null Tue 25 Dec 19:27:56 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 2g0t-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2g0t-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2g0t-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2g0t-3.6-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/2g0t-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2g0t-3.6-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 19:28:11 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/2g0t-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2g0t-3.6-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 897 and 0 Target number of residues in the AU: 897 Target solvent content: 0.5857 Checking the provided sequence file Detected sequence length: 350 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 700 Adjusted target solvent content: 0.68 Input MTZ file: 2g0t-3.6-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: 213 Cell parameters: 191.568 191.568 191.568 90.000 90.000 90.000 Input sequence file: 2g0t-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 5600 target number of atoms Had to go as low as 0.95 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: 29.560 3.601 Wilson plot Bfac: 47.03 14436 reflections ( 99.70 % complete ) and 0 restraints for refining 6261 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3159 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3099 (Rfree = 0.000) for 6261 atoms. Found 40 (40 requested) and removed 52 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.15 2.45 Search for helices and strands: 0 residues in 0 chains, 6423 seeds are put forward NCS extension: 0 residues added, 6423 seeds are put forward Round 1: 415 peptides, 71 chains. Longest chain 16 peptides. Score 0.376 Round 2: 474 peptides, 63 chains. Longest chain 20 peptides. Score 0.502 Round 3: 476 peptides, 57 chains. Longest chain 29 peptides. Score 0.537 Round 4: 484 peptides, 54 chains. Longest chain 34 peptides. Score 0.563 Round 5: 483 peptides, 54 chains. Longest chain 27 peptides. Score 0.562 Taking the results from Round 4 Chains 59, Residues 430, Estimated correctness of the model 0.0 % 6 chains (82 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 9847 restraints for refining 5075 atoms. 7861 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2714 (Rfree = 0.000) for 5075 atoms. Found 32 (32 requested) and removed 42 (16 requested) atoms. Cycle 2: After refmac, R = 0.2581 (Rfree = 0.000) for 4994 atoms. Found 32 (32 requested) and removed 34 (16 requested) atoms. Cycle 3: After refmac, R = 0.2440 (Rfree = 0.000) for 4963 atoms. Found 21 (31 requested) and removed 33 (15 requested) atoms. Cycle 4: After refmac, R = 0.2371 (Rfree = 0.000) for 4931 atoms. Found 21 (31 requested) and removed 27 (15 requested) atoms. Cycle 5: After refmac, R = 0.2264 (Rfree = 0.000) for 4905 atoms. Found 17 (31 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.11 2.42 Search for helices and strands: 0 residues in 0 chains, 5114 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5131 seeds are put forward Round 1: 460 peptides, 63 chains. Longest chain 23 peptides. Score 0.485 Round 2: 472 peptides, 57 chains. Longest chain 18 peptides. Score 0.533 Round 3: 511 peptides, 52 chains. Longest chain 32 peptides. Score 0.602 Round 4: 476 peptides, 51 chains. Longest chain 33 peptides. Score 0.570 Round 5: 488 peptides, 50 chains. Longest chain 44 peptides. Score 0.588 Taking the results from Round 3 Chains 56, Residues 459, Estimated correctness of the model 15.4 % 6 chains (80 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 9759 restraints for refining 5076 atoms. 7693 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2580 (Rfree = 0.000) for 5076 atoms. Found 32 (32 requested) and removed 44 (16 requested) atoms. Cycle 7: After refmac, R = 0.2399 (Rfree = 0.000) for 5029 atoms. Found 31 (32 requested) and removed 41 (16 requested) atoms. Cycle 8: After refmac, R = 0.2278 (Rfree = 0.000) for 4998 atoms. Found 23 (32 requested) and removed 24 (16 requested) atoms. Cycle 9: After refmac, R = 0.2250 (Rfree = 0.000) for 4982 atoms. Found 24 (32 requested) and removed 30 (16 requested) atoms. Cycle 10: After refmac, R = 0.2206 (Rfree = 0.000) for 4964 atoms. Found 21 (31 requested) and removed 28 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.08 2.40 Search for helices and strands: 0 residues in 0 chains, 5132 seeds are put forward NCS extension: 24 residues added (8 deleted due to clashes), 5156 seeds are put forward Round 1: 464 peptides, 58 chains. Longest chain 18 peptides. Score 0.518 Round 2: 510 peptides, 56 chains. Longest chain 30 peptides. Score 0.581 Round 3: 482 peptides, 53 chains. Longest chain 23 peptides. Score 0.566 Round 4: 484 peptides, 56 chains. Longest chain 21 peptides. Score 0.552 Round 5: 493 peptides, 56 chains. Longest chain 30 peptides. Score 0.562 Taking the results from Round 2 Chains 57, Residues 454, Estimated correctness of the model 7.0 % 4 chains (50 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 9947 restraints for refining 5075 atoms. 8015 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2527 (Rfree = 0.000) for 5075 atoms. Found 32 (32 requested) and removed 27 (16 requested) atoms. Cycle 12: After refmac, R = 0.2387 (Rfree = 0.000) for 5045 atoms. Found 30 (32 requested) and removed 35 (16 requested) atoms. Cycle 13: After refmac, R = 0.2304 (Rfree = 0.000) for 5021 atoms. Found 28 (32 requested) and removed 36 (16 requested) atoms. Cycle 14: After refmac, R = 0.2258 (Rfree = 0.000) for 4999 atoms. Found 25 (32 requested) and removed 32 (16 requested) atoms. Cycle 15: After refmac, R = 0.2173 (Rfree = 0.000) for 4981 atoms. Found 22 (32 requested) and removed 25 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.07 2.39 Search for helices and strands: 0 residues in 0 chains, 5198 seeds are put forward NCS extension: 19 residues added (9 deleted due to clashes), 5217 seeds are put forward Round 1: 466 peptides, 57 chains. Longest chain 21 peptides. Score 0.526 Round 2: 489 peptides, 58 chains. Longest chain 31 peptides. Score 0.547 Round 3: 505 peptides, 56 chains. Longest chain 31 peptides. Score 0.576 Round 4: 495 peptides, 55 chains. Longest chain 31 peptides. Score 0.570 Round 5: 489 peptides, 55 chains. Longest chain 38 peptides. Score 0.563 Taking the results from Round 3 Chains 58, Residues 449, Estimated correctness of the model 5.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 10381 restraints for refining 5075 atoms. 8591 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2607 (Rfree = 0.000) for 5075 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. Cycle 17: After refmac, R = 0.2453 (Rfree = 0.000) for 5033 atoms. Found 32 (32 requested) and removed 35 (16 requested) atoms. Cycle 18: After refmac, R = 0.2424 (Rfree = 0.000) for 4998 atoms. Found 25 (32 requested) and removed 37 (16 requested) atoms. Cycle 19: After refmac, R = 0.2306 (Rfree = 0.000) for 4966 atoms. Found 28 (31 requested) and removed 27 (15 requested) atoms. Cycle 20: After refmac, R = 0.2298 (Rfree = 0.000) for 4957 atoms. Found 24 (31 requested) and removed 27 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.06 2.38 Search for helices and strands: 0 residues in 0 chains, 5124 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 5149 seeds are put forward Round 1: 458 peptides, 68 chains. Longest chain 21 peptides. Score 0.453 Round 2: 485 peptides, 56 chains. Longest chain 22 peptides. Score 0.553 Round 3: 487 peptides, 61 chains. Longest chain 37 peptides. Score 0.529 Round 4: 494 peptides, 58 chains. Longest chain 30 peptides. Score 0.553 Round 5: 509 peptides, 62 chains. Longest chain 26 peptides. Score 0.549 Taking the results from Round 4 Chains 63, Residues 436, Estimated correctness of the model 0.0 % 3 chains (41 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 10329 restraints for refining 5075 atoms. 8479 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2589 (Rfree = 0.000) for 5075 atoms. Found 32 (32 requested) and removed 32 (16 requested) atoms. Cycle 22: After refmac, R = 0.2458 (Rfree = 0.000) for 5043 atoms. Found 27 (32 requested) and removed 35 (16 requested) atoms. Cycle 23: After refmac, R = 0.2403 (Rfree = 0.000) for 5022 atoms. Found 21 (32 requested) and removed 35 (16 requested) atoms. Cycle 24: After refmac, R = 0.2427 (Rfree = 0.000) for 4999 atoms. Found 26 (32 requested) and removed 24 (16 requested) atoms. Cycle 25: After refmac, R = 0.2416 (Rfree = 0.000) for 4992 atoms. Found 32 (32 requested) and removed 39 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 2.43 Search for helices and strands: 0 residues in 0 chains, 5166 seeds are put forward NCS extension: 27 residues added (7 deleted due to clashes), 5193 seeds are put forward Round 1: 436 peptides, 63 chains. Longest chain 21 peptides. Score 0.454 Round 2: 474 peptides, 53 chains. Longest chain 35 peptides. Score 0.557 Round 3: 485 peptides, 55 chains. Longest chain 34 peptides. Score 0.559 Round 4: 469 peptides, 55 chains. Longest chain 34 peptides. Score 0.540 Round 5: 479 peptides, 53 chains. Longest chain 40 peptides. Score 0.562 Taking the results from Round 5 Chains 57, Residues 426, Estimated correctness of the model 0.0 % 7 chains (104 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 9815 restraints for refining 5075 atoms. 7779 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2792 (Rfree = 0.000) for 5075 atoms. Found 32 (32 requested) and removed 48 (16 requested) atoms. Cycle 27: After refmac, R = 0.2574 (Rfree = 0.000) for 5030 atoms. Found 31 (32 requested) and removed 28 (16 requested) atoms. Cycle 28: After refmac, R = 0.2446 (Rfree = 0.000) for 5018 atoms. Found 17 (32 requested) and removed 36 (16 requested) atoms. Cycle 29: After refmac, R = 0.2375 (Rfree = 0.000) for 4993 atoms. Found 11 (32 requested) and removed 36 (16 requested) atoms. Cycle 30: After refmac, R = 0.2312 (Rfree = 0.000) for 4960 atoms. Found 14 (31 requested) and removed 27 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.06 2.38 Search for helices and strands: 0 residues in 0 chains, 5135 seeds are put forward NCS extension: 44 residues added (0 deleted due to clashes), 5179 seeds are put forward Round 1: 465 peptides, 67 chains. Longest chain 34 peptides. Score 0.468 Round 2: 489 peptides, 52 chains. Longest chain 23 peptides. Score 0.579 Round 3: 481 peptides, 51 chains. Longest chain 35 peptides. Score 0.575 Round 4: 499 peptides, 54 chains. Longest chain 23 peptides. Score 0.579 Round 5: 493 peptides, 52 chains. Longest chain 23 peptides. Score 0.583 Taking the results from Round 5 Chains 56, Residues 441, Estimated correctness of the model 7.8 % 6 chains (54 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 10292 restraints for refining 5075 atoms. 8385 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2776 (Rfree = 0.000) for 5075 atoms. Found 32 (32 requested) and removed 31 (16 requested) atoms. Cycle 32: After refmac, R = 0.2692 (Rfree = 0.000) for 5040 atoms. Found 32 (32 requested) and removed 36 (16 requested) atoms. Cycle 33: After refmac, R = 0.2504 (Rfree = 0.000) for 5015 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. Cycle 34: After refmac, R = 0.2488 (Rfree = 0.000) for 4999 atoms. Found 32 (32 requested) and removed 30 (16 requested) atoms. Cycle 35: After refmac, R = 0.2364 (Rfree = 0.000) for 4988 atoms. Found 16 (32 requested) and removed 26 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.05 2.37 Search for helices and strands: 0 residues in 0 chains, 5143 seeds are put forward NCS extension: 22 residues added (6 deleted due to clashes), 5165 seeds are put forward Round 1: 462 peptides, 65 chains. Longest chain 20 peptides. Score 0.476 Round 2: 453 peptides, 55 chains. Longest chain 21 peptides. Score 0.521 Round 3: 493 peptides, 58 chains. Longest chain 24 peptides. Score 0.552 Round 4: 483 peptides, 56 chains. Longest chain 21 peptides. Score 0.551 Round 5: 471 peptides, 53 chains. Longest chain 20 peptides. Score 0.553 Taking the results from Round 5 Chains 55, Residues 418, Estimated correctness of the model 0.0 % 4 chains (40 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 10634 restraints for refining 5076 atoms. 8863 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2639 (Rfree = 0.000) for 5076 atoms. Found 32 (32 requested) and removed 26 (16 requested) atoms. Cycle 37: After refmac, R = 0.2642 (Rfree = 0.000) for 5041 atoms. Found 32 (32 requested) and removed 32 (16 requested) atoms. Cycle 38: After refmac, R = 0.2384 (Rfree = 0.000) for 5028 atoms. Found 26 (32 requested) and removed 33 (16 requested) atoms. Cycle 39: After refmac, R = 0.2462 (Rfree = 0.000) for 5012 atoms. Found 32 (32 requested) and removed 31 (16 requested) atoms. Cycle 40: After refmac, R = 0.2304 (Rfree = 0.000) for 5009 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.08 2.40 Search for helices and strands: 0 residues in 0 chains, 5225 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 5243 seeds are put forward Round 1: 436 peptides, 65 chains. Longest chain 18 peptides. Score 0.442 Round 2: 453 peptides, 53 chains. Longest chain 28 peptides. Score 0.532 Round 3: 448 peptides, 50 chains. Longest chain 24 peptides. Score 0.543 Round 4: 456 peptides, 52 chains. Longest chain 42 peptides. Score 0.541 Round 5: 470 peptides, 53 chains. Longest chain 31 peptides. Score 0.552 Taking the results from Round 5 Chains 57, Residues 417, Estimated correctness of the model 0.0 % 5 chains (69 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 10107 restraints for refining 5075 atoms. 8234 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2688 (Rfree = 0.000) for 5075 atoms. Found 32 (32 requested) and removed 43 (16 requested) atoms. Cycle 42: After refmac, R = 0.2563 (Rfree = 0.000) for 5035 atoms. Found 27 (32 requested) and removed 39 (16 requested) atoms. Cycle 43: After refmac, R = 0.2552 (Rfree = 0.000) for 5015 atoms. Found 32 (32 requested) and removed 34 (16 requested) atoms. Cycle 44: After refmac, R = 0.2566 (Rfree = 0.000) for 5001 atoms. Found 32 (32 requested) and removed 42 (16 requested) atoms. Cycle 45: After refmac, R = 0.2371 (Rfree = 0.000) for 4981 atoms. Found 20 (31 requested) and removed 33 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 2.41 Search for helices and strands: 0 residues in 0 chains, 5164 seeds are put forward NCS extension: 49 residues added (3 deleted due to clashes), 5213 seeds are put forward Round 1: 396 peptides, 59 chains. Longest chain 19 peptides. Score 0.424 Round 2: 443 peptides, 53 chains. Longest chain 30 peptides. Score 0.520 Round 3: 463 peptides, 54 chains. Longest chain 23 peptides. Score 0.539 Round 4: 462 peptides, 51 chains. Longest chain 31 peptides. Score 0.554 Round 5: 453 peptides, 46 chains. Longest chain 28 peptides. Score 0.570 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 46, Residues 407, Estimated correctness of the model 2.5 % 5 chains (65 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 2g0t-3_warpNtrace.pdb as input Building loops using Loopy2018 46 chains (407 residues) following loop building 5 chains (65 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14436 reflections ( 99.70 % complete ) and 10312 restraints for refining 5075 atoms. 8482 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2925 (Rfree = 0.000) for 5075 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2672 (Rfree = 0.000) for 5027 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2605 (Rfree = 0.000) for 4996 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2573 (Rfree = 0.000) for 4973 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 23:14:38 GMT 2018 Job finished. TimeTaking 226.71 Used memory is bytes: 9418064