null 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 2ppv-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ppv-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ppv-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ppv-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/2ppv-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ppv-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 22:23:17 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/2ppv-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ppv-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 312 and 0 Target number of residues in the AU: 312 Target solvent content: 0.6701 Checking the provided sequence file Detected sequence length: 332 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 332 Adjusted target solvent content: 0.65 Input MTZ file: 2ppv-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: 20 Cell parameters: 133.390 136.620 56.180 90.000 90.000 90.000 Input sequence file: 2ppv-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2656 target number of atoms Had to go as low as 0.85 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: 29.185 3.200 Wilson plot Bfac: 92.59 8761 reflections ( 99.17 % complete ) and 0 restraints for refining 2947 atoms. Observations/parameters ratio is 0.74 ------------------------------------------------------ Starting model: R = 0.3410 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3480 (Rfree = 0.000) for 2947 atoms. Found 26 (26 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 2.96 Search for helices and strands: 0 residues in 0 chains, 3018 seeds are put forward Round 1: 148 peptides, 24 chains. Longest chain 13 peptides. Score 0.369 Round 2: 198 peptides, 26 chains. Longest chain 17 peptides. Score 0.496 Round 3: 206 peptides, 27 chains. Longest chain 18 peptides. Score 0.506 Round 4: 205 peptides, 21 chains. Longest chain 21 peptides. Score 0.578 Round 5: 207 peptides, 24 chains. Longest chain 20 peptides. Score 0.546 Taking the results from Round 4 Chains 21, Residues 184, Estimated correctness of the model 35.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 8761 reflections ( 99.17 % complete ) and 5302 restraints for refining 2425 atoms. 4546 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3154 (Rfree = 0.000) for 2425 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 2: After refmac, R = 0.3048 (Rfree = 0.000) for 2359 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 3: After refmac, R = 0.2881 (Rfree = 0.000) for 2335 atoms. Found 10 (21 requested) and removed 16 (10 requested) atoms. Cycle 4: After refmac, R = 0.2940 (Rfree = 0.000) for 2290 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 5: After refmac, R = 0.2777 (Rfree = 0.000) for 2280 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.62 2.95 Search for helices and strands: 0 residues in 0 chains, 2395 seeds are put forward Round 1: 201 peptides, 29 chains. Longest chain 16 peptides. Score 0.466 Round 2: 218 peptides, 26 chains. Longest chain 22 peptides. Score 0.551 Round 3: 230 peptides, 21 chains. Longest chain 27 peptides. Score 0.637 Round 4: 232 peptides, 21 chains. Longest chain 33 peptides. Score 0.641 Round 5: 233 peptides, 25 chains. Longest chain 21 peptides. Score 0.600 Taking the results from Round 4 Chains 24, Residues 211, Estimated correctness of the model 51.6 % 2 chains (35 residues) have been docked in sequence ------------------------------------------------------ 8761 reflections ( 99.17 % complete ) and 4720 restraints for refining 2405 atoms. 3782 conditional restraints added. Observations/parameters ratio is 0.91 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2802 (Rfree = 0.000) for 2405 atoms. Found 19 (21 requested) and removed 21 (10 requested) atoms. Cycle 7: After refmac, R = 0.2767 (Rfree = 0.000) for 2367 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. Cycle 8: After refmac, R = 0.2837 (Rfree = 0.000) for 2345 atoms. Found 21 (21 requested) and removed 30 (10 requested) atoms. Cycle 9: After refmac, R = 0.2494 (Rfree = 0.000) for 2322 atoms. Found 17 (20 requested) and removed 12 (10 requested) atoms. Cycle 10: After refmac, R = 0.2414 (Rfree = 0.000) for 2309 atoms. Found 6 (20 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 2.90 Search for helices and strands: 0 residues in 0 chains, 2406 seeds are put forward Round 1: 223 peptides, 29 chains. Longest chain 16 peptides. Score 0.528 Round 2: 236 peptides, 23 chains. Longest chain 26 peptides. Score 0.629 Round 3: 229 peptides, 23 chains. Longest chain 26 peptides. Score 0.613 Round 4: 242 peptides, 22 chains. Longest chain 26 peptides. Score 0.653 Round 5: 228 peptides, 18 chains. Longest chain 30 peptides. Score 0.664 Taking the results from Round 5 Chains 22, Residues 210, Estimated correctness of the model 57.2 % 3 chains (57 residues) have been docked in sequence ------------------------------------------------------ 8761 reflections ( 99.17 % complete ) and 4634 restraints for refining 2425 atoms. 3612 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2863 (Rfree = 0.000) for 2425 atoms. Found 19 (21 requested) and removed 21 (10 requested) atoms. Cycle 12: After refmac, R = 0.2639 (Rfree = 0.000) for 2403 atoms. Found 19 (21 requested) and removed 14 (10 requested) atoms. Cycle 13: After refmac, R = 0.2735 (Rfree = 0.000) for 2388 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 14: After refmac, R = 0.2434 (Rfree = 0.000) for 2357 atoms. Found 15 (21 requested) and removed 12 (10 requested) atoms. Cycle 15: After refmac, R = 0.2385 (Rfree = 0.000) for 2350 atoms. Found 13 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 2.87 Search for helices and strands: 0 residues in 0 chains, 2443 seeds are put forward Round 1: 230 peptides, 27 chains. Longest chain 26 peptides. Score 0.570 Round 2: 253 peptides, 23 chains. Longest chain 35 peptides. Score 0.666 Round 3: 247 peptides, 24 chains. Longest chain 36 peptides. Score 0.643 Round 4: 241 peptides, 22 chains. Longest chain 36 peptides. Score 0.650 Round 5: 242 peptides, 21 chains. Longest chain 36 peptides. Score 0.663 Taking the results from Round 2 Chains 24, Residues 230, Estimated correctness of the model 57.6 % 3 chains (59 residues) have been docked in sequence ------------------------------------------------------ 8761 reflections ( 99.17 % complete ) and 4448 restraints for refining 2425 atoms. 3355 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2490 (Rfree = 0.000) for 2425 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. Cycle 17: After refmac, R = 0.2628 (Rfree = 0.000) for 2403 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 18: After refmac, R = 0.2525 (Rfree = 0.000) for 2393 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 19: After refmac, R = 0.2404 (Rfree = 0.000) for 2374 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. Cycle 20: After refmac, R = 0.2441 (Rfree = 0.000) for 2362 atoms. Found 21 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 2.88 Search for helices and strands: 0 residues in 0 chains, 2440 seeds are put forward Round 1: 217 peptides, 30 chains. Longest chain 23 peptides. Score 0.499 Round 2: 236 peptides, 29 chains. Longest chain 22 peptides. Score 0.562 Round 3: 236 peptides, 22 chains. Longest chain 33 peptides. Score 0.639 Round 4: 245 peptides, 21 chains. Longest chain 23 peptides. Score 0.669 Round 5: 242 peptides, 20 chains. Longest chain 25 peptides. Score 0.673 Taking the results from Round 5 Chains 20, Residues 222, Estimated correctness of the model 59.2 % 3 chains (57 residues) have been docked in sequence ------------------------------------------------------ 8761 reflections ( 99.17 % complete ) and 4579 restraints for refining 2425 atoms. 3499 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2742 (Rfree = 0.000) for 2425 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 22: After refmac, R = 0.2519 (Rfree = 0.000) for 2405 atoms. Found 15 (21 requested) and removed 17 (10 requested) atoms. Cycle 23: After refmac, R = 0.2440 (Rfree = 0.000) for 2391 atoms. Found 17 (21 requested) and removed 15 (10 requested) atoms. Cycle 24: After refmac, R = 0.2428 (Rfree = 0.000) for 2379 atoms. Found 19 (21 requested) and removed 18 (10 requested) atoms. Cycle 25: After refmac, R = 0.2100 (Rfree = 0.000) for 2375 atoms. Found 3 (21 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 2.86 Search for helices and strands: 0 residues in 0 chains, 2437 seeds are put forward Round 1: 220 peptides, 26 chains. Longest chain 22 peptides. Score 0.556 Round 2: 229 peptides, 23 chains. Longest chain 28 peptides. Score 0.613 Round 3: 224 peptides, 24 chains. Longest chain 19 peptides. Score 0.589 Round 4: 241 peptides, 25 chains. Longest chain 28 peptides. Score 0.619 Round 5: 213 peptides, 24 chains. Longest chain 29 peptides. Score 0.562 Taking the results from Round 4 Chains 27, Residues 216, Estimated correctness of the model 46.1 % 2 chains (42 residues) have been docked in sequence ------------------------------------------------------ 8761 reflections ( 99.17 % complete ) and 4605 restraints for refining 2425 atoms. 3610 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2610 (Rfree = 0.000) for 2425 atoms. Found 21 (21 requested) and removed 28 (10 requested) atoms. Cycle 27: After refmac, R = 0.2581 (Rfree = 0.000) for 2395 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 28: After refmac, R = 0.2542 (Rfree = 0.000) for 2386 atoms. Found 21 (21 requested) and removed 13 (10 requested) atoms. Cycle 29: After refmac, R = 0.2182 (Rfree = 0.000) for 2381 atoms. Found 6 (21 requested) and removed 14 (10 requested) atoms. Cycle 30: After refmac, R = 0.2109 (Rfree = 0.000) for 2366 atoms. Found 4 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 2.88 Search for helices and strands: 0 residues in 0 chains, 2436 seeds are put forward Round 1: 220 peptides, 29 chains. Longest chain 28 peptides. Score 0.520 Round 2: 228 peptides, 26 chains. Longest chain 25 peptides. Score 0.576 Round 3: 230 peptides, 26 chains. Longest chain 31 peptides. Score 0.581 Round 4: 224 peptides, 25 chains. Longest chain 27 peptides. Score 0.578 Round 5: 237 peptides, 26 chains. Longest chain 23 peptides. Score 0.598 Taking the results from Round 5 Chains 29, Residues 211, Estimated correctness of the model 40.5 % 4 chains (44 residues) have been docked in sequence ------------------------------------------------------ 8761 reflections ( 99.17 % complete ) and 4673 restraints for refining 2424 atoms. 3705 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2626 (Rfree = 0.000) for 2424 atoms. Found 17 (21 requested) and removed 23 (10 requested) atoms. Cycle 32: After refmac, R = 0.2436 (Rfree = 0.000) for 2390 atoms. Found 9 (21 requested) and removed 13 (10 requested) atoms. Cycle 33: After refmac, R = 0.2667 (Rfree = 0.000) for 2364 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. Cycle 34: After refmac, R = 0.2627 (Rfree = 0.000) for 2355 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. Cycle 35: After refmac, R = 0.2614 (Rfree = 0.000) for 2350 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 2.90 Search for helices and strands: 0 residues in 0 chains, 2448 seeds are put forward Round 1: 191 peptides, 28 chains. Longest chain 22 peptides. Score 0.449 Round 2: 220 peptides, 26 chains. Longest chain 27 peptides. Score 0.556 Round 3: 212 peptides, 25 chains. Longest chain 27 peptides. Score 0.547 Round 4: 226 peptides, 28 chains. Longest chain 28 peptides. Score 0.548 Round 5: 223 peptides, 22 chains. Longest chain 36 peptides. Score 0.610 Taking the results from Round 5 Chains 22, Residues 201, Estimated correctness of the model 43.7 % 2 chains (49 residues) have been docked in sequence ------------------------------------------------------ 8761 reflections ( 99.17 % complete ) and 4719 restraints for refining 2425 atoms. 3779 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2780 (Rfree = 0.000) for 2425 atoms. Found 21 (21 requested) and removed 21 (10 requested) atoms. Cycle 37: After refmac, R = 0.2523 (Rfree = 0.000) for 2404 atoms. Found 14 (21 requested) and removed 13 (10 requested) atoms. Cycle 38: After refmac, R = 0.2669 (Rfree = 0.000) for 2390 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 39: After refmac, R = 0.2810 (Rfree = 0.000) for 2387 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. Cycle 40: After refmac, R = 0.2434 (Rfree = 0.000) for 2378 atoms. Found 13 (21 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.56 2.90 Search for helices and strands: 0 residues in 0 chains, 2450 seeds are put forward Round 1: 210 peptides, 28 chains. Longest chain 24 peptides. Score 0.504 Round 2: 242 peptides, 26 chains. Longest chain 27 peptides. Score 0.610 Round 3: 228 peptides, 23 chains. Longest chain 37 peptides. Score 0.610 Round 4: 233 peptides, 23 chains. Longest chain 24 peptides. Score 0.622 Round 5: 234 peptides, 23 chains. Longest chain 29 peptides. Score 0.624 Taking the results from Round 5 Chains 23, Residues 211, Estimated correctness of the model 47.4 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 8761 reflections ( 99.17 % complete ) and 4774 restraints for refining 2425 atoms. 3856 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2764 (Rfree = 0.000) for 2425 atoms. Found 21 (21 requested) and removed 15 (10 requested) atoms. Cycle 42: After refmac, R = 0.2492 (Rfree = 0.000) for 2421 atoms. Found 8 (21 requested) and removed 13 (10 requested) atoms. Cycle 43: After refmac, R = 0.2327 (Rfree = 0.000) for 2390 atoms. Found 12 (21 requested) and removed 16 (10 requested) atoms. Cycle 44: After refmac, R = 0.2510 (Rfree = 0.000) for 2371 atoms. Found 19 (21 requested) and removed 13 (10 requested) atoms. Cycle 45: After refmac, R = 0.2257 (Rfree = 0.000) for 2367 atoms. Found 5 (21 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 2.88 Search for helices and strands: 0 residues in 0 chains, 2447 seeds are put forward Round 1: 193 peptides, 23 chains. Longest chain 37 peptides. Score 0.521 Round 2: 213 peptides, 26 chains. Longest chain 21 peptides. Score 0.538 Round 3: 229 peptides, 24 chains. Longest chain 37 peptides. Score 0.602 Round 4: 222 peptides, 24 chains. Longest chain 26 peptides. Score 0.585 Round 5: 237 peptides, 23 chains. Longest chain 27 peptides. Score 0.631 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 214, Estimated correctness of the model 49.1 % 2 chains (35 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 2ppv-3_warpNtrace.pdb as input Building loops using Loopy2018 26 chains (214 residues) following loop building 2 chains (35 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8761 reflections ( 99.17 % complete ) and 4773 restraints for refining 2424 atoms. 3804 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3005 (Rfree = 0.000) for 2424 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2569 (Rfree = 0.000) for 2401 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2413 (Rfree = 0.000) for 2383 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2321 (Rfree = 0.000) for 2371 atoms. Found 0 (21 requested) and removed 10 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:15:00 GMT 2018 Job finished. TimeTaking 51.88 Used memory is bytes: 7536392