null Mon 24 Dec 00:40:03 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 2hx1-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hx1-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hx1-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.8-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/2hx1-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.8-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 00:40:12 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/2hx1-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.8-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 831 and 0 Target number of residues in the AU: 831 Target solvent content: 0.6208 Checking the provided sequence file Detected sequence length: 284 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1136 Adjusted target solvent content: 0.48 Input MTZ file: 2hx1-3.8-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: 65.624 119.462 151.274 90.000 90.000 90.000 Input sequence file: 2hx1-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 9088 target number of atoms Had to go as low as 0.75 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: 93.753 3.800 Wilson plot Bfac: 61.72 12229 reflections ( 99.65 % complete ) and 0 restraints for refining 10058 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3324 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3472 (Rfree = 0.000) for 10058 atoms. Found 55 (55 requested) and removed 98 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.50 Search for helices and strands: 0 residues in 0 chains, 10215 seeds are put forward NCS extension: 0 residues added, 10215 seeds are put forward Round 1: 446 peptides, 91 chains. Longest chain 11 peptides. Score 0.296 Round 2: 533 peptides, 87 chains. Longest chain 16 peptides. Score 0.440 Round 3: 569 peptides, 93 chains. Longest chain 17 peptides. Score 0.453 Round 4: 638 peptides, 88 chains. Longest chain 20 peptides. Score 0.559 Round 5: 659 peptides, 90 chains. Longest chain 19 peptides. Score 0.572 Taking the results from Round 5 Chains 93, Residues 569, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 18326 restraints for refining 8217 atoms. 16077 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3128 (Rfree = 0.000) for 8217 atoms. Found 45 (45 requested) and removed 61 (22 requested) atoms. Cycle 2: After refmac, R = 0.2663 (Rfree = 0.000) for 8020 atoms. Found 45 (45 requested) and removed 52 (22 requested) atoms. Cycle 3: After refmac, R = 0.2626 (Rfree = 0.000) for 7949 atoms. Found 44 (44 requested) and removed 52 (22 requested) atoms. Cycle 4: After refmac, R = 0.2245 (Rfree = 0.000) for 7900 atoms. Found 43 (43 requested) and removed 46 (21 requested) atoms. Cycle 5: After refmac, R = 0.2362 (Rfree = 0.000) for 7871 atoms. Found 43 (43 requested) and removed 37 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.41 3.50 Search for helices and strands: 0 residues in 0 chains, 8198 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 8218 seeds are put forward Round 1: 556 peptides, 97 chains. Longest chain 13 peptides. Score 0.414 Round 2: 625 peptides, 87 chains. Longest chain 21 peptides. Score 0.550 Round 3: 621 peptides, 85 chains. Longest chain 20 peptides. Score 0.555 Round 4: 631 peptides, 76 chains. Longest chain 23 peptides. Score 0.608 Round 5: 624 peptides, 89 chains. Longest chain 28 peptides. Score 0.539 Taking the results from Round 4 Chains 76, Residues 555, Estimated correctness of the model 2.6 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 18570 restraints for refining 8219 atoms. 16405 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2805 (Rfree = 0.000) for 8219 atoms. Found 45 (45 requested) and removed 59 (22 requested) atoms. Cycle 7: After refmac, R = 0.2580 (Rfree = 0.000) for 8118 atoms. Found 45 (45 requested) and removed 63 (22 requested) atoms. Cycle 8: After refmac, R = 0.2318 (Rfree = 0.000) for 8062 atoms. Found 44 (44 requested) and removed 54 (22 requested) atoms. Cycle 9: After refmac, R = 0.2135 (Rfree = 0.000) for 8039 atoms. Found 44 (44 requested) and removed 47 (22 requested) atoms. Cycle 10: After refmac, R = 0.1704 (Rfree = 0.000) for 8022 atoms. Found 28 (44 requested) and removed 37 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 8291 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 8325 seeds are put forward Round 1: 562 peptides, 101 chains. Longest chain 13 peptides. Score 0.399 Round 2: 637 peptides, 96 chains. Longest chain 19 peptides. Score 0.519 Round 3: 642 peptides, 94 chains. Longest chain 23 peptides. Score 0.534 Round 4: 651 peptides, 93 chains. Longest chain 22 peptides. Score 0.549 Round 5: 674 peptides, 89 chains. Longest chain 19 peptides. Score 0.592 Taking the results from Round 5 Chains 89, Residues 585, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 18819 restraints for refining 8218 atoms. 16568 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2912 (Rfree = 0.000) for 8218 atoms. Found 45 (45 requested) and removed 43 (22 requested) atoms. Cycle 12: After refmac, R = 0.2524 (Rfree = 0.000) for 8148 atoms. Found 45 (45 requested) and removed 44 (22 requested) atoms. Cycle 13: After refmac, R = 0.2298 (Rfree = 0.000) for 8136 atoms. Found 44 (44 requested) and removed 45 (22 requested) atoms. Cycle 14: After refmac, R = 0.2077 (Rfree = 0.000) for 8120 atoms. Found 44 (44 requested) and removed 40 (22 requested) atoms. Cycle 15: After refmac, R = 0.1776 (Rfree = 0.000) for 8112 atoms. Found 16 (44 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 8374 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 8398 seeds are put forward Round 1: 537 peptides, 95 chains. Longest chain 21 peptides. Score 0.400 Round 2: 588 peptides, 92 chains. Longest chain 19 peptides. Score 0.482 Round 3: 611 peptides, 90 chains. Longest chain 19 peptides. Score 0.519 Round 4: 630 peptides, 91 chains. Longest chain 22 peptides. Score 0.536 Round 5: 649 peptides, 89 chains. Longest chain 19 peptides. Score 0.566 Taking the results from Round 5 Chains 90, Residues 560, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 18481 restraints for refining 8218 atoms. 16269 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2502 (Rfree = 0.000) for 8218 atoms. Found 45 (45 requested) and removed 50 (22 requested) atoms. Cycle 17: After refmac, R = 0.2222 (Rfree = 0.000) for 8140 atoms. Found 45 (45 requested) and removed 37 (22 requested) atoms. Cycle 18: After refmac, R = 0.2087 (Rfree = 0.000) for 8105 atoms. Found 44 (44 requested) and removed 38 (22 requested) atoms. Cycle 19: After refmac, R = 0.2038 (Rfree = 0.000) for 8087 atoms. Found 44 (44 requested) and removed 35 (22 requested) atoms. Cycle 20: After refmac, R = 0.1904 (Rfree = 0.000) for 8076 atoms. Found 44 (44 requested) and removed 33 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 8320 seeds are put forward NCS extension: 15 residues added (5 deleted due to clashes), 8335 seeds are put forward Round 1: 521 peptides, 92 chains. Longest chain 14 peptides. Score 0.396 Round 2: 593 peptides, 91 chains. Longest chain 15 peptides. Score 0.493 Round 3: 582 peptides, 82 chains. Longest chain 30 peptides. Score 0.526 Round 4: 587 peptides, 89 chains. Longest chain 27 peptides. Score 0.496 Round 5: 599 peptides, 85 chains. Longest chain 28 peptides. Score 0.531 Taking the results from Round 5 Chains 85, Residues 514, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 19101 restraints for refining 8219 atoms. 17130 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2416 (Rfree = 0.000) for 8219 atoms. Found 45 (45 requested) and removed 47 (22 requested) atoms. Cycle 22: After refmac, R = 0.2144 (Rfree = 0.000) for 8167 atoms. Found 45 (45 requested) and removed 38 (22 requested) atoms. Cycle 23: After refmac, R = 0.1933 (Rfree = 0.000) for 8142 atoms. Found 40 (44 requested) and removed 35 (22 requested) atoms. Cycle 24: After refmac, R = 0.1934 (Rfree = 0.000) for 8131 atoms. Found 44 (44 requested) and removed 37 (22 requested) atoms. Cycle 25: After refmac, R = 0.1839 (Rfree = 0.000) for 8125 atoms. Found 44 (44 requested) and removed 29 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 8416 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 8446 seeds are put forward Round 1: 497 peptides, 99 chains. Longest chain 14 peptides. Score 0.321 Round 2: 545 peptides, 79 chains. Longest chain 20 peptides. Score 0.499 Round 3: 565 peptides, 92 chains. Longest chain 25 peptides. Score 0.453 Round 4: 579 peptides, 83 chains. Longest chain 23 peptides. Score 0.518 Round 5: 564 peptides, 86 chains. Longest chain 25 peptides. Score 0.484 Taking the results from Round 4 Chains 83, Residues 496, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 18884 restraints for refining 8218 atoms. 16973 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2218 (Rfree = 0.000) for 8218 atoms. Found 45 (45 requested) and removed 46 (22 requested) atoms. Cycle 27: After refmac, R = 0.2063 (Rfree = 0.000) for 8155 atoms. Found 45 (45 requested) and removed 45 (22 requested) atoms. Cycle 28: After refmac, R = 0.1916 (Rfree = 0.000) for 8133 atoms. Found 44 (44 requested) and removed 37 (22 requested) atoms. Cycle 29: After refmac, R = 0.1874 (Rfree = 0.000) for 8127 atoms. Found 44 (44 requested) and removed 41 (22 requested) atoms. Cycle 30: After refmac, R = 0.1555 (Rfree = 0.000) for 8114 atoms. Found 18 (44 requested) and removed 30 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 8376 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 8399 seeds are put forward Round 1: 500 peptides, 96 chains. Longest chain 14 peptides. Score 0.344 Round 2: 519 peptides, 89 chains. Longest chain 14 peptides. Score 0.410 Round 3: 568 peptides, 93 chains. Longest chain 18 peptides. Score 0.452 Round 4: 556 peptides, 89 chains. Longest chain 19 peptides. Score 0.458 Round 5: 554 peptides, 83 chains. Longest chain 19 peptides. Score 0.488 Taking the results from Round 5 Chains 84, Residues 471, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 19249 restraints for refining 8219 atoms. 17432 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2442 (Rfree = 0.000) for 8219 atoms. Found 45 (45 requested) and removed 39 (22 requested) atoms. Cycle 32: After refmac, R = 0.2129 (Rfree = 0.000) for 8179 atoms. Found 45 (45 requested) and removed 40 (22 requested) atoms. Cycle 33: After refmac, R = 0.2045 (Rfree = 0.000) for 8158 atoms. Found 45 (45 requested) and removed 33 (22 requested) atoms. Cycle 34: After refmac, R = 0.1663 (Rfree = 0.000) for 8157 atoms. Found 25 (44 requested) and removed 28 (22 requested) atoms. Cycle 35: After refmac, R = 0.1573 (Rfree = 0.000) for 8142 atoms. Found 18 (44 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 8385 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8400 seeds are put forward Round 1: 424 peptides, 86 chains. Longest chain 10 peptides. Score 0.294 Round 2: 513 peptides, 89 chains. Longest chain 15 peptides. Score 0.402 Round 3: 501 peptides, 81 chains. Longest chain 19 peptides. Score 0.432 Round 4: 514 peptides, 83 chains. Longest chain 18 peptides. Score 0.438 Round 5: 494 peptides, 74 chains. Longest chain 15 peptides. Score 0.463 Taking the results from Round 5 Chains 75, Residues 420, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 19372 restraints for refining 8219 atoms. 17728 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2285 (Rfree = 0.000) for 8219 atoms. Found 45 (45 requested) and removed 47 (22 requested) atoms. Cycle 37: After refmac, R = 0.2095 (Rfree = 0.000) for 8182 atoms. Found 45 (45 requested) and removed 44 (22 requested) atoms. Cycle 38: After refmac, R = 0.2000 (Rfree = 0.000) for 8166 atoms. Found 45 (45 requested) and removed 34 (22 requested) atoms. Cycle 39: After refmac, R = 0.1950 (Rfree = 0.000) for 8170 atoms. Found 44 (44 requested) and removed 41 (22 requested) atoms. Cycle 40: After refmac, R = 0.1935 (Rfree = 0.000) for 8165 atoms. Found 44 (44 requested) and removed 36 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 8394 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 8411 seeds are put forward Round 1: 423 peptides, 90 chains. Longest chain 10 peptides. Score 0.267 Round 2: 451 peptides, 75 chains. Longest chain 12 peptides. Score 0.401 Round 3: 478 peptides, 79 chains. Longest chain 16 peptides. Score 0.414 Round 4: 465 peptides, 79 chains. Longest chain 20 peptides. Score 0.396 Round 5: 466 peptides, 76 chains. Longest chain 18 peptides. Score 0.415 Taking the results from Round 5 Chains 76, Residues 390, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 19482 restraints for refining 8219 atoms. 17938 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2329 (Rfree = 0.000) for 8219 atoms. Found 45 (45 requested) and removed 43 (22 requested) atoms. Cycle 42: After refmac, R = 0.2141 (Rfree = 0.000) for 8192 atoms. Found 45 (45 requested) and removed 41 (22 requested) atoms. Cycle 43: After refmac, R = 0.1870 (Rfree = 0.000) for 8172 atoms. Found 45 (45 requested) and removed 30 (22 requested) atoms. Cycle 44: After refmac, R = 0.1479 (Rfree = 0.000) for 8178 atoms. Found 20 (45 requested) and removed 28 (22 requested) atoms. Cycle 45: After refmac, R = 0.1365 (Rfree = 0.000) for 8167 atoms. Found 13 (44 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 8346 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 8363 seeds are put forward Round 1: 371 peptides, 76 chains. Longest chain 11 peptides. Score 0.277 Round 2: 421 peptides, 76 chains. Longest chain 13 peptides. Score 0.352 Round 3: 433 peptides, 74 chains. Longest chain 16 peptides. Score 0.382 Round 4: 423 peptides, 69 chains. Longest chain 13 peptides. Score 0.398 Round 5: 421 peptides, 72 chains. Longest chain 14 peptides. Score 0.377 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 69, Residues 354, 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 2hx1-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12229 reflections ( 99.65 % complete ) and 19783 restraints for refining 8218 atoms. 18436 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2101 (Rfree = 0.000) for 8218 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 47: After refmac, R = 0.2160 (Rfree = 0.000) for 8162 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 48: After refmac, R = 0.1874 (Rfree = 0.000) for 8123 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Cycle 49: After refmac, R = 0.1941 (Rfree = 0.000) for 8080 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 02:18:38 GMT 2018 Job finished. TimeTaking 98.59 Used memory is bytes: 9823312