Sun 23 Dec 22:23:08 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2awa-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2awa-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2awa-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2awa-3.4-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 22:23:18 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2awa-3.4-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 1201 and 0 Target number of residues in the AU: 1201 Target solvent content: 0.6414 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-3.4-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-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 12480 target number of atoms Had to go as low as 0.80 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 3.400 Wilson plot Bfac: 72.77 23980 reflections ( 95.89 % complete ) and 0 restraints for refining 13782 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3583 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2891 (Rfree = 0.000) for 13782 atoms. Found 72 (104 requested) and removed 147 (52 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.22 Search for helices and strands: 0 residues in 0 chains, 13856 seeds are put forward NCS extension: 0 residues added, 13856 seeds are put forward Round 1: 480 peptides, 96 chains. Longest chain 13 peptides. Score 0.276 Round 2: 633 peptides, 119 chains. Longest chain 14 peptides. Score 0.331 Round 3: 711 peptides, 124 chains. Longest chain 14 peptides. Score 0.384 Round 4: 709 peptides, 122 chains. Longest chain 13 peptides. Score 0.389 Round 5: 736 peptides, 123 chains. Longest chain 14 peptides. Score 0.410 Taking the results from Round 5 Chains 123, Residues 613, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 23980 reflections ( 95.89 % complete ) and 26477 restraints for refining 11345 atoms. 24081 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2491 (Rfree = 0.000) for 11345 atoms. Found 52 (85 requested) and removed 65 (42 requested) atoms. Cycle 2: After refmac, R = 0.2332 (Rfree = 0.000) for 11225 atoms. Found 24 (85 requested) and removed 48 (42 requested) atoms. Cycle 3: After refmac, R = 0.2259 (Rfree = 0.000) for 11169 atoms. Found 11 (84 requested) and removed 48 (42 requested) atoms. Cycle 4: After refmac, R = 0.2243 (Rfree = 0.000) for 11115 atoms. Found 13 (84 requested) and removed 49 (42 requested) atoms. Cycle 5: After refmac, R = 0.2213 (Rfree = 0.000) for 11064 atoms. Found 11 (83 requested) and removed 43 (41 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.21 Search for helices and strands: 0 residues in 0 chains, 11282 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 11299 seeds are put forward Round 1: 679 peptides, 124 chains. Longest chain 11 peptides. Score 0.354 Round 2: 759 peptides, 121 chains. Longest chain 17 peptides. Score 0.437 Round 3: 793 peptides, 122 chains. Longest chain 17 peptides. Score 0.462 Round 4: 818 peptides, 124 chains. Longest chain 20 peptides. Score 0.475 Round 5: 806 peptides, 115 chains. Longest chain 20 peptides. Score 0.497 Taking the results from Round 5 Chains 117, Residues 691, Estimated correctness of the model 0.0 % 3 chains (50 residues) have been docked in sequence ------------------------------------------------------ 23980 reflections ( 95.89 % complete ) and 25339 restraints for refining 11346 atoms. 22497 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2361 (Rfree = 0.000) for 11346 atoms. Found 59 (85 requested) and removed 64 (42 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2215 (Rfree = 0.000) for 11268 atoms. Found 14 (85 requested) and removed 53 (42 requested) atoms. Cycle 8: After refmac, R = 0.2151 (Rfree = 0.000) for 11207 atoms. Found 13 (84 requested) and removed 47 (42 requested) atoms. Cycle 9: After refmac, R = 0.2116 (Rfree = 0.000) for 11164 atoms. Found 14 (84 requested) and removed 46 (42 requested) atoms. Cycle 10: After refmac, R = 0.2179 (Rfree = 0.000) for 11123 atoms. Found 20 (84 requested) and removed 53 (42 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 3.19 Search for helices and strands: 0 residues in 0 chains, 11329 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 11347 seeds are put forward Round 1: 688 peptides, 131 chains. Longest chain 12 peptides. Score 0.334 Round 2: 794 peptides, 125 chains. Longest chain 20 peptides. Score 0.452 Round 3: 808 peptides, 122 chains. Longest chain 23 peptides. Score 0.474 Round 4: 821 peptides, 123 chains. Longest chain 23 peptides. Score 0.481 Round 5: 824 peptides, 127 chains. Longest chain 21 peptides. Score 0.469 Taking the results from Round 4 Chains 125, Residues 698, Estimated correctness of the model 0.0 % 5 chains (43 residues) have been docked in sequence ------------------------------------------------------ 23980 reflections ( 95.89 % complete ) and 25200 restraints for refining 11348 atoms. 22398 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2250 (Rfree = 0.000) for 11348 atoms. Found 33 (85 requested) and removed 58 (42 requested) atoms. Cycle 12: After refmac, R = 0.2173 (Rfree = 0.000) for 11281 atoms. Found 22 (85 requested) and removed 50 (42 requested) atoms. Cycle 13: After refmac, R = 0.2113 (Rfree = 0.000) for 11236 atoms. Found 20 (84 requested) and removed 47 (42 requested) atoms. Cycle 14: After refmac, R = 0.2073 (Rfree = 0.000) for 11195 atoms. Found 11 (84 requested) and removed 48 (42 requested) atoms. Cycle 15: After refmac, R = 0.2020 (Rfree = 0.000) for 11145 atoms. Found 9 (84 requested) and removed 44 (42 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 11350 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 11377 seeds are put forward Round 1: 701 peptides, 131 chains. Longest chain 13 peptides. Score 0.347 Round 2: 758 peptides, 123 chains. Longest chain 23 peptides. Score 0.429 Round 3: 773 peptides, 117 chains. Longest chain 24 peptides. Score 0.464 Round 4: 783 peptides, 127 chains. Longest chain 17 peptides. Score 0.435 Round 5: 780 peptides, 122 chains. Longest chain 20 peptides. Score 0.451 Taking the results from Round 3 Chains 120, Residues 656, Estimated correctness of the model 0.0 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 23980 reflections ( 95.89 % complete ) and 25622 restraints for refining 11347 atoms. 23004 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2235 (Rfree = 0.000) for 11347 atoms. Found 36 (85 requested) and removed 56 (42 requested) atoms. Cycle 17: After refmac, R = 0.2147 (Rfree = 0.000) for 11292 atoms. Found 25 (85 requested) and removed 54 (42 requested) atoms. Cycle 18: After refmac, R = 0.2133 (Rfree = 0.000) for 11249 atoms. Found 10 (85 requested) and removed 48 (42 requested) atoms. Cycle 19: After refmac, R = 0.2091 (Rfree = 0.000) for 11198 atoms. Found 10 (84 requested) and removed 43 (42 requested) atoms. Cycle 20: After refmac, R = 0.2070 (Rfree = 0.000) for 11155 atoms. Found 12 (84 requested) and removed 42 (42 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 11363 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 11389 seeds are put forward Round 1: 670 peptides, 124 chains. Longest chain 14 peptides. Score 0.346 Round 2: 749 peptides, 123 chains. Longest chain 17 peptides. Score 0.421 Round 3: 768 peptides, 121 chains. Longest chain 18 peptides. Score 0.445 Round 4: 764 peptides, 117 chains. Longest chain 19 peptides. Score 0.456 Round 5: 762 peptides, 113 chains. Longest chain 18 peptides. Score 0.469 Taking the results from Round 5 Chains 114, Residues 649, Estimated correctness of the model 0.0 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 23980 reflections ( 95.89 % complete ) and 25551 restraints for refining 11347 atoms. 22970 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2164 (Rfree = 0.000) for 11347 atoms. Found 40 (85 requested) and removed 56 (42 requested) atoms. Cycle 22: After refmac, R = 0.2084 (Rfree = 0.000) for 11294 atoms. Found 27 (85 requested) and removed 50 (42 requested) atoms. Cycle 23: After refmac, R = 0.2080 (Rfree = 0.000) for 11252 atoms. Found 29 (85 requested) and removed 50 (42 requested) atoms. Cycle 24: After refmac, R = 0.2025 (Rfree = 0.000) for 11212 atoms. Found 31 (84 requested) and removed 46 (42 requested) atoms. Cycle 25: After refmac, R = 0.2004 (Rfree = 0.000) for 11192 atoms. Found 25 (84 requested) and removed 48 (42 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 3.23 Search for helices and strands: 0 residues in 0 chains, 11410 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 11443 seeds are put forward Round 1: 652 peptides, 125 chains. Longest chain 15 peptides. Score 0.324 Round 2: 728 peptides, 122 chains. Longest chain 16 peptides. Score 0.406 Round 3: 713 peptides, 112 chains. Longest chain 19 peptides. Score 0.432 Round 4: 688 peptides, 110 chains. Longest chain 20 peptides. Score 0.417 Round 5: 696 peptides, 110 chains. Longest chain 14 peptides. Score 0.424 Taking the results from Round 3 Chains 114, Residues 601, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 23980 reflections ( 95.89 % complete ) and 25732 restraints for refining 11347 atoms. 23363 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2058 (Rfree = 0.000) for 11347 atoms. Found 42 (85 requested) and removed 46 (42 requested) atoms. Cycle 27: After refmac, R = 0.1978 (Rfree = 0.000) for 11314 atoms. Found 20 (85 requested) and removed 46 (42 requested) atoms. Cycle 28: After refmac, R = 0.2020 (Rfree = 0.000) for 11271 atoms. Found 31 (85 requested) and removed 46 (42 requested) atoms. Cycle 29: After refmac, R = 0.1962 (Rfree = 0.000) for 11243 atoms. Found 32 (84 requested) and removed 47 (42 requested) atoms. Cycle 30: After refmac, R = 0.1961 (Rfree = 0.000) for 11214 atoms. Found 35 (84 requested) and removed 48 (42 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 11425 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 11441 seeds are put forward Round 1: 624 peptides, 121 chains. Longest chain 13 peptides. Score 0.314 Round 2: 695 peptides, 120 chains. Longest chain 18 peptides. Score 0.385 Round 3: 725 peptides, 116 chains. Longest chain 18 peptides. Score 0.427 Round 4: 735 peptides, 117 chains. Longest chain 17 peptides. Score 0.432 Round 5: 720 peptides, 116 chains. Longest chain 18 peptides. Score 0.422 Taking the results from Round 4 Chains 117, Residues 618, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 23980 reflections ( 95.89 % complete ) and 25832 restraints for refining 11347 atoms. 23477 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2074 (Rfree = 0.000) for 11347 atoms. Found 40 (85 requested) and removed 49 (42 requested) atoms. Cycle 32: After refmac, R = 0.2020 (Rfree = 0.000) for 11308 atoms. Found 38 (85 requested) and removed 47 (42 requested) atoms. Cycle 33: After refmac, R = 0.1925 (Rfree = 0.000) for 11287 atoms. Found 24 (85 requested) and removed 46 (42 requested) atoms. Cycle 34: After refmac, R = 0.1907 (Rfree = 0.000) for 11257 atoms. Found 33 (85 requested) and removed 45 (42 requested) atoms. Cycle 35: After refmac, R = 0.1834 (Rfree = 0.000) for 11232 atoms. Found 18 (84 requested) and removed 47 (42 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 11435 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 11449 seeds are put forward Round 1: 573 peptides, 112 chains. Longest chain 11 peptides. Score 0.301 Round 2: 701 peptides, 116 chains. Longest chain 19 peptides. Score 0.406 Round 3: 718 peptides, 114 chains. Longest chain 17 peptides. Score 0.428 Round 4: 720 peptides, 114 chains. Longest chain 15 peptides. Score 0.430 Round 5: 695 peptides, 110 chains. Longest chain 15 peptides. Score 0.424 Taking the results from Round 4 Chains 114, Residues 606, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 23980 reflections ( 95.89 % complete ) and 25819 restraints for refining 11348 atoms. 23509 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1974 (Rfree = 0.000) for 11348 atoms. Found 37 (85 requested) and removed 48 (42 requested) atoms. Cycle 37: After refmac, R = 0.1924 (Rfree = 0.000) for 11315 atoms. Found 21 (85 requested) and removed 44 (42 requested) atoms. Cycle 38: After refmac, R = 0.1940 (Rfree = 0.000) for 11278 atoms. Found 25 (85 requested) and removed 44 (42 requested) atoms. Cycle 39: After refmac, R = 0.1911 (Rfree = 0.000) for 11250 atoms. Found 24 (85 requested) and removed 47 (42 requested) atoms. Cycle 40: After refmac, R = 0.1884 (Rfree = 0.000) for 11216 atoms. Found 21 (84 requested) and removed 44 (42 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 3.23 Search for helices and strands: 0 residues in 0 chains, 11423 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 11440 seeds are put forward Round 1: 580 peptides, 118 chains. Longest chain 12 peptides. Score 0.283 Round 2: 653 peptides, 107 chains. Longest chain 15 peptides. Score 0.398 Round 3: 665 peptides, 105 chains. Longest chain 28 peptides. Score 0.417 Round 4: 666 peptides, 106 chains. Longest chain 16 peptides. Score 0.413 Round 5: 669 peptides, 105 chains. Longest chain 17 peptides. Score 0.420 Taking the results from Round 5 Chains 105, Residues 564, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 23980 reflections ( 95.89 % complete ) and 25974 restraints for refining 11347 atoms. 23823 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1981 (Rfree = 0.000) for 11347 atoms. Found 31 (85 requested) and removed 43 (42 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1904 (Rfree = 0.000) for 11306 atoms. Found 33 (85 requested) and removed 45 (42 requested) atoms. Cycle 43: After refmac, R = 0.1875 (Rfree = 0.000) for 11281 atoms. Found 28 (85 requested) and removed 44 (42 requested) atoms. Cycle 44: After refmac, R = 0.1803 (Rfree = 0.000) for 11253 atoms. Found 14 (85 requested) and removed 45 (42 requested) atoms. Cycle 45: After refmac, R = 0.1804 (Rfree = 0.000) for 11210 atoms. Found 22 (84 requested) and removed 45 (42 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 11415 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 11430 seeds are put forward Round 1: 551 peptides, 108 chains. Longest chain 13 peptides. Score 0.296 Round 2: 631 peptides, 110 chains. Longest chain 17 peptides. Score 0.366 Round 3: 643 peptides, 104 chains. Longest chain 16 peptides. Score 0.401 Round 4: 639 peptides, 110 chains. Longest chain 19 peptides. Score 0.373 Round 5: 649 peptides, 105 chains. Longest chain 20 peptides. Score 0.402 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 105, Residues 544, 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. 23980 reflections ( 95.89 % complete ) and 26375 restraints for refining 11347 atoms. 24304 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1902 (Rfree = 0.000) for 11347 atoms. Found 0 (85 requested) and removed 42 (42 requested) atoms. Cycle 47: After refmac, R = 0.1889 (Rfree = 0.000) for 11286 atoms. Found 0 (85 requested) and removed 42 (42 requested) atoms. Cycle 48: After refmac, R = 0.1892 (Rfree = 0.000) for 11230 atoms. Found 0 (84 requested) and removed 42 (42 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1891 (Rfree = 0.000) for 11179 atoms. TimeTaking 124.47