Sun 23 Dec 22:23:10 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 2hx1-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hx1-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hx1-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hx1-3.8-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/2hx1-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hx1-3.8-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 22:23:20 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/2hx1-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hx1-3.8-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 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-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: 19 Cell parameters: 65.624 119.462 151.274 90.000 90.000 90.000 Input sequence file: 2hx1-3.8-parrot-hancs.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 10008 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3312 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3488 (Rfree = 0.000) for 10008 atoms. Found 55 (55 requested) and removed 77 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 10188 seeds are put forward NCS extension: 0 residues added, 10188 seeds are put forward Round 1: 403 peptides, 84 chains. Longest chain 9 peptides. Score 0.275 Round 2: 532 peptides, 89 chains. Longest chain 26 peptides. Score 0.428 Round 3: 592 peptides, 97 chains. Longest chain 14 peptides. Score 0.460 Round 4: 622 peptides, 89 chains. Longest chain 22 peptides. Score 0.537 Round 5: 658 peptides, 87 chains. Longest chain 31 peptides. Score 0.585 Taking the results from Round 5 Chains 89, Residues 571, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 18483 restraints for refining 8220 atoms. 16221 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3135 (Rfree = 0.000) for 8220 atoms. Found 45 (45 requested) and removed 58 (22 requested) atoms. Cycle 2: After refmac, R = 0.2927 (Rfree = 0.000) for 8021 atoms. Found 45 (45 requested) and removed 88 (22 requested) atoms. Cycle 3: After refmac, R = 0.2608 (Rfree = 0.000) for 7887 atoms. Found 18 (43 requested) and removed 56 (21 requested) atoms. Cycle 4: After refmac, R = 0.2580 (Rfree = 0.000) for 7803 atoms. Found 28 (43 requested) and removed 38 (21 requested) atoms. Cycle 5: After refmac, R = 0.2730 (Rfree = 0.000) for 7778 atoms. Found 38 (42 requested) and removed 62 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.55 Search for helices and strands: 0 residues in 0 chains, 8018 seeds are put forward NCS extension: 19 residues added (7 deleted due to clashes), 8037 seeds are put forward Round 1: 501 peptides, 93 chains. Longest chain 14 peptides. Score 0.363 Round 2: 569 peptides, 87 chains. Longest chain 17 peptides. Score 0.485 Round 3: 615 peptides, 86 chains. Longest chain 20 peptides. Score 0.544 Round 4: 602 peptides, 81 chains. Longest chain 28 peptides. Score 0.554 Round 5: 622 peptides, 85 chains. Longest chain 27 peptides. Score 0.556 Taking the results from Round 5 Chains 85, Residues 537, Estimated correctness of the model 0.0 % 3 chains (38 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 18476 restraints for refining 8220 atoms. 16295 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2907 (Rfree = 0.000) for 8220 atoms. Found 45 (45 requested) and removed 102 (22 requested) atoms. Cycle 7: After refmac, R = 0.2619 (Rfree = 0.000) for 8082 atoms. Found 44 (44 requested) and removed 57 (22 requested) atoms. Cycle 8: After refmac, R = 0.2116 (Rfree = 0.000) for 8006 atoms. Found 25 (44 requested) and removed 41 (22 requested) atoms. Cycle 9: After refmac, R = 0.1941 (Rfree = 0.000) for 7962 atoms. Found 11 (43 requested) and removed 38 (21 requested) atoms. Cycle 10: After refmac, R = 0.1917 (Rfree = 0.000) for 7918 atoms. Found 5 (43 requested) and removed 38 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 8192 seeds are put forward NCS extension: 27 residues added (5 deleted due to clashes), 8219 seeds are put forward Round 1: 504 peptides, 90 chains. Longest chain 11 peptides. Score 0.385 Round 2: 571 peptides, 90 chains. Longest chain 24 peptides. Score 0.472 Round 3: 584 peptides, 93 chains. Longest chain 20 peptides. Score 0.471 Round 4: 583 peptides, 89 chains. Longest chain 17 peptides. Score 0.491 Round 5: 607 peptides, 86 chains. Longest chain 20 peptides. Score 0.535 Taking the results from Round 5 Chains 86, Residues 521, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 18698 restraints for refining 8218 atoms. 16671 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2911 (Rfree = 0.000) for 8218 atoms. Found 45 (45 requested) and removed 46 (22 requested) atoms. Cycle 12: After refmac, R = 0.2455 (Rfree = 0.000) for 8136 atoms. Found 45 (45 requested) and removed 48 (22 requested) atoms. Cycle 13: After refmac, R = 0.2042 (Rfree = 0.000) for 8093 atoms. Found 27 (44 requested) and removed 36 (22 requested) atoms. Cycle 14: After refmac, R = 0.1931 (Rfree = 0.000) for 8053 atoms. Found 21 (44 requested) and removed 32 (22 requested) atoms. Cycle 15: After refmac, R = 0.1922 (Rfree = 0.000) for 8027 atoms. Found 17 (44 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 8264 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 8288 seeds are put forward Round 1: 513 peptides, 100 chains. Longest chain 10 peptides. Score 0.338 Round 2: 573 peptides, 91 chains. Longest chain 19 peptides. Score 0.469 Round 3: 572 peptides, 89 chains. Longest chain 20 peptides. Score 0.478 Round 4: 604 peptides, 85 chains. Longest chain 28 peptides. Score 0.536 Round 5: 604 peptides, 90 chains. Longest chain 17 peptides. Score 0.511 Taking the results from Round 4 Chains 86, Residues 519, Estimated correctness of the model 0.0 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 18453 restraints for refining 8219 atoms. 16364 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2797 (Rfree = 0.000) for 8219 atoms. Found 45 (45 requested) and removed 53 (22 requested) atoms. Cycle 17: After refmac, R = 0.2443 (Rfree = 0.000) for 8140 atoms. Found 45 (45 requested) and removed 38 (22 requested) atoms. Cycle 18: After refmac, R = 0.2371 (Rfree = 0.000) for 8096 atoms. Found 44 (44 requested) and removed 37 (22 requested) atoms. Cycle 19: After refmac, R = 0.1891 (Rfree = 0.000) for 8070 atoms. Found 22 (44 requested) and removed 35 (22 requested) atoms. Cycle 20: After refmac, R = 0.1780 (Rfree = 0.000) for 8034 atoms. Found 16 (44 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 8240 seeds are put forward NCS extension: 32 residues added (1 deleted due to clashes), 8272 seeds are put forward Round 1: 477 peptides, 94 chains. Longest chain 10 peptides. Score 0.323 Round 2: 562 peptides, 92 chains. Longest chain 16 peptides. Score 0.449 Round 3: 562 peptides, 89 chains. Longest chain 19 peptides. Score 0.466 Round 4: 595 peptides, 83 chains. Longest chain 18 peptides. Score 0.536 Round 5: 573 peptides, 83 chains. Longest chain 16 peptides. Score 0.511 Taking the results from Round 4 Chains 83, Residues 512, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 18865 restraints for refining 8216 atoms. 16900 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2758 (Rfree = 0.000) for 8216 atoms. Found 45 (45 requested) and removed 55 (22 requested) atoms. Cycle 22: After refmac, R = 0.2494 (Rfree = 0.000) for 8142 atoms. Found 45 (45 requested) and removed 44 (22 requested) atoms. Cycle 23: After refmac, R = 0.2303 (Rfree = 0.000) for 8096 atoms. Found 44 (44 requested) and removed 40 (22 requested) atoms. Cycle 24: After refmac, R = 0.2147 (Rfree = 0.000) for 8080 atoms. Found 35 (44 requested) and removed 39 (22 requested) atoms. Cycle 25: After refmac, R = 0.1942 (Rfree = 0.000) for 8059 atoms. Found 19 (44 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 8278 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 8291 seeds are put forward Round 1: 469 peptides, 90 chains. Longest chain 12 peptides. Score 0.335 Round 2: 544 peptides, 86 chains. Longest chain 14 peptides. Score 0.460 Round 3: 564 peptides, 86 chains. Longest chain 16 peptides. Score 0.484 Round 4: 564 peptides, 86 chains. Longest chain 16 peptides. Score 0.484 Round 5: 565 peptides, 83 chains. Longest chain 16 peptides. Score 0.501 Taking the results from Round 5 Chains 83, Residues 482, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 18912 restraints for refining 8219 atoms. 17058 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2628 (Rfree = 0.000) for 8219 atoms. Found 45 (45 requested) and removed 45 (22 requested) atoms. Cycle 27: After refmac, R = 0.2280 (Rfree = 0.000) for 8167 atoms. Found 45 (45 requested) and removed 38 (22 requested) atoms. Cycle 28: After refmac, R = 0.1927 (Rfree = 0.000) for 8141 atoms. Found 27 (44 requested) and removed 35 (22 requested) atoms. Cycle 29: After refmac, R = 0.1826 (Rfree = 0.000) for 8121 atoms. Found 11 (44 requested) and removed 32 (22 requested) atoms. Cycle 30: After refmac, R = 0.1938 (Rfree = 0.000) for 8095 atoms. Found 8 (44 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.52 Search for helices and strands: 0 residues in 0 chains, 8299 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 8320 seeds are put forward Round 1: 486 peptides, 96 chains. Longest chain 10 peptides. Score 0.324 Round 2: 534 peptides, 88 chains. Longest chain 14 peptides. Score 0.436 Round 3: 541 peptides, 83 chains. Longest chain 16 peptides. Score 0.472 Round 4: 528 peptides, 84 chains. Longest chain 14 peptides. Score 0.450 Round 5: 526 peptides, 88 chains. Longest chain 16 peptides. Score 0.425 Taking the results from Round 3 Chains 84, Residues 458, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 18821 restraints for refining 8220 atoms. 17044 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2438 (Rfree = 0.000) for 8220 atoms. Found 45 (45 requested) and removed 39 (22 requested) atoms. Cycle 32: After refmac, R = 0.2303 (Rfree = 0.000) for 8195 atoms. Found 45 (45 requested) and removed 49 (22 requested) atoms. Cycle 33: After refmac, R = 0.2074 (Rfree = 0.000) for 8166 atoms. Found 45 (45 requested) and removed 34 (22 requested) atoms. Cycle 34: After refmac, R = 0.2124 (Rfree = 0.000) for 8164 atoms. Found 44 (44 requested) and removed 39 (22 requested) atoms. Cycle 35: After refmac, R = 0.1732 (Rfree = 0.000) for 8157 atoms. Found 17 (44 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 8398 seeds are put forward NCS extension: 20 residues added (6 deleted due to clashes), 8418 seeds are put forward Round 1: 450 peptides, 89 chains. Longest chain 11 peptides. Score 0.314 Round 2: 489 peptides, 77 chains. Longest chain 15 peptides. Score 0.440 Round 3: 510 peptides, 80 chains. Longest chain 17 peptides. Score 0.450 Round 4: 518 peptides, 80 chains. Longest chain 14 peptides. Score 0.460 Round 5: 502 peptides, 75 chains. Longest chain 14 peptides. Score 0.468 Taking the results from Round 5 Chains 75, Residues 427, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 19048 restraints for refining 8218 atoms. 17339 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2639 (Rfree = 0.000) for 8218 atoms. Found 45 (45 requested) and removed 56 (22 requested) atoms. Cycle 37: After refmac, R = 0.2271 (Rfree = 0.000) for 8158 atoms. Found 45 (45 requested) and removed 41 (22 requested) atoms. Cycle 38: After refmac, R = 0.2432 (Rfree = 0.000) for 8132 atoms. Found 44 (44 requested) and removed 38 (22 requested) atoms. Cycle 39: After refmac, R = 0.2184 (Rfree = 0.000) for 8100 atoms. Found 44 (44 requested) and removed 36 (22 requested) atoms. Cycle 40: After refmac, R = 0.1771 (Rfree = 0.000) for 8088 atoms. Found 30 (44 requested) and removed 29 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 8268 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 8287 seeds are put forward Round 1: 381 peptides, 78 chains. Longest chain 11 peptides. Score 0.280 Round 2: 455 peptides, 80 chains. Longest chain 14 peptides. Score 0.376 Round 3: 466 peptides, 76 chains. Longest chain 14 peptides. Score 0.415 Round 4: 474 peptides, 79 chains. Longest chain 15 peptides. Score 0.408 Round 5: 488 peptides, 83 chains. Longest chain 12 peptides. Score 0.404 Taking the results from Round 3 Chains 76, Residues 390, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12229 reflections ( 99.65 % complete ) and 19279 restraints for refining 8145 atoms. 17795 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2342 (Rfree = 0.000) for 8145 atoms. Found 44 (44 requested) and removed 51 (22 requested) atoms. Cycle 42: After refmac, R = 0.2236 (Rfree = 0.000) for 8099 atoms. Found 44 (44 requested) and removed 39 (22 requested) atoms. Cycle 43: After refmac, R = 0.1705 (Rfree = 0.000) for 8082 atoms. Found 23 (44 requested) and removed 31 (22 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1551 (Rfree = 0.000) for 8059 atoms. Found 13 (44 requested) and removed 28 (22 requested) atoms. Cycle 45: After refmac, R = 0.1668 (Rfree = 0.000) for 8035 atoms. Found 14 (44 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 3.50 Search for helices and strands: 0 residues in 0 chains, 8201 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 8215 seeds are put forward Round 1: 398 peptides, 81 chains. Longest chain 10 peptides. Score 0.287 Round 2: 466 peptides, 82 chains. Longest chain 14 peptides. Score 0.379 Round 3: 438 peptides, 77 chains. Longest chain 12 peptides. Score 0.370 Round 4: 431 peptides, 75 chains. Longest chain 12 peptides. Score 0.373 Round 5: 434 peptides, 72 chains. Longest chain 15 peptides. Score 0.395 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 72, Residues 362, 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 19530 restraints for refining 8220 atoms. 18154 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2409 (Rfree = 0.000) for 8220 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 47: After refmac, R = 0.2459 (Rfree = 0.000) for 8171 atoms. Found 0 (45 requested) and removed 22 (22 requested) atoms. Cycle 48: After refmac, R = 0.2177 (Rfree = 0.000) for 8133 atoms. Found 0 (44 requested) and removed 22 (22 requested) atoms. Cycle 49: After refmac, R = 0.2057 (Rfree = 0.000) for 8076 atoms. TimeTaking 94.3