Sun 23 Dec 22:23:08 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 1ztc-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1ztc-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1ztc-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1ztc-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/1ztc-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1ztc-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 22:23:18 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/1ztc-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1ztc-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 1095 and 0 Target number of residues in the AU: 1095 Target solvent content: 0.6595 Checking the provided sequence file Detected sequence length: 221 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 884 Adjusted target solvent content: 0.73 Input MTZ file: 1ztc-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: 89.783 127.343 152.224 90.000 90.000 90.000 Input sequence file: 1ztc-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 7072 target number of atoms Had to go as low as 1.10 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: 97.673 3.800 Wilson plot Bfac: 84.57 17528 reflections ( 98.52 % complete ) and 0 restraints for refining 7874 atoms. Observations/parameters ratio is 0.56 ------------------------------------------------------ Starting model: R = 0.3318 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3217 (Rfree = 0.000) for 7874 atoms. Found 43 (43 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 2.64 Search for helices and strands: 0 residues in 0 chains, 8039 seeds are put forward NCS extension: 0 residues added, 8039 seeds are put forward Round 1: 551 peptides, 72 chains. Longest chain 25 peptides. Score 0.456 Round 2: 610 peptides, 62 chains. Longest chain 46 peptides. Score 0.545 Round 3: 620 peptides, 59 chains. Longest chain 35 peptides. Score 0.564 Round 4: 634 peptides, 60 chains. Longest chain 31 peptides. Score 0.571 Round 5: 622 peptides, 53 chains. Longest chain 44 peptides. Score 0.588 Taking the results from Round 5 Chains 58, Residues 569, Estimated correctness of the model 0.0 % 4 chains (79 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 12759 restraints for refining 6393 atoms. 10166 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2880 (Rfree = 0.000) for 6393 atoms. Found 35 (35 requested) and removed 36 (17 requested) atoms. Cycle 2: After refmac, R = 0.2582 (Rfree = 0.000) for 6292 atoms. Found 35 (35 requested) and removed 26 (17 requested) atoms. Cycle 3: After refmac, R = 0.2430 (Rfree = 0.000) for 6262 atoms. Found 26 (34 requested) and removed 30 (17 requested) atoms. Cycle 4: After refmac, R = 0.2342 (Rfree = 0.000) for 6239 atoms. Found 14 (34 requested) and removed 23 (17 requested) atoms. Cycle 5: After refmac, R = 0.2299 (Rfree = 0.000) for 6217 atoms. Found 8 (34 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 2.64 Search for helices and strands: 0 residues in 0 chains, 6430 seeds are put forward NCS extension: 17 residues added (22 deleted due to clashes), 6447 seeds are put forward Round 1: 602 peptides, 63 chains. Longest chain 33 peptides. Score 0.535 Round 2: 624 peptides, 55 chains. Longest chain 36 peptides. Score 0.582 Round 3: 630 peptides, 51 chains. Longest chain 36 peptides. Score 0.601 Round 4: 637 peptides, 50 chains. Longest chain 45 peptides. Score 0.610 Round 5: 633 peptides, 54 chains. Longest chain 47 peptides. Score 0.592 Taking the results from Round 4 Chains 53, Residues 587, Estimated correctness of the model 3.5 % 3 chains (55 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13062 restraints for refining 6396 atoms. 10512 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2682 (Rfree = 0.000) for 6396 atoms. Found 35 (35 requested) and removed 28 (17 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2505 (Rfree = 0.000) for 6314 atoms. Found 35 (35 requested) and removed 25 (17 requested) atoms. Cycle 8: After refmac, R = 0.2407 (Rfree = 0.000) for 6263 atoms. Found 34 (34 requested) and removed 32 (17 requested) atoms. Cycle 9: After refmac, R = 0.2402 (Rfree = 0.000) for 6224 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. Cycle 10: After refmac, R = 0.2310 (Rfree = 0.000) for 6195 atoms. Found 34 (34 requested) and removed 52 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.66 2.63 Search for helices and strands: 0 residues in 0 chains, 6448 seeds are put forward NCS extension: 49 residues added (17 deleted due to clashes), 6497 seeds are put forward Round 1: 618 peptides, 64 chains. Longest chain 30 peptides. Score 0.544 Round 2: 621 peptides, 59 chains. Longest chain 34 peptides. Score 0.565 Round 3: 605 peptides, 62 chains. Longest chain 29 peptides. Score 0.541 Round 4: 623 peptides, 58 chains. Longest chain 30 peptides. Score 0.570 Round 5: 615 peptides, 56 chains. Longest chain 39 peptides. Score 0.572 Taking the results from Round 5 Chains 56, Residues 559, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13634 restraints for refining 6397 atoms. 11394 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2896 (Rfree = 0.000) for 6397 atoms. Found 35 (35 requested) and removed 54 (17 requested) atoms. Cycle 12: After refmac, R = 0.2517 (Rfree = 0.000) for 6321 atoms. Found 35 (35 requested) and removed 24 (17 requested) atoms. Cycle 13: After refmac, R = 0.2373 (Rfree = 0.000) for 6316 atoms. Found 34 (34 requested) and removed 23 (17 requested) atoms. Cycle 14: After refmac, R = 0.2341 (Rfree = 0.000) for 6313 atoms. Found 34 (34 requested) and removed 25 (17 requested) atoms. Cycle 15: After refmac, R = 0.2297 (Rfree = 0.000) for 6307 atoms. Found 34 (34 requested) and removed 39 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.65 2.62 Search for helices and strands: 0 residues in 0 chains, 6510 seeds are put forward NCS extension: 24 residues added (11 deleted due to clashes), 6534 seeds are put forward Round 1: 596 peptides, 75 chains. Longest chain 26 peptides. Score 0.483 Round 2: 613 peptides, 62 chains. Longest chain 27 peptides. Score 0.548 Round 3: 611 peptides, 63 chains. Longest chain 30 peptides. Score 0.542 Failed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDB Round 4: 620 peptides, 61 chains. Longest chain 40 peptides. Score 0.557 Round 5: 620 peptides, 59 chains. Longest chain 43 peptides. Score 0.564 Taking the results from Round 5 Chains 61, Residues 561, Estimated correctness of the model 0.0 % 3 chains (39 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13436 restraints for refining 6395 atoms. 11074 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2812 (Rfree = 0.000) for 6395 atoms. Found 35 (35 requested) and removed 29 (17 requested) atoms. Cycle 17: After refmac, R = 0.2425 (Rfree = 0.000) for 6344 atoms. Found 31 (35 requested) and removed 24 (17 requested) atoms. Cycle 18: After refmac, R = 0.2361 (Rfree = 0.000) for 6324 atoms. Found 29 (34 requested) and removed 31 (17 requested) atoms. Cycle 19: After refmac, R = 0.2322 (Rfree = 0.000) for 6307 atoms. Found 31 (34 requested) and removed 27 (17 requested) atoms. Cycle 20: After refmac, R = 0.2243 (Rfree = 0.000) for 6295 atoms. Found 25 (34 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.70 2.66 Search for helices and strands: 0 residues in 0 chains, 6543 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 6560 seeds are put forward Round 1: 583 peptides, 75 chains. Longest chain 29 peptides. Score 0.472 Round 2: 609 peptides, 64 chains. Longest chain 32 peptides. Score 0.537 Round 3: 621 peptides, 64 chains. Longest chain 29 peptides. Score 0.546 Round 4: 625 peptides, 61 chains. Longest chain 27 peptides. Score 0.561 Round 5: 596 peptides, 61 chains. Longest chain 30 peptides. Score 0.538 Taking the results from Round 4 Chains 63, Residues 564, Estimated correctness of the model 0.0 % 4 chains (50 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13102 restraints for refining 6397 atoms. 10678 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2581 (Rfree = 0.000) for 6397 atoms. Found 35 (35 requested) and removed 28 (17 requested) atoms. Cycle 22: After refmac, R = 0.2462 (Rfree = 0.000) for 6338 atoms. Found 35 (35 requested) and removed 25 (17 requested) atoms. Cycle 23: After refmac, R = 0.2458 (Rfree = 0.000) for 6317 atoms. Found 34 (34 requested) and removed 26 (17 requested) atoms. Cycle 24: After refmac, R = 0.2389 (Rfree = 0.000) for 6292 atoms. Found 34 (34 requested) and removed 30 (17 requested) atoms. Cycle 25: After refmac, R = 0.2329 (Rfree = 0.000) for 6277 atoms. Found 34 (34 requested) and removed 23 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.69 2.65 Search for helices and strands: 0 residues in 0 chains, 6498 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 6515 seeds are put forward Round 1: 571 peptides, 71 chains. Longest chain 32 peptides. Score 0.477 Round 2: 601 peptides, 65 chains. Longest chain 38 peptides. Score 0.527 Round 3: 576 peptides, 54 chains. Longest chain 29 peptides. Score 0.549 Round 4: 596 peptides, 61 chains. Longest chain 29 peptides. Score 0.538 Round 5: 586 peptides, 59 chains. Longest chain 31 peptides. Score 0.538 Taking the results from Round 3 Chains 57, Residues 522, Estimated correctness of the model 0.0 % 3 chains (45 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13610 restraints for refining 6397 atoms. 11376 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2640 (Rfree = 0.000) for 6397 atoms. Found 35 (35 requested) and removed 27 (17 requested) atoms. Cycle 27: After refmac, R = 0.2413 (Rfree = 0.000) for 6352 atoms. Found 31 (35 requested) and removed 22 (17 requested) atoms. Cycle 28: After refmac, R = 0.2355 (Rfree = 0.000) for 6337 atoms. Found 30 (34 requested) and removed 22 (17 requested) atoms. Cycle 29: After refmac, R = 0.2262 (Rfree = 0.000) for 6322 atoms. Found 19 (34 requested) and removed 20 (17 requested) atoms. Cycle 30: After refmac, R = 0.2253 (Rfree = 0.000) for 6301 atoms. Found 22 (34 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.68 2.64 Search for helices and strands: 0 residues in 0 chains, 6521 seeds are put forward NCS extension: 25 residues added (4 deleted due to clashes), 6546 seeds are put forward Round 1: 574 peptides, 69 chains. Longest chain 29 peptides. Score 0.488 Round 2: 612 peptides, 62 chains. Longest chain 32 peptides. Score 0.547 Round 3: 626 peptides, 61 chains. Longest chain 35 peptides. Score 0.561 Round 4: 634 peptides, 63 chains. Longest chain 37 peptides. Score 0.560 Round 5: 621 peptides, 57 chains. Longest chain 26 peptides. Score 0.573 Taking the results from Round 5 Chains 60, Residues 564, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13662 restraints for refining 6395 atoms. 11384 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2604 (Rfree = 0.000) for 6395 atoms. Found 35 (35 requested) and removed 32 (17 requested) atoms. Cycle 32: After refmac, R = 0.2533 (Rfree = 0.000) for 6347 atoms. Found 35 (35 requested) and removed 19 (17 requested) atoms. Cycle 33: After refmac, R = 0.2452 (Rfree = 0.000) for 6346 atoms. Found 34 (34 requested) and removed 25 (17 requested) atoms. Cycle 34: After refmac, R = 0.2371 (Rfree = 0.000) for 6339 atoms. Found 33 (34 requested) and removed 21 (17 requested) atoms. Cycle 35: After refmac, R = 0.2323 (Rfree = 0.000) for 6341 atoms. Found 29 (34 requested) and removed 23 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.69 2.65 Search for helices and strands: 0 residues in 0 chains, 6565 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 6581 seeds are put forward Round 1: 548 peptides, 68 chains. Longest chain 21 peptides. Score 0.469 Round 2: 603 peptides, 66 chains. Longest chain 22 peptides. Score 0.524 Round 3: 597 peptides, 62 chains. Longest chain 30 peptides. Score 0.535 Round 4: 612 peptides, 62 chains. Longest chain 34 peptides. Score 0.547 Round 5: 593 peptides, 62 chains. Longest chain 34 peptides. Score 0.532 Taking the results from Round 4 Chains 65, Residues 550, Estimated correctness of the model 0.0 % 3 chains (57 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13287 restraints for refining 6395 atoms. 10895 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2681 (Rfree = 0.000) for 6395 atoms. Found 35 (35 requested) and removed 33 (17 requested) atoms. Cycle 37: After refmac, R = 0.2508 (Rfree = 0.000) for 6324 atoms. Found 35 (35 requested) and removed 27 (17 requested) atoms. Cycle 38: After refmac, R = 0.2440 (Rfree = 0.000) for 6298 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. Cycle 39: After refmac, R = 0.2388 (Rfree = 0.000) for 6291 atoms. Found 34 (34 requested) and removed 26 (17 requested) atoms. Cycle 40: After refmac, R = 0.2347 (Rfree = 0.000) for 6283 atoms. Found 34 (34 requested) and removed 23 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.69 2.65 Search for helices and strands: 0 residues in 0 chains, 6497 seeds are put forward NCS extension: 21 residues added (7 deleted due to clashes), 6518 seeds are put forward Round 1: 558 peptides, 72 chains. Longest chain 23 peptides. Score 0.462 Round 2: 577 peptides, 63 chains. Longest chain 24 peptides. Score 0.515 Round 3: 584 peptides, 63 chains. Longest chain 25 peptides. Score 0.520 Round 4: 596 peptides, 60 chains. Longest chain 37 peptides. Score 0.542 Round 5: 607 peptides, 58 chains. Longest chain 36 peptides. Score 0.558 Taking the results from Round 5 Chains 60, Residues 549, Estimated correctness of the model 0.0 % 3 chains (76 residues) have been docked in sequence ------------------------------------------------------ 17528 reflections ( 98.52 % complete ) and 13166 restraints for refining 6396 atoms. 10684 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2817 (Rfree = 0.000) for 6396 atoms. Found 35 (35 requested) and removed 31 (17 requested) atoms. Cycle 42: After refmac, R = 0.2640 (Rfree = 0.000) for 6343 atoms. Found 35 (35 requested) and removed 28 (17 requested) atoms. Cycle 43: After refmac, R = 0.2533 (Rfree = 0.000) for 6326 atoms. Found 34 (34 requested) and removed 24 (17 requested) atoms. Cycle 44: After refmac, R = 0.2429 (Rfree = 0.000) for 6316 atoms. Found 34 (34 requested) and removed 21 (17 requested) atoms. Cycle 45: After refmac, R = 0.2351 (Rfree = 0.000) for 6311 atoms. Found 19 (34 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.68 2.64 Search for helices and strands: 0 residues in 0 chains, 6493 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 6526 seeds are put forward Round 1: 538 peptides, 78 chains. Longest chain 19 peptides. Score 0.418 Round 2: 562 peptides, 64 chains. Longest chain 36 peptides. Score 0.498 Round 3: 573 peptides, 60 chains. Longest chain 26 peptides. Score 0.523 Round 4: 583 peptides, 66 chains. Longest chain 22 peptides. Score 0.508 Round 5: 583 peptides, 64 chains. Longest chain 32 peptides. Score 0.516 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 60, Residues 513, Estimated correctness of the model 0.0 % 1 chains (25 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1ztc-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17528 reflections ( 98.52 % complete ) and 14006 restraints for refining 6395 atoms. 11902 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2760 (Rfree = 0.000) for 6395 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2563 (Rfree = 0.000) for 6342 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.2470 (Rfree = 0.000) for 6307 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.2446 (Rfree = 0.000) for 6281 atoms. TimeTaking 92.88