null Mon 24 Dec 08:00:04 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 2hx1-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2hx1-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2hx1-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.8-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/2hx1-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.8-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 08:00:08 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/2hx1-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.8-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 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-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: 65.624 119.462 151.274 90.000 90.000 90.000 Input sequence file: 2hx1-3.8-parrot-noncs.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 10062 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3437 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3630 (Rfree = 0.000) for 10062 atoms. Found 55 (55 requested) and removed 150 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 3.56 Search for helices and strands: 0 residues in 0 chains, 10181 seeds are put forward NCS extension: 0 residues added, 10181 seeds are put forward Round 1: 346 peptides, 75 chains. Longest chain 9 peptides. Score 0.244 Round 2: 482 peptides, 90 chains. Longest chain 13 peptides. Score 0.354 Round 3: 502 peptides, 89 chains. Longest chain 14 peptides. Score 0.388 Round 4: 543 peptides, 90 chains. Longest chain 17 peptides. Score 0.436 Round 5: 577 peptides, 90 chains. Longest chain 19 peptides. Score 0.479 Taking the results from Round 5 Chains 92, Residues 487, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 18777 restraints for refining 8219 atoms. 16886 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3249 (Rfree = 0.000) for 8219 atoms. Found 45 (45 requested) and removed 70 (22 requested) atoms. Cycle 2: After refmac, R = 0.2907 (Rfree = 0.000) for 8016 atoms. Found 45 (45 requested) and removed 64 (22 requested) atoms. Cycle 3: After refmac, R = 0.2476 (Rfree = 0.000) for 7893 atoms. Found 34 (43 requested) and removed 35 (21 requested) atoms. Cycle 4: After refmac, R = 0.2392 (Rfree = 0.000) for 7837 atoms. Found 25 (43 requested) and removed 36 (21 requested) atoms. Cycle 5: After refmac, R = 0.2491 (Rfree = 0.000) for 7798 atoms. Found 43 (43 requested) and removed 32 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 8047 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 8072 seeds are put forward Round 1: 480 peptides, 94 chains. Longest chain 17 peptides. Score 0.327 Round 2: 578 peptides, 90 chains. Longest chain 23 peptides. Score 0.480 Round 3: 613 peptides, 98 chains. Longest chain 15 peptides. Score 0.480 Round 4: 611 peptides, 91 chains. Longest chain 25 peptides. Score 0.514 Round 5: 611 peptides, 90 chains. Longest chain 19 peptides. Score 0.519 Taking the results from Round 5 Chains 90, Residues 521, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 18860 restraints for refining 8186 atoms. 16866 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2865 (Rfree = 0.000) for 8186 atoms. Found 45 (45 requested) and removed 66 (22 requested) atoms. Cycle 7: After refmac, R = 0.2654 (Rfree = 0.000) for 8057 atoms. Found 44 (44 requested) and removed 64 (22 requested) atoms. Cycle 8: After refmac, R = 0.2652 (Rfree = 0.000) for 7974 atoms. Found 44 (44 requested) and removed 50 (22 requested) atoms. Cycle 9: After refmac, R = 0.2597 (Rfree = 0.000) for 7921 atoms. Found 43 (43 requested) and removed 49 (21 requested) atoms. Cycle 10: After refmac, R = 0.2284 (Rfree = 0.000) for 7888 atoms. Found 39 (43 requested) and removed 38 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.54 Search for helices and strands: 0 residues in 0 chains, 8147 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 8170 seeds are put forward Round 1: 492 peptides, 96 chains. Longest chain 12 peptides. Score 0.332 Round 2: 562 peptides, 93 chains. Longest chain 13 peptides. Score 0.444 Round 3: 592 peptides, 94 chains. Longest chain 15 peptides. Score 0.476 Round 4: 594 peptides, 96 chains. Longest chain 13 peptides. Score 0.468 Round 5: 594 peptides, 89 chains. Longest chain 17 peptides. Score 0.505 Taking the results from Round 5 Chains 89, Residues 505, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 18879 restraints for refining 8218 atoms. 16948 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2893 (Rfree = 0.000) for 8218 atoms. Found 45 (45 requested) and removed 58 (22 requested) atoms. Cycle 12: After refmac, R = 0.2613 (Rfree = 0.000) for 8130 atoms. Found 45 (45 requested) and removed 53 (22 requested) atoms. Cycle 13: After refmac, R = 0.2503 (Rfree = 0.000) for 8050 atoms. Found 44 (44 requested) and removed 37 (22 requested) atoms. Cycle 14: After refmac, R = 0.2406 (Rfree = 0.000) for 8025 atoms. Found 44 (44 requested) and removed 35 (22 requested) atoms. Cycle 15: After refmac, R = 0.2333 (Rfree = 0.000) for 8008 atoms. Found 44 (44 requested) and removed 39 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 8245 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 8264 seeds are put forward Round 1: 454 peptides, 88 chains. Longest chain 13 peptides. Score 0.326 Round 2: 529 peptides, 86 chains. Longest chain 16 peptides. Score 0.441 Round 3: 559 peptides, 90 chains. Longest chain 14 peptides. Score 0.457 Round 4: 564 peptides, 89 chains. Longest chain 15 peptides. Score 0.468 Round 5: 596 peptides, 92 chains. Longest chain 21 peptides. Score 0.491 Taking the results from Round 5 Chains 93, Residues 504, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 18719 restraints for refining 8219 atoms. 16758 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2753 (Rfree = 0.000) for 8219 atoms. Found 45 (45 requested) and removed 38 (22 requested) atoms. Cycle 17: After refmac, R = 0.2387 (Rfree = 0.000) for 8126 atoms. Found 45 (45 requested) and removed 54 (22 requested) atoms. Cycle 18: After refmac, R = 0.2216 (Rfree = 0.000) for 8071 atoms. Found 44 (44 requested) and removed 50 (22 requested) atoms. Cycle 19: After refmac, R = 0.2109 (Rfree = 0.000) for 8045 atoms. Found 44 (44 requested) and removed 44 (22 requested) atoms. Cycle 20: After refmac, R = 0.1727 (Rfree = 0.000) for 8035 atoms. Found 14 (44 requested) and removed 41 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.50 Search for helices and strands: 0 residues in 0 chains, 8269 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 8290 seeds are put forward Round 1: 490 peptides, 94 chains. Longest chain 11 peptides. Score 0.341 Round 2: 550 peptides, 86 chains. Longest chain 22 peptides. Score 0.467 Round 3: 550 peptides, 85 chains. Longest chain 14 peptides. Score 0.473 Round 4: 589 peptides, 82 chains. Longest chain 15 peptides. Score 0.534 Round 5: 592 peptides, 91 chains. Longest chain 20 peptides. Score 0.492 Taking the results from Round 4 Chains 82, Residues 507, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 18713 restraints for refining 8219 atoms. 16709 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2410 (Rfree = 0.000) for 8219 atoms. Found 45 (45 requested) and removed 61 (22 requested) atoms. Cycle 22: After refmac, R = 0.2099 (Rfree = 0.000) for 8144 atoms. Found 45 (45 requested) and removed 43 (22 requested) atoms. Cycle 23: After refmac, R = 0.1726 (Rfree = 0.000) for 8104 atoms. Found 27 (44 requested) and removed 29 (22 requested) atoms. Cycle 24: After refmac, R = 0.1608 (Rfree = 0.000) for 8079 atoms. Found 16 (44 requested) and removed 33 (22 requested) atoms. Cycle 25: After refmac, R = 0.1581 (Rfree = 0.000) for 8053 atoms. Found 7 (44 requested) and removed 29 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.50 Search for helices and strands: 0 residues in 0 chains, 8249 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 8263 seeds are put forward Round 1: 473 peptides, 92 chains. Longest chain 16 peptides. Score 0.329 Round 2: 540 peptides, 82 chains. Longest chain 18 peptides. Score 0.476 Round 3: 562 peptides, 90 chains. Longest chain 17 peptides. Score 0.460 Round 4: 563 peptides, 78 chains. Longest chain 25 peptides. Score 0.525 Round 5: 552 peptides, 80 chains. Longest chain 22 peptides. Score 0.502 Taking the results from Round 4 Chains 80, Residues 485, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 18689 restraints for refining 8218 atoms. 16732 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2442 (Rfree = 0.000) for 8218 atoms. Found 45 (45 requested) and removed 54 (22 requested) atoms. Cycle 27: After refmac, R = 0.2187 (Rfree = 0.000) for 8147 atoms. Found 45 (45 requested) and removed 38 (22 requested) atoms. Cycle 28: After refmac, R = 0.2082 (Rfree = 0.000) for 8120 atoms. Found 44 (44 requested) and removed 38 (22 requested) atoms. Cycle 29: After refmac, R = 0.1938 (Rfree = 0.000) for 8102 atoms. Found 33 (44 requested) and removed 32 (22 requested) atoms. Cycle 30: After refmac, R = 0.1914 (Rfree = 0.000) for 8079 atoms. Found 38 (44 requested) and removed 35 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 8312 seeds are put forward NCS extension: 54 residues added (2 deleted due to clashes), 8366 seeds are put forward Round 1: 458 peptides, 88 chains. Longest chain 10 peptides. Score 0.332 Round 2: 508 peptides, 81 chains. Longest chain 18 peptides. Score 0.442 Round 3: 515 peptides, 80 chains. Longest chain 18 peptides. Score 0.456 Round 4: 506 peptides, 83 chains. Longest chain 14 peptides. Score 0.428 Round 5: 491 peptides, 74 chains. Longest chain 21 peptides. Score 0.459 Taking the results from Round 5 Chains 74, Residues 417, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 19359 restraints for refining 8220 atoms. 17765 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2516 (Rfree = 0.000) for 8220 atoms. Found 45 (45 requested) and removed 42 (22 requested) atoms. Cycle 32: After refmac, R = 0.2266 (Rfree = 0.000) for 8156 atoms. Found 45 (45 requested) and removed 46 (22 requested) atoms. Cycle 33: After refmac, R = 0.1810 (Rfree = 0.000) for 8117 atoms. Found 19 (44 requested) and removed 25 (22 requested) atoms. Cycle 34: After refmac, R = 0.1591 (Rfree = 0.000) for 8090 atoms. Found 13 (44 requested) and removed 25 (22 requested) atoms. Cycle 35: After refmac, R = 0.1520 (Rfree = 0.000) for 8066 atoms. Found 11 (44 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 8239 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 8269 seeds are put forward Round 1: 411 peptides, 85 chains. Longest chain 11 peptides. Score 0.281 Round 2: 444 peptides, 79 chains. Longest chain 14 peptides. Score 0.367 Round 3: 460 peptides, 78 chains. Longest chain 14 peptides. Score 0.395 Round 4: 474 peptides, 78 chains. Longest chain 13 peptides. Score 0.414 Round 5: 479 peptides, 73 chains. Longest chain 15 peptides. Score 0.450 Taking the results from Round 5 Chains 73, Residues 406, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 19368 restraints for refining 8220 atoms. 17817 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2380 (Rfree = 0.000) for 8220 atoms. Found 45 (45 requested) and removed 40 (22 requested) atoms. Cycle 37: After refmac, R = 0.2088 (Rfree = 0.000) for 8179 atoms. Found 45 (45 requested) and removed 41 (22 requested) atoms. Cycle 38: After refmac, R = 0.1677 (Rfree = 0.000) for 8157 atoms. Found 21 (45 requested) and removed 36 (22 requested) atoms. Cycle 39: After refmac, R = 0.1514 (Rfree = 0.000) for 8118 atoms. Found 19 (44 requested) and removed 26 (22 requested) atoms. Cycle 40: After refmac, R = 0.1480 (Rfree = 0.000) for 8097 atoms. Found 16 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 8287 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8302 seeds are put forward Round 1: 390 peptides, 77 chains. Longest chain 10 peptides. Score 0.300 Round 2: 464 peptides, 80 chains. Longest chain 14 peptides. Score 0.389 Round 3: 433 peptides, 73 chains. Longest chain 15 peptides. Score 0.388 Round 4: 448 peptides, 72 chains. Longest chain 17 peptides. Score 0.414 Round 5: 457 peptides, 75 chains. Longest chain 19 peptides. Score 0.409 Taking the results from Round 4 Chains 72, Residues 376, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 19381 restraints for refining 8220 atoms. 17928 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2391 (Rfree = 0.000) for 8220 atoms. Found 45 (45 requested) and removed 47 (22 requested) atoms. Cycle 42: After refmac, R = 0.2359 (Rfree = 0.000) for 8175 atoms. Found 45 (45 requested) and removed 45 (22 requested) atoms. Cycle 43: After refmac, R = 0.2156 (Rfree = 0.000) for 8151 atoms. Found 44 (44 requested) and removed 39 (22 requested) atoms. Cycle 44: After refmac, R = 0.1635 (Rfree = 0.000) for 8128 atoms. Found 24 (44 requested) and removed 30 (22 requested) atoms. Cycle 45: After refmac, R = 0.1468 (Rfree = 0.000) for 8112 atoms. Found 11 (44 requested) and removed 29 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 3.50 Search for helices and strands: 0 residues in 0 chains, 8266 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 8294 seeds are put forward Round 1: 349 peptides, 74 chains. Longest chain 9 peptides. Score 0.256 Round 2: 395 peptides, 74 chains. Longest chain 12 peptides. Score 0.327 Round 3: 409 peptides, 71 chains. Longest chain 18 peptides. Score 0.366 Round 4: 415 peptides, 70 chains. Longest chain 18 peptides. Score 0.381 Round 5: 401 peptides, 69 chains. Longest chain 14 peptides. Score 0.367 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 71, Residues 345, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2hx1-3_warpNtrace.pdb as input Building loops using Loopy2018 71 chains (345 residues) following loop building 4 chains (22 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12229 reflections ( 99.65 % complete ) and 19340 restraints for refining 8219 atoms. 17955 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2411 (Rfree = 0.000) for 8219 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 47: After refmac, R = 0.2298 (Rfree = 0.000) for 8151 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 48: After refmac, R = 0.2184 (Rfree = 0.000) for 8089 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Cycle 49: After refmac, R = 0.2115 (Rfree = 0.000) for 8037 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:16:36 GMT 2018 Job finished. TimeTaking 76.54 Used memory is bytes: 9184200