null Sun 23 Dec 22:22:43 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 1vjz-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjz-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjz-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjz-3.2-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/1vjz-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjz-3.2-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 22:22:53 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/1vjz-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjz-3.2-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 325 and 0 Target number of residues in the AU: 325 Target solvent content: 0.5844 Checking the provided sequence file Detected sequence length: 341 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 341 Adjusted target solvent content: 0.56 Input MTZ file: 1vjz-3.2-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: 96 Cell parameters: 64.677 64.677 202.367 90.000 90.000 90.000 Input sequence file: 1vjz-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2728 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 Loops will be built when appropriate and at the last cycle Resolution range: 61.607 3.200 Wilson plot Bfac: 46.52 7644 reflections ( 99.64 % complete ) and 0 restraints for refining 3027 atoms. Observations/parameters ratio is 0.63 ------------------------------------------------------ Starting model: R = 0.3209 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3009 (Rfree = 0.000) for 3027 atoms. Found 27 (27 requested) and removed 45 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.93 2.70 Search for helices and strands: 0 residues in 0 chains, 3062 seeds are put forward Round 1: 187 peptides, 37 chains. Longest chain 10 peptides. Score 0.332 Round 2: 209 peptides, 30 chains. Longest chain 16 peptides. Score 0.520 Round 3: 217 peptides, 31 chains. Longest chain 22 peptides. Score 0.531 Round 4: 223 peptides, 30 chains. Longest chain 18 peptides. Score 0.564 Round 5: 213 peptides, 29 chains. Longest chain 19 peptides. Score 0.547 Taking the results from Round 4 Chains 30, Residues 193, Estimated correctness of the model 31.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7644 reflections ( 99.64 % complete ) and 5327 restraints for refining 2490 atoms. 4585 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2722 (Rfree = 0.000) for 2490 atoms. Found 22 (22 requested) and removed 17 (11 requested) atoms. Cycle 2: After refmac, R = 0.2771 (Rfree = 0.000) for 2469 atoms. Found 15 (22 requested) and removed 16 (11 requested) atoms. Cycle 3: After refmac, R = 0.2925 (Rfree = 0.000) for 2453 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 4: After refmac, R = 0.2629 (Rfree = 0.000) for 2450 atoms. Found 14 (22 requested) and removed 16 (11 requested) atoms. Cycle 5: After refmac, R = 0.2735 (Rfree = 0.000) for 2442 atoms. Found 15 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.99 2.76 Search for helices and strands: 0 residues in 0 chains, 2557 seeds are put forward Round 1: 208 peptides, 33 chains. Longest chain 14 peptides. Score 0.473 Round 2: 228 peptides, 29 chains. Longest chain 17 peptides. Score 0.591 Round 3: 219 peptides, 29 chains. Longest chain 17 peptides. Score 0.565 Round 4: 232 peptides, 27 chains. Longest chain 17 peptides. Score 0.628 Round 5: 229 peptides, 27 chains. Longest chain 22 peptides. Score 0.619 Taking the results from Round 4 Chains 27, Residues 205, Estimated correctness of the model 48.4 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7644 reflections ( 99.64 % complete ) and 5313 restraints for refining 2491 atoms. 4506 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2760 (Rfree = 0.000) for 2491 atoms. Found 22 (22 requested) and removed 15 (11 requested) atoms. Cycle 7: After refmac, R = 0.2718 (Rfree = 0.000) for 2487 atoms. Found 10 (22 requested) and removed 16 (11 requested) atoms. Cycle 8: After refmac, R = 0.2435 (Rfree = 0.000) for 2475 atoms. Found 9 (22 requested) and removed 13 (11 requested) atoms. Cycle 9: After refmac, R = 0.2566 (Rfree = 0.000) for 2469 atoms. Found 11 (22 requested) and removed 15 (11 requested) atoms. Cycle 10: After refmac, R = 0.2393 (Rfree = 0.000) for 2461 atoms. Found 8 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.98 2.75 Search for helices and strands: 0 residues in 0 chains, 2563 seeds are put forward Round 1: 218 peptides, 30 chains. Longest chain 25 peptides. Score 0.548 Round 2: 219 peptides, 26 chains. Longest chain 20 peptides. Score 0.604 Round 3: 222 peptides, 26 chains. Longest chain 27 peptides. Score 0.613 Round 4: 222 peptides, 28 chains. Longest chain 21 peptides. Score 0.587 Round 5: 228 peptides, 25 chains. Longest chain 24 peptides. Score 0.641 Taking the results from Round 5 Chains 25, Residues 203, Estimated correctness of the model 51.6 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7644 reflections ( 99.64 % complete ) and 5195 restraints for refining 2491 atoms. 4310 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3204 (Rfree = 0.000) for 2491 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. Cycle 12: After refmac, R = 0.2682 (Rfree = 0.000) for 2468 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 13: After refmac, R = 0.2567 (Rfree = 0.000) for 2465 atoms. Found 17 (22 requested) and removed 14 (11 requested) atoms. Cycle 14: After refmac, R = 0.2564 (Rfree = 0.000) for 2466 atoms. Found 12 (22 requested) and removed 14 (11 requested) atoms. Cycle 15: After refmac, R = 0.2518 (Rfree = 0.000) for 2462 atoms. Found 13 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.98 2.75 Search for helices and strands: 0 residues in 0 chains, 2539 seeds are put forward Round 1: 201 peptides, 27 chains. Longest chain 25 peptides. Score 0.537 Round 2: 207 peptides, 26 chains. Longest chain 26 peptides. Score 0.570 Round 3: 221 peptides, 28 chains. Longest chain 27 peptides. Score 0.584 Round 4: 220 peptides, 24 chains. Longest chain 25 peptides. Score 0.632 Round 5: 231 peptides, 26 chains. Longest chain 29 peptides. Score 0.637 Taking the results from Round 5 Chains 27, Residues 205, Estimated correctness of the model 50.7 % 2 chains (49 residues) have been docked in sequence ------------------------------------------------------ 7644 reflections ( 99.64 % complete ) and 4835 restraints for refining 2491 atoms. 3803 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2747 (Rfree = 0.000) for 2491 atoms. Found 22 (22 requested) and removed 14 (11 requested) atoms. Cycle 17: After refmac, R = 0.2573 (Rfree = 0.000) for 2491 atoms. Found 16 (22 requested) and removed 13 (11 requested) atoms. Cycle 18: After refmac, R = 0.2458 (Rfree = 0.000) for 2490 atoms. Found 10 (22 requested) and removed 12 (11 requested) atoms. Cycle 19: After refmac, R = 0.2375 (Rfree = 0.000) for 2482 atoms. Found 7 (22 requested) and removed 12 (11 requested) atoms. Cycle 20: After refmac, R = 0.2328 (Rfree = 0.000) for 2472 atoms. Found 10 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.96 2.73 Search for helices and strands: 0 residues in 0 chains, 2563 seeds are put forward Round 1: 217 peptides, 29 chains. Longest chain 22 peptides. Score 0.559 Round 2: 225 peptides, 25 chains. Longest chain 27 peptides. Score 0.633 Round 3: 228 peptides, 24 chains. Longest chain 29 peptides. Score 0.653 Round 4: 238 peptides, 29 chains. Longest chain 20 peptides. Score 0.619 Round 5: 224 peptides, 24 chains. Longest chain 23 peptides. Score 0.643 Taking the results from Round 3 Chains 25, Residues 204, Estimated correctness of the model 54.6 % 2 chains (47 residues) have been docked in sequence ------------------------------------------------------ 7644 reflections ( 99.64 % complete ) and 4759 restraints for refining 2491 atoms. 3749 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2831 (Rfree = 0.000) for 2491 atoms. Found 21 (22 requested) and removed 17 (11 requested) atoms. Cycle 22: After refmac, R = 0.2653 (Rfree = 0.000) for 2486 atoms. Found 12 (22 requested) and removed 15 (11 requested) atoms. Cycle 23: After refmac, R = 0.2493 (Rfree = 0.000) for 2481 atoms. Found 7 (22 requested) and removed 13 (11 requested) atoms. Cycle 24: After refmac, R = 0.2387 (Rfree = 0.000) for 2473 atoms. Found 4 (22 requested) and removed 11 (11 requested) atoms. Cycle 25: After refmac, R = 0.2424 (Rfree = 0.000) for 2465 atoms. Found 7 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.91 2.69 Search for helices and strands: 0 residues in 0 chains, 2518 seeds are put forward Round 1: 213 peptides, 25 chains. Longest chain 24 peptides. Score 0.600 Round 2: 242 peptides, 23 chains. Longest chain 33 peptides. Score 0.698 Round 3: 233 peptides, 27 chains. Longest chain 24 peptides. Score 0.630 Round 4: 228 peptides, 22 chains. Longest chain 29 peptides. Score 0.676 Round 5: 226 peptides, 23 chains. Longest chain 25 peptides. Score 0.660 Taking the results from Round 2 Chains 25, Residues 219, Estimated correctness of the model 64.8 % 4 chains (73 residues) have been docked in sequence ------------------------------------------------------ 7644 reflections ( 99.64 % complete ) and 4418 restraints for refining 2491 atoms. 3215 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2838 (Rfree = 0.000) for 2491 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. Cycle 27: After refmac, R = 0.2817 (Rfree = 0.000) for 2471 atoms. Found 22 (22 requested) and removed 14 (11 requested) atoms. Cycle 28: After refmac, R = 0.2619 (Rfree = 0.000) for 2473 atoms. Found 13 (22 requested) and removed 13 (11 requested) atoms. Cycle 29: After refmac, R = 0.2429 (Rfree = 0.000) for 2473 atoms. Found 12 (22 requested) and removed 11 (11 requested) atoms. Cycle 30: After refmac, R = 0.2384 (Rfree = 0.000) for 2472 atoms. Found 8 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.94 2.71 Search for helices and strands: 0 residues in 0 chains, 2540 seeds are put forward Round 1: 208 peptides, 28 chains. Longest chain 16 peptides. Score 0.545 Round 2: 216 peptides, 22 chains. Longest chain 21 peptides. Score 0.646 Round 3: 218 peptides, 25 chains. Longest chain 18 peptides. Score 0.614 Round 4: 217 peptides, 25 chains. Longest chain 24 peptides. Score 0.612 Round 5: 228 peptides, 24 chains. Longest chain 21 peptides. Score 0.653 Taking the results from Round 5 Chains 26, Residues 204, Estimated correctness of the model 54.6 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 7644 reflections ( 99.64 % complete ) and 4967 restraints for refining 2491 atoms. 4000 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2598 (Rfree = 0.000) for 2491 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 32: After refmac, R = 0.2498 (Rfree = 0.000) for 2493 atoms. Found 12 (22 requested) and removed 17 (11 requested) atoms. Cycle 33: After refmac, R = 0.2438 (Rfree = 0.000) for 2487 atoms. Found 9 (22 requested) and removed 14 (11 requested) atoms. Cycle 34: After refmac, R = 0.2496 (Rfree = 0.000) for 2479 atoms. Found 10 (22 requested) and removed 14 (11 requested) atoms. Cycle 35: After refmac, R = 0.2353 (Rfree = 0.000) for 2475 atoms. Found 7 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.93 2.70 Search for helices and strands: 0 residues in 0 chains, 2532 seeds are put forward Round 1: 192 peptides, 26 chains. Longest chain 20 peptides. Score 0.523 Round 2: 218 peptides, 26 chains. Longest chain 29 peptides. Score 0.602 Round 3: 227 peptides, 27 chains. Longest chain 20 peptides. Score 0.614 Round 4: 230 peptides, 27 chains. Longest chain 20 peptides. Score 0.622 Round 5: 230 peptides, 25 chains. Longest chain 26 peptides. Score 0.646 Taking the results from Round 5 Chains 25, Residues 205, Estimated correctness of the model 52.9 % 2 chains (44 residues) have been docked in sequence ------------------------------------------------------ 7644 reflections ( 99.64 % complete ) and 4781 restraints for refining 2491 atoms. 3793 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2897 (Rfree = 0.000) for 2491 atoms. Found 17 (22 requested) and removed 26 (11 requested) atoms. Cycle 37: After refmac, R = 0.2543 (Rfree = 0.000) for 2476 atoms. Found 13 (22 requested) and removed 16 (11 requested) atoms. Cycle 38: After refmac, R = 0.2441 (Rfree = 0.000) for 2468 atoms. Found 3 (22 requested) and removed 13 (11 requested) atoms. Cycle 39: After refmac, R = 0.2418 (Rfree = 0.000) for 2456 atoms. Found 8 (22 requested) and removed 11 (11 requested) atoms. Cycle 40: After refmac, R = 0.2318 (Rfree = 0.000) for 2450 atoms. Found 6 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.94 2.71 Search for helices and strands: 0 residues in 0 chains, 2521 seeds are put forward Round 1: 192 peptides, 28 chains. Longest chain 13 peptides. Score 0.493 Round 2: 209 peptides, 27 chains. Longest chain 21 peptides. Score 0.562 Round 3: 219 peptides, 27 chains. Longest chain 20 peptides. Score 0.591 Round 4: 217 peptides, 26 chains. Longest chain 24 peptides. Score 0.599 Round 5: 213 peptides, 27 chains. Longest chain 21 peptides. Score 0.574 Taking the results from Round 4 Chains 28, Residues 191, Estimated correctness of the model 40.8 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7644 reflections ( 99.64 % complete ) and 5152 restraints for refining 2491 atoms. 4336 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2779 (Rfree = 0.000) for 2491 atoms. Found 7 (22 requested) and removed 17 (11 requested) atoms. Cycle 42: After refmac, R = 0.2461 (Rfree = 0.000) for 2477 atoms. Found 9 (22 requested) and removed 16 (11 requested) atoms. Cycle 43: After refmac, R = 0.2392 (Rfree = 0.000) for 2466 atoms. Found 5 (22 requested) and removed 13 (11 requested) atoms. Cycle 44: After refmac, R = 0.2342 (Rfree = 0.000) for 2455 atoms. Found 7 (22 requested) and removed 12 (11 requested) atoms. Cycle 45: After refmac, R = 0.2290 (Rfree = 0.000) for 2449 atoms. Found 4 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.92 2.69 Search for helices and strands: 0 residues in 0 chains, 2504 seeds are put forward Round 1: 192 peptides, 27 chains. Longest chain 23 peptides. Score 0.508 Round 2: 210 peptides, 24 chains. Longest chain 19 peptides. Score 0.605 Round 3: 214 peptides, 25 chains. Longest chain 27 peptides. Score 0.603 Round 4: 212 peptides, 26 chains. Longest chain 25 peptides. Score 0.584 Round 5: 218 peptides, 28 chains. Longest chain 28 peptides. Score 0.575 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 186, Estimated correctness of the model 42.4 % 3 chains (33 residues) have been docked in sequence Sequence coverage is 17 % Consider running further cycles of model building using 1vjz-3_warpNtrace.pdb as input Building loops using Loopy2018 27 chains (186 residues) following loop building 3 chains (33 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7644 reflections ( 99.64 % complete ) and 4919 restraints for refining 2491 atoms. 4050 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2607 (Rfree = 0.000) for 2491 atoms. Found 0 (22 requested) and removed 2 (11 requested) atoms. Cycle 47: After refmac, R = 0.2588 (Rfree = 0.000) for 2485 atoms. Found 0 (22 requested) and removed 1 (11 requested) atoms. Cycle 48: After refmac, R = 0.2522 (Rfree = 0.000) for 2481 atoms. Found 0 (22 requested) and removed 4 (11 requested) atoms. Cycle 49: After refmac, R = 0.2566 (Rfree = 0.000) for 2476 atoms. Found 0 (22 requested) and removed 6 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:12:48 GMT 2018 Job finished. TimeTaking 50.08 Used memory is bytes: 15666672