. Score 0.270 Round 2: 603 peptides, 110 chains. Longest chain 11 peptides. Score 0.339 Round 3: 607 peptides, 106 chains. Longest chain 11 peptides. Score 0.359 Round 4: 617 peptides, 108 chains. Longest chain 16 peptides. Score 0.361 Round 5: 610 peptides, 106 chains. Longest chain 14 peptides. Score 0.362 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 106, Residues 504, 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 2awa-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20163 reflections ( 95.48 % complete ) and 26312 restraints for refining 11312 atoms. 24402 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1986 (Rfree = 0.000) for 11312 atoms. Found 0 (72 requested) and removed 36 (36 requested) atoms. Cycle 47: After refmac, R = 0.1987 (Rfree = 0.000) for 11242 atoms. Found 0 (72 requested) and removed 36 (36 requested) atoms. Cycle 48: After refmac, R = 0.1939 (Rfree = 0.000) for 11177 atoms. Found 0 (71 requested) and removed 35 (35 requested) atoms. Cycle 49: After refmac, R = 0.1894 (Rfree = 0.000) for 11125 atoms. TimeTaking 121.93