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 1zbt-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zbt-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zbt-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-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/1zbt-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-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 22:22:53 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/1zbt-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-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 312 and 0 Target number of residues in the AU: 312 Target solvent content: 0.6502 Checking the provided sequence file Detected sequence length: 371 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 371 Adjusted target solvent content: 0.58 Input MTZ file: 1zbt-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: 96 Cell parameters: 71.823 71.823 187.134 90.000 90.000 90.000 Input sequence file: 1zbt-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2968 target number of atoms Had to go as low as 0.60 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: 28.608 3.800 Wilson plot Bfac: 78.15 5251 reflections ( 99.62 % complete ) and 0 restraints for refining 3293 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3396 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3746 (Rfree = 0.000) for 3293 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.95 3.55 Search for helices and strands: 0 residues in 0 chains, 3330 seeds are put forward Round 1: 138 peptides, 20 chains. Longest chain 17 peptides. Score 0.405 Round 2: 174 peptides, 19 chains. Longest chain 23 peptides. Score 0.534 Round 3: 180 peptides, 18 chains. Longest chain 29 peptides. Score 0.565 Round 4: 182 peptides, 18 chains. Longest chain 23 peptides. Score 0.570 Round 5: 180 peptides, 20 chains. Longest chain 24 peptides. Score 0.538 Taking the results from Round 4 Chains 19, Residues 164, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 5251 reflections ( 99.62 % complete ) and 5964 restraints for refining 2592 atoms. 5286 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3260 (Rfree = 0.000) for 2592 atoms. Found 14 (14 requested) and removed 31 (7 requested) atoms. Cycle 2: After refmac, R = 0.3179 (Rfree = 0.000) for 2498 atoms. Found 14 (14 requested) and removed 29 (7 requested) atoms. Cycle 3: After refmac, R = 0.3090 (Rfree = 0.000) for 2425 atoms. Found 13 (13 requested) and removed 23 (6 requested) atoms. Cycle 4: After refmac, R = 0.3023 (Rfree = 0.000) for 2382 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 5: After refmac, R = 0.3006 (Rfree = 0.000) for 2340 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 3.34 Search for helices and strands: 0 residues in 0 chains, 2455 seeds are put forward Round 1: 170 peptides, 23 chains. Longest chain 19 peptides. Score 0.466 Round 2: 194 peptides, 21 chains. Longest chain 38 peptides. Score 0.564 Round 3: 187 peptides, 15 chains. Longest chain 50 peptides. Score 0.621 Round 4: 179 peptides, 17 chains. Longest chain 31 peptides. Score 0.575 Round 5: 171 peptides, 15 chains. Longest chain 32 peptides. Score 0.580 Taking the results from Round 3 Chains 16, Residues 172, Estimated correctness of the model 8.4 % 2 chains (57 residues) have been docked in sequence ------------------------------------------------------ 5251 reflections ( 99.62 % complete ) and 4792 restraints for refining 2446 atoms. 3881 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3094 (Rfree = 0.000) for 2446 atoms. Found 13 (13 requested) and removed 30 (6 requested) atoms. Cycle 7: After refmac, R = 0.2791 (Rfree = 0.000) for 2386 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 8: After refmac, R = 0.2805 (Rfree = 0.000) for 2350 atoms. Found 13 (13 requested) and removed 25 (6 requested) atoms. Cycle 9: After refmac, R = 0.2695 (Rfree = 0.000) for 2329 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 10: After refmac, R = 0.2622 (Rfree = 0.000) for 2314 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.68 3.30 Search for helices and strands: 0 residues in 0 chains, 2399 seeds are put forward Round 1: 180 peptides, 27 chains. Longest chain 24 peptides. Score 0.440 Round 2: 191 peptides, 22 chains. Longest chain 27 peptides. Score 0.543 Round 3: 195 peptides, 19 chains. Longest chain 25 peptides. Score 0.592 Round 4: 191 peptides, 18 chains. Longest chain 33 peptides. Score 0.594 Round 5: 189 peptides, 22 chains. Longest chain 17 peptides. Score 0.537 Taking the results from Round 4 Chains 19, Residues 173, Estimated correctness of the model 0.0 % 4 chains (58 residues) have been docked in sequence ------------------------------------------------------ 5251 reflections ( 99.62 % complete ) and 4992 restraints for refining 2569 atoms. 4114 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2909 (Rfree = 0.000) for 2569 atoms. Found 14 (14 requested) and removed 57 (7 requested) atoms. Cycle 12: After refmac, R = 0.2923 (Rfree = 0.000) for 2490 atoms. Found 13 (13 requested) and removed 27 (6 requested) atoms. Cycle 13: After refmac, R = 0.2868 (Rfree = 0.000) for 2441 atoms. Found 13 (13 requested) and removed 30 (6 requested) atoms. Cycle 14: After refmac, R = 0.2624 (Rfree = 0.000) for 2399 atoms. Found 8 (13 requested) and removed 18 (6 requested) atoms. Cycle 15: After refmac, R = 0.2485 (Rfree = 0.000) for 2378 atoms. Found 5 (13 requested) and removed 21 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.25 Search for helices and strands: 0 residues in 0 chains, 2487 seeds are put forward Round 1: 181 peptides, 28 chains. Longest chain 18 peptides. Score 0.429 Round 2: 175 peptides, 24 chains. Longest chain 16 peptides. Score 0.467 Round 3: 179 peptides, 23 chains. Longest chain 17 peptides. Score 0.494 Round 4: 176 peptides, 21 chains. Longest chain 19 peptides. Score 0.513 Round 5: 178 peptides, 24 chains. Longest chain 20 peptides. Score 0.477 Taking the results from Round 4 Chains 21, Residues 155, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5251 reflections ( 99.62 % complete ) and 5607 restraints for refining 2543 atoms. 4989 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3054 (Rfree = 0.000) for 2543 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 17: After refmac, R = 0.2767 (Rfree = 0.000) for 2488 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 18: After refmac, R = 0.2417 (Rfree = 0.000) for 2463 atoms. Found 12 (13 requested) and removed 18 (6 requested) atoms. Cycle 19: After refmac, R = 0.2364 (Rfree = 0.000) for 2445 atoms. Found 6 (13 requested) and removed 11 (6 requested) atoms. Cycle 20: After refmac, R = 0.2435 (Rfree = 0.000) for 2430 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.65 3.28 Search for helices and strands: 0 residues in 0 chains, 2531 seeds are put forward Round 1: 174 peptides, 29 chains. Longest chain 17 peptides. Score 0.391 Round 2: 174 peptides, 24 chains. Longest chain 19 peptides. Score 0.464 Round 3: 193 peptides, 26 chains. Longest chain 19 peptides. Score 0.495 Round 4: 188 peptides, 24 chains. Longest chain 19 peptides. Score 0.507 Round 5: 200 peptides, 25 chains. Longest chain 23 peptides. Score 0.529 Taking the results from Round 5 Chains 25, Residues 175, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 5251 reflections ( 99.62 % complete ) and 5535 restraints for refining 2650 atoms. 4761 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2947 (Rfree = 0.000) for 2650 atoms. Found 14 (14 requested) and removed 46 (7 requested) atoms. Cycle 22: After refmac, R = 0.2645 (Rfree = 0.000) for 2588 atoms. Found 6 (14 requested) and removed 20 (7 requested) atoms. Cycle 23: After refmac, R = 0.2515 (Rfree = 0.000) for 2556 atoms. Found 8 (14 requested) and removed 17 (7 requested) atoms. Cycle 24: After refmac, R = 0.2448 (Rfree = 0.000) for 2537 atoms. Found 4 (14 requested) and removed 15 (7 requested) atoms. Cycle 25: After refmac, R = 0.2498 (Rfree = 0.000) for 2518 atoms. Found 7 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.72 3.34 Search for helices and strands: 0 residues in 0 chains, 2621 seeds are put forward Round 1: 149 peptides, 24 chains. Longest chain 17 peptides. Score 0.381 Round 2: 170 peptides, 24 chains. Longest chain 24 peptides. Score 0.451 Round 3: 193 peptides, 25 chains. Longest chain 20 peptides. Score 0.508 Round 4: 191 peptides, 25 chains. Longest chain 26 peptides. Score 0.502 Round 5: 188 peptides, 22 chains. Longest chain 20 peptides. Score 0.534 Taking the results from Round 5 Chains 22, Residues 166, Estimated correctness of the model 0.0 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 5251 reflections ( 99.62 % complete ) and 5689 restraints for refining 2646 atoms. 4958 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2772 (Rfree = 0.000) for 2646 atoms. Found 14 (14 requested) and removed 30 (7 requested) atoms. Cycle 27: After refmac, R = 0.2665 (Rfree = 0.000) for 2609 atoms. Found 10 (14 requested) and removed 17 (7 requested) atoms. Cycle 28: After refmac, R = 0.2530 (Rfree = 0.000) for 2594 atoms. Found 2 (14 requested) and removed 15 (7 requested) atoms. Cycle 29: After refmac, R = 0.2532 (Rfree = 0.000) for 2577 atoms. Found 4 (14 requested) and removed 11 (7 requested) atoms. Cycle 30: After refmac, R = 0.2486 (Rfree = 0.000) for 2567 atoms. Found 5 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.73 3.35 Search for helices and strands: 0 residues in 0 chains, 2639 seeds are put forward Round 1: 158 peptides, 25 chains. Longest chain 11 peptides. Score 0.396 Round 2: 160 peptides, 22 chains. Longest chain 19 peptides. Score 0.448 Round 3: 163 peptides, 21 chains. Longest chain 16 peptides. Score 0.473 Round 4: 162 peptides, 22 chains. Longest chain 16 peptides. Score 0.455 Round 5: 172 peptides, 21 chains. Longest chain 15 peptides. Score 0.501 Taking the results from Round 5 Chains 21, Residues 151, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5251 reflections ( 99.62 % complete ) and 6055 restraints for refining 2683 atoms. 5450 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2905 (Rfree = 0.000) for 2683 atoms. Found 9 (14 requested) and removed 29 (7 requested) atoms. Cycle 32: After refmac, R = 0.2741 (Rfree = 0.000) for 2638 atoms. Found 6 (14 requested) and removed 18 (7 requested) atoms. Cycle 33: After refmac, R = 0.2689 (Rfree = 0.000) for 2607 atoms. Found 6 (14 requested) and removed 21 (7 requested) atoms. Cycle 34: After refmac, R = 0.2625 (Rfree = 0.000) for 2579 atoms. Found 9 (14 requested) and removed 14 (7 requested) atoms. Cycle 35: After refmac, R = 0.2624 (Rfree = 0.000) for 2563 atoms. Found 7 (14 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 3.28 Search for helices and strands: 0 residues in 0 chains, 2647 seeds are put forward Round 1: 138 peptides, 25 chains. Longest chain 14 peptides. Score 0.324 Round 2: 160 peptides, 29 chains. Longest chain 14 peptides. Score 0.341 Round 3: 166 peptides, 25 chains. Longest chain 19 peptides. Score 0.423 Round 4: 154 peptides, 23 chains. Longest chain 16 peptides. Score 0.413 Round 5: 155 peptides, 24 chains. Longest chain 14 peptides. Score 0.401 Taking the results from Round 3 Chains 25, Residues 141, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5251 reflections ( 99.62 % complete ) and 5864 restraints for refining 2632 atoms. 5325 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2982 (Rfree = 0.000) for 2632 atoms. Found 14 (14 requested) and removed 36 (7 requested) atoms. Cycle 37: After refmac, R = 0.2604 (Rfree = 0.000) for 2584 atoms. Found 9 (14 requested) and removed 15 (7 requested) atoms. Cycle 38: After refmac, R = 0.2542 (Rfree = 0.000) for 2566 atoms. Found 8 (14 requested) and removed 13 (7 requested) atoms. Cycle 39: After refmac, R = 0.2346 (Rfree = 0.000) for 2554 atoms. Found 5 (14 requested) and removed 10 (7 requested) atoms. Cycle 40: After refmac, R = 0.2345 (Rfree = 0.000) for 2545 atoms. Found 3 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.68 3.30 Search for helices and strands: 0 residues in 0 chains, 2614 seeds are put forward Round 1: 150 peptides, 29 chains. Longest chain 9 peptides. Score 0.305 Round 2: 167 peptides, 27 chains. Longest chain 17 peptides. Score 0.397 Round 3: 179 peptides, 28 chains. Longest chain 11 peptides. Score 0.422 Round 4: 176 peptides, 26 chains. Longest chain 18 peptides. Score 0.442 Round 5: 179 peptides, 24 chains. Longest chain 23 peptides. Score 0.480 Taking the results from Round 5 Chains 27, Residues 155, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5251 reflections ( 99.62 % complete ) and 5663 restraints for refining 2684 atoms. 4989 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2765 (Rfree = 0.000) for 2684 atoms. Found 11 (14 requested) and removed 23 (7 requested) atoms. Cycle 42: After refmac, R = 0.2625 (Rfree = 0.000) for 2637 atoms. Found 6 (14 requested) and removed 14 (7 requested) atoms. Cycle 43: After refmac, R = 0.2478 (Rfree = 0.000) for 2608 atoms. Found 3 (14 requested) and removed 15 (7 requested) atoms. Cycle 44: After refmac, R = 0.2437 (Rfree = 0.000) for 2586 atoms. Found 3 (14 requested) and removed 13 (7 requested) atoms. Cycle 45: After refmac, R = 0.2162 (Rfree = 0.000) for 2571 atoms. Found 1 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 3.29 Search for helices and strands: 0 residues in 0 chains, 2672 seeds are put forward Round 1: 127 peptides, 27 chains. Longest chain 9 peptides. Score 0.248 Round 2: 152 peptides, 28 chains. Longest chain 11 peptides. Score 0.328 Round 3: 160 peptides, 27 chains. Longest chain 11 peptides. Score 0.373 Round 4: 149 peptides, 24 chains. Longest chain 13 peptides. Score 0.381 Round 5: 161 peptides, 23 chains. Longest chain 16 peptides. Score 0.437 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 138, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 1zbt-3_warpNtrace.pdb as input Building loops using Loopy2018 24 chains (138 residues) following loop building 3 chains (17 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5251 reflections ( 99.62 % complete ) and 5919 restraints for refining 2678 atoms. 5353 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2853 (Rfree = 0.000) for 2678 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2576 (Rfree = 0.000) for 2655 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2470 (Rfree = 0.000) for 2638 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2390 (Rfree = 0.000) for 2620 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:12:28 GMT 2018 Job finished. TimeTaking 49.76 Used memory is bytes: 17153120