Tue 25 Dec 19:27:57 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1ztc-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1ztc-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1ztc-4.0-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-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1ztc-4.0-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 ============================================================ Tue 25 Dec 19:28:06 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1ztc-4.0-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 1067 and 0 Target number of residues in the AU: 1067 Target solvent content: 0.6682 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-4.0-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-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 7072 target number of atoms Had to go as low as 1.15 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 4.000 Wilson plot Bfac: 91.02 15050 reflections ( 98.31 % complete ) and 0 restraints for refining 7806 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3391 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3343 (Rfree = 0.000) for 7806 atoms. Found 37 (37 requested) and removed 50 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.85 2.76 Search for helices and strands: 0 residues in 0 chains, 7903 seeds are put forward NCS extension: 0 residues added, 7903 seeds are put forward Round 1: 462 peptides, 69 chains. Longest chain 16 peptides. Score 0.384 Round 2: 585 peptides, 62 chains. Longest chain 27 peptides. Score 0.525 Round 3: 577 peptides, 66 chains. Longest chain 24 peptides. Score 0.503 Round 4: 597 peptides, 59 chains. Longest chain 33 peptides. Score 0.546 Round 5: 594 peptides, 59 chains. Longest chain 31 peptides. Score 0.544 Taking the results from Round 4 Chains 59, Residues 538, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 15050 reflections ( 98.31 % complete ) and 14188 restraints for refining 6382 atoms. 12095 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2800 (Rfree = 0.000) for 6382 atoms. Found 30 (30 requested) and removed 33 (15 requested) atoms. Cycle 2: After refmac, R = 0.2599 (Rfree = 0.000) for 6284 atoms. Found 30 (30 requested) and removed 85 (15 requested) atoms. Cycle 3: After refmac, R = 0.2477 (Rfree = 0.000) for 6176 atoms. Found 29 (29 requested) and removed 40 (14 requested) atoms. Cycle 4: After refmac, R = 0.2516 (Rfree = 0.000) for 6126 atoms. Found 29 (29 requested) and removed 27 (14 requested) atoms. Cycle 5: After refmac, R = 0.2445 (Rfree = 0.000) for 6100 atoms. Found 29 (29 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.78 2.71 Search for helices and strands: 0 residues in 0 chains, 6393 seeds are put forward NCS extension: 21 residues added (8 deleted due to clashes), 6414 seeds are put forward Round 1: 572 peptides, 66 chains. Longest chain 29 peptides. Score 0.498 Round 2: 598 peptides, 57 chains. Longest chain 32 peptides. Score 0.555 Round 3: 611 peptides, 56 chains. Longest chain 30 peptides. Score 0.569 Round 4: 606 peptides, 56 chains. Longest chain 46 peptides. Score 0.565 Round 5: 595 peptides, 56 chains. Longest chain 49 peptides. Score 0.556 Taking the results from Round 3 Chains 57, Residues 555, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 13595 restraints for refining 6385 atoms. 11365 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2639 (Rfree = 0.000) for 6385 atoms. Found 30 (30 requested) and removed 31 (15 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2361 (Rfree = 0.000) for 6325 atoms. Found 30 (30 requested) and removed 35 (15 requested) atoms. Cycle 8: After refmac, R = 0.2436 (Rfree = 0.000) for 6281 atoms. Found 30 (30 requested) and removed 29 (15 requested) atoms. Cycle 9: After refmac, R = 0.2252 (Rfree = 0.000) for 6246 atoms. Found 29 (29 requested) and removed 30 (14 requested) atoms. Cycle 10: After refmac, R = 0.2231 (Rfree = 0.000) for 6211 atoms. Found 29 (29 requested) and removed 35 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.77 2.71 Search for helices and strands: 0 residues in 0 chains, 6485 seeds are put forward NCS extension: 15 residues added (10 deleted due to clashes), 6500 seeds are put forward Round 1: 575 peptides, 70 chains. Longest chain 35 peptides. Score 0.485 Round 2: 616 peptides, 59 chains. Longest chain 38 peptides. Score 0.561 Round 3: 589 peptides, 57 chains. Longest chain 30 peptides. Score 0.548 Round 4: 579 peptides, 53 chains. Longest chain 46 peptides. Score 0.555 Round 5: 576 peptides, 55 chains. Longest chain 35 peptides. Score 0.545 Taking the results from Round 2 Chains 63, Residues 557, Estimated correctness of the model 0.0 % 2 chains (59 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 13186 restraints for refining 6387 atoms. 10734 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2580 (Rfree = 0.000) for 6387 atoms. Found 30 (30 requested) and removed 39 (15 requested) atoms. Cycle 12: After refmac, R = 0.2346 (Rfree = 0.000) for 6301 atoms. Found 30 (30 requested) and removed 34 (15 requested) atoms. Cycle 13: After refmac, R = 0.2191 (Rfree = 0.000) for 6253 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2153 (Rfree = 0.000) for 6235 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. Cycle 15: After refmac, R = 0.2088 (Rfree = 0.000) for 6222 atoms. Found 22 (29 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.80 2.73 Search for helices and strands: 0 residues in 0 chains, 6473 seeds are put forward NCS extension: 9 residues added (11 deleted due to clashes), 6482 seeds are put forward Round 1: 579 peptides, 62 chains. Longest chain 29 peptides. Score 0.520 Round 2: 620 peptides, 57 chains. Longest chain 37 peptides. Score 0.572 Round 3: 598 peptides, 62 chains. Longest chain 29 peptides. Score 0.536 Round 4: 608 peptides, 58 chains. Longest chain 39 peptides. Score 0.559 Round 5: 612 peptides, 54 chains. Longest chain 35 peptides. Score 0.577 Taking the results from Round 5 Chains 56, Residues 558, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 13830 restraints for refining 6387 atoms. 11582 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2735 (Rfree = 0.000) for 6387 atoms. Found 30 (30 requested) and removed 82 (15 requested) atoms. Cycle 17: After refmac, R = 0.2433 (Rfree = 0.000) for 6250 atoms. Found 30 (30 requested) and removed 87 (15 requested) atoms. Cycle 18: After refmac, R = 0.2229 (Rfree = 0.000) for 6161 atoms. Found 28 (29 requested) and removed 18 (14 requested) atoms. Cycle 19: After refmac, R = 0.2152 (Rfree = 0.000) for 6151 atoms. Found 21 (29 requested) and removed 17 (14 requested) atoms. Cycle 20: After refmac, R = 0.2125 (Rfree = 0.000) for 6141 atoms. Found 8 (29 requested) and removed 22 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.83 2.75 Search for helices and strands: 0 residues in 0 chains, 6362 seeds are put forward NCS extension: 41 residues added (10 deleted due to clashes), 6403 seeds are put forward Round 1: 565 peptides, 69 chains. Longest chain 24 peptides. Score 0.480 Round 2: 585 peptides, 60 chains. Longest chain 24 peptides. Score 0.533 Round 3: 573 peptides, 56 chains. Longest chain 32 peptides. Score 0.539 Round 4: 583 peptides, 56 chains. Longest chain 31 peptides. Score 0.547 Round 5: 581 peptides, 57 chains. Longest chain 26 peptides. Score 0.542 Taking the results from Round 4 Chains 59, Residues 527, Estimated correctness of the model 0.0 % 3 chains (64 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 13413 restraints for refining 6387 atoms. 11092 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2571 (Rfree = 0.000) for 6387 atoms. Found 30 (30 requested) and removed 24 (15 requested) atoms. Cycle 22: After refmac, R = 0.2299 (Rfree = 0.000) for 6313 atoms. Found 17 (30 requested) and removed 23 (15 requested) atoms. Cycle 23: After refmac, R = 0.2205 (Rfree = 0.000) for 6269 atoms. Found 13 (29 requested) and removed 16 (14 requested) atoms. Cycle 24: After refmac, R = 0.2132 (Rfree = 0.000) for 6247 atoms. Found 10 (29 requested) and removed 23 (14 requested) atoms. Cycle 25: After refmac, R = 0.2101 (Rfree = 0.000) for 6214 atoms. Found 11 (29 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.84 2.76 Search for helices and strands: 0 residues in 0 chains, 6443 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 6464 seeds are put forward Round 1: 555 peptides, 71 chains. Longest chain 24 peptides. Score 0.463 Round 2: 585 peptides, 71 chains. Longest chain 25 peptides. Score 0.490 Round 3: 573 peptides, 62 chains. Longest chain 24 peptides. Score 0.515 Round 4: 570 peptides, 56 chains. Longest chain 27 peptides. Score 0.537 Round 5: 583 peptides, 62 chains. Longest chain 30 peptides. Score 0.524 Taking the results from Round 4 Chains 56, Residues 514, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 14333 restraints for refining 6385 atoms. 12333 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2786 (Rfree = 0.000) for 6385 atoms. Found 30 (30 requested) and removed 18 (15 requested) atoms. Cycle 27: After refmac, R = 0.2535 (Rfree = 0.000) for 6354 atoms. Found 30 (30 requested) and removed 21 (15 requested) atoms. Cycle 28: After refmac, R = 0.2410 (Rfree = 0.000) for 6342 atoms. Found 30 (30 requested) and removed 22 (15 requested) atoms. Cycle 29: After refmac, R = 0.2410 (Rfree = 0.000) for 6318 atoms. Found 30 (30 requested) and removed 28 (15 requested) atoms. Cycle 30: After refmac, R = 0.2300 (Rfree = 0.000) for 6291 atoms. Found 29 (30 requested) and removed 25 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 2.69 Search for helices and strands: 0 residues in 0 chains, 6574 seeds are put forward NCS extension: 17 residues added (10 deleted due to clashes), 6591 seeds are put forward Round 1: 539 peptides, 67 chains. Longest chain 26 peptides. Score 0.466 Round 2: 585 peptides, 66 chains. Longest chain 27 peptides. Score 0.509 Round 3: 576 peptides, 57 chains. Longest chain 31 peptides. Score 0.537 Round 4: 592 peptides, 59 chains. Longest chain 37 peptides. Score 0.543 Round 5: 600 peptides, 59 chains. Longest chain 33 peptides. Score 0.549 Taking the results from Round 5 Chains 59, Residues 541, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 13948 restraints for refining 6387 atoms. 11843 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2698 (Rfree = 0.000) for 6387 atoms. Found 30 (30 requested) and removed 17 (15 requested) atoms. Cycle 32: After refmac, R = 0.2483 (Rfree = 0.000) for 6335 atoms. Found 30 (30 requested) and removed 24 (15 requested) atoms. Cycle 33: After refmac, R = 0.2547 (Rfree = 0.000) for 6306 atoms. Found 30 (30 requested) and removed 72 (15 requested) atoms. Cycle 34: After refmac, R = 0.2572 (Rfree = 0.000) for 6231 atoms. Found 29 (29 requested) and removed 55 (14 requested) atoms. Cycle 35: After refmac, R = 0.2462 (Rfree = 0.000) for 6156 atoms. Found 29 (29 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.75 2.69 Search for helices and strands: 0 residues in 0 chains, 6427 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 6440 seeds are put forward Round 1: 547 peptides, 75 chains. Longest chain 22 peptides. Score 0.439 Round 2: 559 peptides, 61 chains. Longest chain 28 peptides. Score 0.508 Round 3: 590 peptides, 61 chains. Longest chain 32 peptides. Score 0.533 Round 4: 588 peptides, 63 chains. Longest chain 32 peptides. Score 0.524 Round 5: 588 peptides, 62 chains. Longest chain 35 peptides. Score 0.528 Taking the results from Round 3 Chains 64, Residues 529, Estimated correctness of the model 0.0 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 13575 restraints for refining 6387 atoms. 11368 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2580 (Rfree = 0.000) for 6387 atoms. Found 30 (30 requested) and removed 25 (15 requested) atoms. Cycle 37: After refmac, R = 0.2430 (Rfree = 0.000) for 6339 atoms. Found 30 (30 requested) and removed 27 (15 requested) atoms. Cycle 38: After refmac, R = 0.2345 (Rfree = 0.000) for 6315 atoms. Found 30 (30 requested) and removed 41 (15 requested) atoms. Cycle 39: After refmac, R = 0.2326 (Rfree = 0.000) for 6279 atoms. Found 29 (29 requested) and removed 34 (14 requested) atoms. Cycle 40: After refmac, R = 0.2255 (Rfree = 0.000) for 6257 atoms. Found 29 (29 requested) and removed 28 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.77 2.71 Search for helices and strands: 0 residues in 0 chains, 6460 seeds are put forward NCS extension: 32 residues added (3 deleted due to clashes), 6492 seeds are put forward Round 1: 520 peptides, 70 chains. Longest chain 21 peptides. Score 0.436 Round 2: 583 peptides, 68 chains. Longest chain 21 peptides. Score 0.500 Round 3: 572 peptides, 63 chains. Longest chain 32 peptides. Score 0.510 Round 4: 578 peptides, 62 chains. Longest chain 26 peptides. Score 0.519 Round 5: 561 peptides, 65 chains. Longest chain 27 peptides. Score 0.493 Taking the results from Round 4 Chains 62, Residues 516, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 15050 reflections ( 98.31 % complete ) and 14125 restraints for refining 6384 atoms. 12066 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2639 (Rfree = 0.000) for 6384 atoms. Found 30 (30 requested) and removed 27 (15 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2440 (Rfree = 0.000) for 6350 atoms. Found 30 (30 requested) and removed 29 (15 requested) atoms. Cycle 43: After refmac, R = 0.2313 (Rfree = 0.000) for 6331 atoms. Found 25 (30 requested) and removed 23 (15 requested) atoms. Cycle 44: After refmac, R = 0.2194 (Rfree = 0.000) for 6316 atoms. Found 30 (30 requested) and removed 23 (15 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 45: After refmac, R = 0.2168 (Rfree = 0.000) for 6315 atoms. Found 16 (30 requested) and removed 24 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.81 2.74 Search for helices and strands: 0 residues in 0 chains, 6508 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 6530 seeds are put forward Round 1: 498 peptides, 74 chains. Longest chain 23 peptides. Score 0.397 Round 2: 534 peptides, 62 chains. Longest chain 27 peptides. Score 0.482 Round 3: 544 peptides, 67 chains. Longest chain 29 peptides. Score 0.470 Round 4: 548 peptides, 60 chains. Longest chain 28 peptides. Score 0.502 Round 5: 557 peptides, 59 chains. Longest chain 31 peptides. Score 0.514 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 60, Residues 498, Estimated correctness of the model 0.0 % 1 chains (24 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1ztc-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15050 reflections ( 98.31 % complete ) and 14292 restraints for refining 6386 atoms. 12268 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2644 (Rfree = 0.000) for 6386 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2474 (Rfree = 0.000) for 6316 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2415 (Rfree = 0.000) for 6271 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2263 (Rfree = 0.000) for 6229 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 21:14:33 GMT 2018 Job finished. TimeTaking 106.61