null Sun 23 Dec 23:44:32 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 2hx1-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hx1-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hx1-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.6-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/2hx1-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.6-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 ============================================================ Sun 23 Dec 23:44:37 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/2hx1-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.6-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 849 and 0 Target number of residues in the AU: 849 Target solvent content: 0.6126 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: 2hx1-3.6-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: 2hx1-3.6-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 3.600 Wilson plot Bfac: 58.00 14332 reflections ( 99.70 % complete ) and 0 restraints for refining 10070 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3272 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3157 (Rfree = 0.000) for 10070 atoms. Found 64 (64 requested) and removed 70 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 10281 seeds are put forward NCS extension: 0 residues added, 10281 seeds are put forward Round 1: 497 peptides, 100 chains. Longest chain 11 peptides. Score 0.315 Round 2: 635 peptides, 95 chains. Longest chain 21 peptides. Score 0.522 Round 3: 676 peptides, 96 chains. Longest chain 21 peptides. Score 0.562 Round 4: 699 peptides, 92 chains. Longest chain 23 peptides. Score 0.604 Round 5: 698 peptides, 85 chains. Longest chain 29 peptides. Score 0.633 Taking the results from Round 5 Chains 86, Residues 613, Estimated correctness of the model 27.1 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 18079 restraints for refining 8237 atoms. 15635 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2825 (Rfree = 0.000) for 8237 atoms. Found 47 (52 requested) and removed 46 (26 requested) atoms. Cycle 2: After refmac, R = 0.2442 (Rfree = 0.000) for 8125 atoms. Found 34 (52 requested) and removed 50 (26 requested) atoms. Cycle 3: After refmac, R = 0.2359 (Rfree = 0.000) for 8068 atoms. Found 36 (52 requested) and removed 45 (26 requested) atoms. Cycle 4: After refmac, R = 0.2148 (Rfree = 0.000) for 8030 atoms. Found 24 (51 requested) and removed 38 (25 requested) atoms. Cycle 5: After refmac, R = 0.2105 (Rfree = 0.000) for 7995 atoms. Found 30 (51 requested) and removed 36 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 8287 seeds are put forward NCS extension: 37 residues added (13 deleted due to clashes), 8324 seeds are put forward Round 1: 604 peptides, 97 chains. Longest chain 21 peptides. Score 0.475 Round 2: 692 peptides, 86 chains. Longest chain 27 peptides. Score 0.623 Round 3: 721 peptides, 90 chains. Longest chain 23 peptides. Score 0.633 Round 4: 721 peptides, 82 chains. Longest chain 25 peptides. Score 0.666 Round 5: 721 peptides, 89 chains. Longest chain 25 peptides. Score 0.637 Taking the results from Round 4 Chains 85, Residues 639, Estimated correctness of the model 38.6 % 4 chains (39 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 17745 restraints for refining 8236 atoms. 15141 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2714 (Rfree = 0.000) for 8236 atoms. Found 52 (52 requested) and removed 50 (26 requested) atoms. Cycle 7: After refmac, R = 0.2418 (Rfree = 0.000) for 8171 atoms. Found 43 (52 requested) and removed 39 (26 requested) atoms. Cycle 8: After refmac, R = 0.2212 (Rfree = 0.000) for 8120 atoms. Found 30 (52 requested) and removed 38 (26 requested) atoms. Cycle 9: After refmac, R = 0.2151 (Rfree = 0.000) for 8077 atoms. Found 34 (52 requested) and removed 36 (26 requested) atoms. Cycle 10: After refmac, R = 0.2071 (Rfree = 0.000) for 8062 atoms. Found 23 (51 requested) and removed 39 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.28 3.37 Search for helices and strands: 0 residues in 0 chains, 8291 seeds are put forward NCS extension: 10 residues added (4 deleted due to clashes), 8301 seeds are put forward Round 1: 640 peptides, 109 chains. Longest chain 20 peptides. Score 0.456 Round 2: 678 peptides, 92 chains. Longest chain 28 peptides. Score 0.583 Round 3: 698 peptides, 96 chains. Longest chain 20 peptides. Score 0.585 Round 4: 690 peptides, 94 chains. Longest chain 29 peptides. Score 0.586 Round 5: 695 peptides, 95 chains. Longest chain 23 peptides. Score 0.586 Taking the results from Round 5 Chains 98, Residues 600, Estimated correctness of the model 9.1 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 18226 restraints for refining 8238 atoms. 15836 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2567 (Rfree = 0.000) for 8238 atoms. Found 52 (52 requested) and removed 61 (26 requested) atoms. Cycle 12: After refmac, R = 0.2378 (Rfree = 0.000) for 8190 atoms. Found 52 (52 requested) and removed 50 (26 requested) atoms. Cycle 13: After refmac, R = 0.2292 (Rfree = 0.000) for 8175 atoms. Found 38 (52 requested) and removed 53 (26 requested) atoms. Cycle 14: After refmac, R = 0.2241 (Rfree = 0.000) for 8152 atoms. Found 41 (52 requested) and removed 51 (26 requested) atoms. Cycle 15: After refmac, R = 0.2004 (Rfree = 0.000) for 8133 atoms. Found 16 (52 requested) and removed 41 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 8378 seeds are put forward NCS extension: 18 residues added (8 deleted due to clashes), 8396 seeds are put forward Round 1: 609 peptides, 105 chains. Longest chain 23 peptides. Score 0.438 Round 2: 668 peptides, 95 chains. Longest chain 17 peptides. Score 0.558 Round 3: 668 peptides, 94 chains. Longest chain 15 peptides. Score 0.563 Round 4: 666 peptides, 90 chains. Longest chain 20 peptides. Score 0.579 Round 5: 700 peptides, 94 chains. Longest chain 21 peptides. Score 0.596 Taking the results from Round 5 Chains 95, Residues 606, Estimated correctness of the model 13.1 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 18219 restraints for refining 8237 atoms. 15828 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2544 (Rfree = 0.000) for 8237 atoms. Found 52 (52 requested) and removed 55 (26 requested) atoms. Cycle 17: After refmac, R = 0.2267 (Rfree = 0.000) for 8170 atoms. Found 40 (52 requested) and removed 50 (26 requested) atoms. Cycle 18: After refmac, R = 0.2137 (Rfree = 0.000) for 8129 atoms. Found 23 (52 requested) and removed 34 (26 requested) atoms. Cycle 19: After refmac, R = 0.2029 (Rfree = 0.000) for 8102 atoms. Found 31 (52 requested) and removed 33 (26 requested) atoms. Cycle 20: After refmac, R = 0.1958 (Rfree = 0.000) for 8088 atoms. Found 29 (51 requested) and removed 31 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 8355 seeds are put forward NCS extension: 9 residues added (6 deleted due to clashes), 8364 seeds are put forward Round 1: 570 peptides, 102 chains. Longest chain 14 peptides. Score 0.404 Round 2: 608 peptides, 89 chains. Longest chain 19 peptides. Score 0.521 Round 3: 626 peptides, 87 chains. Longest chain 17 peptides. Score 0.551 Round 4: 657 peptides, 90 chains. Longest chain 22 peptides. Score 0.570 Round 5: 672 peptides, 89 chains. Longest chain 22 peptides. Score 0.590 Taking the results from Round 5 Chains 89, Residues 583, Estimated correctness of the model 10.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 18418 restraints for refining 8237 atoms. 16175 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2376 (Rfree = 0.000) for 8237 atoms. Found 52 (52 requested) and removed 36 (26 requested) atoms. Cycle 22: After refmac, R = 0.2158 (Rfree = 0.000) for 8230 atoms. Found 20 (52 requested) and removed 38 (26 requested) atoms. Cycle 23: After refmac, R = 0.2047 (Rfree = 0.000) for 8202 atoms. Found 19 (52 requested) and removed 31 (26 requested) atoms. Cycle 24: After refmac, R = 0.1997 (Rfree = 0.000) for 8177 atoms. Found 17 (52 requested) and removed 31 (26 requested) atoms. Cycle 25: After refmac, R = 0.1942 (Rfree = 0.000) for 8159 atoms. Found 19 (52 requested) and removed 31 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 3.35 Search for helices and strands: 0 residues in 0 chains, 8426 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 8446 seeds are put forward Round 1: 537 peptides, 99 chains. Longest chain 16 peptides. Score 0.377 Round 2: 591 peptides, 82 chains. Longest chain 20 peptides. Score 0.537 Round 3: 586 peptides, 79 chains. Longest chain 21 peptides. Score 0.546 Round 4: 640 peptides, 85 chains. Longest chain 17 peptides. Score 0.575 Round 5: 645 peptides, 91 chains. Longest chain 18 peptides. Score 0.552 Taking the results from Round 4 Chains 86, Residues 555, Estimated correctness of the model 4.6 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 18543 restraints for refining 8238 atoms. 16378 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2281 (Rfree = 0.000) for 8238 atoms. Found 52 (52 requested) and removed 40 (26 requested) atoms. Cycle 27: After refmac, R = 0.2265 (Rfree = 0.000) for 8230 atoms. Found 52 (52 requested) and removed 42 (26 requested) atoms. Cycle 28: After refmac, R = 0.2138 (Rfree = 0.000) for 8226 atoms. Found 52 (52 requested) and removed 36 (26 requested) atoms. Cycle 29: After refmac, R = 0.2067 (Rfree = 0.000) for 8233 atoms. Found 36 (52 requested) and removed 38 (26 requested) atoms. Cycle 30: After refmac, R = 0.2045 (Rfree = 0.000) for 8225 atoms. Found 52 (52 requested) and removed 33 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 8511 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 8531 seeds are put forward Round 1: 550 peptides, 100 chains. Longest chain 13 peptides. Score 0.389 Round 2: 630 peptides, 91 chains. Longest chain 20 peptides. Score 0.536 Round 3: 662 peptides, 97 chains. Longest chain 18 peptides. Score 0.542 Round 4: 656 peptides, 94 chains. Longest chain 18 peptides. Score 0.550 Round 5: 641 peptides, 89 chains. Longest chain 25 peptides. Score 0.558 Taking the results from Round 5 Chains 89, Residues 552, Estimated correctness of the model 0.0 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 18370 restraints for refining 8238 atoms. 16169 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2512 (Rfree = 0.000) for 8238 atoms. Found 52 (52 requested) and removed 41 (26 requested) atoms. Cycle 32: After refmac, R = 0.2322 (Rfree = 0.000) for 8216 atoms. Found 45 (52 requested) and removed 40 (26 requested) atoms. Cycle 33: After refmac, R = 0.2238 (Rfree = 0.000) for 8193 atoms. Found 43 (52 requested) and removed 37 (26 requested) atoms. Cycle 34: After refmac, R = 0.2074 (Rfree = 0.000) for 8189 atoms. Found 30 (52 requested) and removed 38 (26 requested) atoms. Cycle 35: After refmac, R = 0.2113 (Rfree = 0.000) for 8171 atoms. Found 31 (52 requested) and removed 30 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.38 Search for helices and strands: 0 residues in 0 chains, 8429 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 8447 seeds are put forward Round 1: 525 peptides, 99 chains. Longest chain 11 peptides. Score 0.361 Round 2: 593 peptides, 94 chains. Longest chain 17 peptides. Score 0.477 Round 3: 597 peptides, 90 chains. Longest chain 22 peptides. Score 0.503 Round 4: 607 peptides, 88 chains. Longest chain 17 peptides. Score 0.525 Round 5: 586 peptides, 82 chains. Longest chain 23 peptides. Score 0.531 Taking the results from Round 5 Chains 82, Residues 504, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 18876 restraints for refining 8238 atoms. 16942 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2297 (Rfree = 0.000) for 8238 atoms. Found 52 (52 requested) and removed 45 (26 requested) atoms. Cycle 37: After refmac, R = 0.2229 (Rfree = 0.000) for 8217 atoms. Found 48 (52 requested) and removed 31 (26 requested) atoms. Cycle 38: After refmac, R = 0.2117 (Rfree = 0.000) for 8210 atoms. Found 52 (52 requested) and removed 36 (26 requested) atoms. Cycle 39: After refmac, R = 0.2032 (Rfree = 0.000) for 8218 atoms. Found 48 (52 requested) and removed 31 (26 requested) atoms. Cycle 40: After refmac, R = 0.1798 (Rfree = 0.000) for 8228 atoms. Found 24 (52 requested) and removed 30 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 8443 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 8460 seeds are put forward Round 1: 501 peptides, 85 chains. Longest chain 14 peptides. Score 0.409 Round 2: 529 peptides, 81 chains. Longest chain 19 peptides. Score 0.468 Round 3: 566 peptides, 79 chains. Longest chain 21 peptides. Score 0.523 Round 4: 564 peptides, 78 chains. Longest chain 18 peptides. Score 0.526 Round 5: 577 peptides, 78 chains. Longest chain 17 peptides. Score 0.541 Taking the results from Round 5 Chains 78, Residues 499, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 18926 restraints for refining 8238 atoms. 16971 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2440 (Rfree = 0.000) for 8238 atoms. Found 52 (52 requested) and removed 41 (26 requested) atoms. Cycle 42: After refmac, R = 0.2315 (Rfree = 0.000) for 8218 atoms. Found 52 (52 requested) and removed 32 (26 requested) atoms. Cycle 43: After refmac, R = 0.2191 (Rfree = 0.000) for 8225 atoms. Found 44 (52 requested) and removed 33 (26 requested) atoms. Cycle 44: After refmac, R = 0.2113 (Rfree = 0.000) for 8222 atoms. Found 52 (52 requested) and removed 33 (26 requested) atoms. Cycle 45: After refmac, R = 0.2200 (Rfree = 0.000) for 8230 atoms. Found 52 (52 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 8482 seeds are put forward NCS extension: 8 residues added (4 deleted due to clashes), 8490 seeds are put forward Round 1: 455 peptides, 87 chains. Longest chain 16 peptides. Score 0.334 Round 2: 521 peptides, 85 chains. Longest chain 20 peptides. Score 0.436 Round 3: 556 peptides, 83 chains. Longest chain 27 peptides. Score 0.491 Round 4: 549 peptides, 84 chains. Longest chain 18 peptides. Score 0.477 Round 5: 559 peptides, 86 chains. Longest chain 15 peptides. Score 0.478 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 84, Residues 473, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2hx1-3_warpNtrace.pdb as input Building loops using Loopy2018 84 chains (473 residues) following loop building 3 chains (24 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14332 reflections ( 99.70 % complete ) and 18773 restraints for refining 8237 atoms. 16899 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2327 (Rfree = 0.000) for 8237 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 47: After refmac, R = 0.2153 (Rfree = 0.000) for 8178 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 48: After refmac, R = 0.2029 (Rfree = 0.000) for 8137 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 49: After refmac, R = 0.2051 (Rfree = 0.000) for 8099 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:18:44 GMT 2018 Job finished. TimeTaking 94.22 Used memory is bytes: 21375944