Sun 23 Dec 22:22:53 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 2hx1-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hx1-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hx1-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hx1-3.6-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/2hx1-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hx1-3.6-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 22:23:03 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/2hx1-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hx1-3.6-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 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-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: 2hx1-3.6-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 3.600 Wilson plot Bfac: 58.00 Failed to save intermediate PDB 14332 reflections ( 99.70 % complete ) and 0 restraints for refining 10013 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3280 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3119 (Rfree = 0.000) for 10013 atoms. Found 64 (64 requested) and removed 68 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.37 Search for helices and strands: 0 residues in 0 chains, 10226 seeds are put forward NCS extension: 0 residues added, 10226 seeds are put forward Round 1: 481 peptides, 97 chains. Longest chain 11 peptides. Score 0.310 Round 2: 645 peptides, 99 chains. Longest chain 19 peptides. Score 0.513 Round 3: 691 peptides, 94 chains. Longest chain 28 peptides. Score 0.587 Round 4: 710 peptides, 97 chains. Longest chain 22 peptides. Score 0.593 Round 5: 714 peptides, 88 chains. Longest chain 44 peptides. Score 0.635 Taking the results from Round 5 Chains 91, Residues 626, Estimated correctness of the model 27.8 % 4 chains (46 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 14332 reflections ( 99.70 % complete ) and 18077 restraints for refining 8233 atoms. 15515 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2935 (Rfree = 0.000) for 8233 atoms. Found 52 (52 requested) and removed 63 (26 requested) atoms. Cycle 2: After refmac, R = 0.2679 (Rfree = 0.000) for 8103 atoms. Found 49 (52 requested) and removed 97 (26 requested) atoms. Cycle 3: After refmac, R = 0.2537 (Rfree = 0.000) for 8011 atoms. Found 35 (51 requested) and removed 74 (25 requested) atoms. Cycle 4: After refmac, R = 0.2387 (Rfree = 0.000) for 7949 atoms. Found 41 (51 requested) and removed 103 (25 requested) atoms. Cycle 5: After refmac, R = 0.2346 (Rfree = 0.000) for 7874 atoms. Found 34 (50 requested) and removed 38 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 8164 seeds are put forward NCS extension: 22 residues added (21 deleted due to clashes), 8186 seeds are put forward Round 1: 617 peptides, 98 chains. Longest chain 24 peptides. Score 0.485 Round 2: 693 peptides, 91 chains. Longest chain 25 peptides. Score 0.602 Round 3: 718 peptides, 88 chains. Longest chain 41 peptides. Score 0.639 Round 4: 709 peptides, 82 chains. Longest chain 27 peptides. Score 0.655 Round 5: 713 peptides, 89 chains. Longest chain 32 peptides. Score 0.630 Taking the results from Round 4 Chains 86, Residues 627, Estimated correctness of the model 34.9 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 14332 reflections ( 99.70 % complete ) and 18092 restraints for refining 8238 atoms. 15533 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2648 (Rfree = 0.000) for 8238 atoms. Found 44 (52 requested) and removed 51 (26 requested) atoms. Cycle 7: After refmac, R = 0.2406 (Rfree = 0.000) for 8185 atoms. Found 41 (52 requested) and removed 41 (26 requested) atoms. Cycle 8: After refmac, R = 0.2346 (Rfree = 0.000) for 8167 atoms. Found 38 (52 requested) and removed 45 (26 requested) atoms. Cycle 9: After refmac, R = 0.2162 (Rfree = 0.000) for 8141 atoms. Found 33 (52 requested) and removed 37 (26 requested) atoms. Cycle 10: After refmac, R = 0.2080 (Rfree = 0.000) for 8126 atoms. Found 16 (52 requested) and removed 41 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 8355 seeds are put forward NCS extension: 26 residues added (15 deleted due to clashes), 8381 seeds are put forward Round 1: 628 peptides, 98 chains. Longest chain 20 peptides. Score 0.498 Round 2: 701 peptides, 85 chains. Longest chain 29 peptides. Score 0.636 Round 3: 697 peptides, 86 chains. Longest chain 28 peptides. Score 0.628 Round 4: 706 peptides, 76 chains. Longest chain 32 peptides. Score 0.676 Round 5: 683 peptides, 82 chains. Longest chain 26 peptides. Score 0.632 Taking the results from Round 4 Chains 76, Residues 630, Estimated correctness of the model 42.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 17977 restraints for refining 8238 atoms. 15462 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2765 (Rfree = 0.000) for 8238 atoms. Found 52 (52 requested) and removed 39 (26 requested) atoms. Cycle 12: After refmac, R = 0.2503 (Rfree = 0.000) for 8211 atoms. Found 36 (52 requested) and removed 51 (26 requested) atoms. Cycle 13: After refmac, R = 0.2352 (Rfree = 0.000) for 8178 atoms. Found 44 (52 requested) and removed 38 (26 requested) atoms. Cycle 14: After refmac, R = 0.2385 (Rfree = 0.000) for 8173 atoms. Found 34 (52 requested) and removed 38 (26 requested) atoms. Cycle 15: After refmac, R = 0.2083 (Rfree = 0.000) for 8155 atoms. Found 14 (52 requested) and removed 36 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 8393 seeds are put forward NCS extension: 11 residues added (13 deleted due to clashes), 8404 seeds are put forward Round 1: 622 peptides, 98 chains. Longest chain 20 peptides. Score 0.491 Round 2: 671 peptides, 87 chains. Longest chain 22 peptides. Score 0.598 Round 3: 643 peptides, 83 chains. Longest chain 21 peptides. Score 0.588 Round 4: 678 peptides, 81 chains. Longest chain 27 peptides. Score 0.631 Round 5: 663 peptides, 86 chains. Longest chain 22 peptides. Score 0.595 Taking the results from Round 4 Chains 83, Residues 597, Estimated correctness of the model 26.4 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 18513 restraints for refining 8237 atoms. 16180 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2748 (Rfree = 0.000) for 8237 atoms. Found 52 (52 requested) and removed 38 (26 requested) atoms. Cycle 17: After refmac, R = 0.2417 (Rfree = 0.000) for 8221 atoms. Found 43 (52 requested) and removed 41 (26 requested) atoms. Cycle 18: After refmac, R = 0.2376 (Rfree = 0.000) for 8199 atoms. Found 52 (52 requested) and removed 34 (26 requested) atoms. Cycle 19: After refmac, R = 0.2598 (Rfree = 0.000) for 8203 atoms. Found 52 (52 requested) and removed 38 (26 requested) atoms. Cycle 20: After refmac, R = 0.2582 (Rfree = 0.000) for 8209 atoms. Found 52 (52 requested) and removed 44 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 8466 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 8488 seeds are put forward Round 1: 582 peptides, 98 chains. Longest chain 17 peptides. Score 0.442 Round 2: 644 peptides, 95 chains. Longest chain 18 peptides. Score 0.532 Round 3: 681 peptides, 96 chains. Longest chain 23 peptides. Score 0.567 Round 4: 694 peptides, 92 chains. Longest chain 31 peptides. Score 0.599 Round 5: 678 peptides, 95 chains. Longest chain 23 peptides. Score 0.569 Taking the results from Round 4 Chains 92, Residues 602, Estimated correctness of the model 14.3 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 18155 restraints for refining 8237 atoms. 15768 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2915 (Rfree = 0.000) for 8237 atoms. Found 52 (52 requested) and removed 40 (26 requested) atoms. Cycle 22: After refmac, R = 0.2748 (Rfree = 0.000) for 8215 atoms. Found 52 (52 requested) and removed 38 (26 requested) atoms. Cycle 23: After refmac, R = 0.2704 (Rfree = 0.000) for 8202 atoms. Found 52 (52 requested) and removed 36 (26 requested) atoms. Cycle 24: After refmac, R = 0.2596 (Rfree = 0.000) for 8199 atoms. Found 47 (52 requested) and removed 33 (26 requested) atoms. Cycle 25: After refmac, R = 0.2592 (Rfree = 0.000) for 8193 atoms. Found 52 (52 requested) and removed 32 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 8466 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 8485 seeds are put forward Round 1: 553 peptides, 96 chains. Longest chain 15 peptides. Score 0.416 Round 2: 620 peptides, 91 chains. Longest chain 21 peptides. Score 0.525 Round 3: 600 peptides, 84 chains. Longest chain 22 peptides. Score 0.537 Round 4: 611 peptides, 84 chains. Longest chain 26 peptides. Score 0.549 Round 5: 613 peptides, 88 chains. Longest chain 17 peptides. Score 0.531 Taking the results from Round 4 Chains 84, Residues 527, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 19018 restraints for refining 8238 atoms. 16994 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2628 (Rfree = 0.000) for 8238 atoms. Found 52 (52 requested) and removed 37 (26 requested) atoms. Cycle 27: After refmac, R = 0.2491 (Rfree = 0.000) for 8204 atoms. Found 52 (52 requested) and removed 41 (26 requested) atoms. Cycle 28: After refmac, R = 0.2530 (Rfree = 0.000) for 8194 atoms. Found 52 (52 requested) and removed 32 (26 requested) atoms. Cycle 29: After refmac, R = 0.2321 (Rfree = 0.000) for 8189 atoms. Found 52 (52 requested) and removed 35 (26 requested) atoms. Cycle 30: After refmac, R = 0.2224 (Rfree = 0.000) for 8198 atoms. Found 44 (52 requested) and removed 32 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 3.37 Search for helices and strands: 0 residues in 0 chains, 8428 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 8446 seeds are put forward Round 1: 503 peptides, 94 chains. Longest chain 13 peptides. Score 0.360 Round 2: 612 peptides, 91 chains. Longest chain 19 peptides. Score 0.515 Round 3: 611 peptides, 90 chains. Longest chain 19 peptides. Score 0.519 Round 4: 617 peptides, 83 chains. Longest chain 21 peptides. Score 0.560 Round 5: 629 peptides, 88 chains. Longest chain 19 peptides. Score 0.549 Taking the results from Round 4 Chains 83, Residues 534, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 18968 restraints for refining 8237 atoms. 16915 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2624 (Rfree = 0.000) for 8237 atoms. Found 52 (52 requested) and removed 40 (26 requested) atoms. Cycle 32: After refmac, R = 0.2292 (Rfree = 0.000) for 8230 atoms. Found 52 (52 requested) and removed 36 (26 requested) atoms. Cycle 33: After refmac, R = 0.2411 (Rfree = 0.000) for 8219 atoms. Found 52 (52 requested) and removed 31 (26 requested) atoms. Cycle 34: After refmac, R = 0.2309 (Rfree = 0.000) for 8214 atoms. Found 52 (52 requested) and removed 30 (26 requested) atoms. Cycle 35: After refmac, R = 0.2055 (Rfree = 0.000) for 8219 atoms. Found 20 (52 requested) and removed 30 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 3.44 Search for helices and strands: 0 residues in 0 chains, 8430 seeds are put forward NCS extension: 15 residues added (4 deleted due to clashes), 8445 seeds are put forward Round 1: 496 peptides, 96 chains. Longest chain 12 peptides. Score 0.338 Round 2: 589 peptides, 90 chains. Longest chain 15 peptides. Score 0.493 Round 3: 578 peptides, 91 chains. Longest chain 21 peptides. Score 0.475 Round 4: 584 peptides, 95 chains. Longest chain 16 peptides. Score 0.461 Round 5: 586 peptides, 87 chains. Longest chain 22 peptides. Score 0.505 Taking the results from Round 5 Chains 87, Residues 499, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 19149 restraints for refining 8237 atoms. 17240 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2579 (Rfree = 0.000) for 8237 atoms. Found 52 (52 requested) and removed 29 (26 requested) atoms. Cycle 37: After refmac, R = 0.2399 (Rfree = 0.000) for 8238 atoms. Found 52 (52 requested) and removed 34 (26 requested) atoms. Cycle 38: After refmac, R = 0.2336 (Rfree = 0.000) for 8237 atoms. Found 52 (52 requested) and removed 31 (26 requested) atoms. Cycle 39: After refmac, R = 0.1968 (Rfree = 0.000) for 8245 atoms. Found 24 (52 requested) and removed 32 (26 requested) atoms. Cycle 40: After refmac, R = 0.1930 (Rfree = 0.000) for 8225 atoms. Found 15 (52 requested) and removed 31 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.44 Search for helices and strands: 0 residues in 0 chains, 8444 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 8467 seeds are put forward Round 1: 471 peptides, 88 chains. Longest chain 16 peptides. Score 0.350 Round 2: 543 peptides, 88 chains. Longest chain 13 peptides. Score 0.447 Round 3: 557 peptides, 81 chains. Longest chain 26 peptides. Score 0.502 Round 4: 542 peptides, 78 chains. Longest chain 19 peptides. Score 0.500 Round 5: 520 peptides, 81 chains. Longest chain 18 peptides. Score 0.457 Taking the results from Round 3 Chains 82, Residues 476, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 14332 reflections ( 99.70 % complete ) and 19150 restraints for refining 8237 atoms. 17281 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2609 (Rfree = 0.000) for 8237 atoms. Found 52 (52 requested) and removed 36 (26 requested) atoms. Cycle 42: After refmac, R = 0.2257 (Rfree = 0.000) for 8237 atoms. Found 52 (52 requested) and removed 32 (26 requested) atoms. Cycle 43: After refmac, R = 0.2028 (Rfree = 0.000) for 8245 atoms. Found 33 (52 requested) and removed 31 (26 requested) atoms. Cycle 44: After refmac, R = 0.2172 (Rfree = 0.000) for 8232 atoms. Found 52 (52 requested) and removed 39 (26 requested) atoms. Cycle 45: After refmac, R = 0.2256 (Rfree = 0.000) for 8231 atoms. Found 52 (52 requested) and removed 39 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 3.36 Search for helices and strands: 0 residues in 0 chains, 8437 seeds are put forward NCS extension: 31 residues added (2 deleted due to clashes), 8468 seeds are put forward Round 1: 413 peptides, 78 chains. Longest chain 13 peptides. Score 0.328 Round 2: 472 peptides, 76 chains. Longest chain 14 peptides. Score 0.423 Round 3: 483 peptides, 75 chains. Longest chain 17 peptides. Score 0.443 Round 4: 497 peptides, 73 chains. Longest chain 19 peptides. Score 0.472 Round 5: 494 peptides, 72 chains. Longest chain 17 peptides. Score 0.474 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 72, Residues 422, 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. 14332 reflections ( 99.70 % complete ) and 19454 restraints for refining 8238 atoms. 17838 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2490 (Rfree = 0.000) for 8238 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 47: After refmac, R = 0.2371 (Rfree = 0.000) for 8189 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 48: After refmac, R = 0.2361 (Rfree = 0.000) for 8145 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2083 (Rfree = 0.000) for 8104 atoms. TimeTaking 98.13