Tue 25 Dec 19:27:55 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2g0t-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2g0t-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2g0t-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/2g0t-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2g0t-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 ============================================================ Tue 25 Dec 19:28:04 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2g0t-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 853 and 0 Target number of residues in the AU: 853 Target solvent content: 0.6060 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-3.8-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: 213 Cell parameters: 191.568 191.568 191.568 90.000 90.000 90.000 Input sequence file: 2g0t-3.8-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 3.800 Wilson plot Bfac: 55.01 12351 reflections ( 99.65 % complete ) and 0 restraints for refining 6225 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3252 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3363 (Rfree = 0.000) for 6225 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 2.57 Search for helices and strands: 0 residues in 0 chains, 6383 seeds are put forward NCS extension: 0 residues added, 6383 seeds are put forward Round 1: 380 peptides, 59 chains. Longest chain 27 peptides. Score 0.402 Round 2: 425 peptides, 54 chains. Longest chain 23 peptides. Score 0.492 Round 3: 450 peptides, 51 chains. Longest chain 26 peptides. Score 0.540 Round 4: 480 peptides, 57 chains. Longest chain 22 peptides. Score 0.542 Round 5: 467 peptides, 47 chains. Longest chain 38 peptides. Score 0.580 Taking the results from Round 5 Chains 50, Residues 420, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10888 restraints for refining 5063 atoms. 9193 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2674 (Rfree = 0.000) for 5063 atoms. Found 27 (27 requested) and removed 29 (13 requested) atoms. Cycle 2: After refmac, R = 0.2478 (Rfree = 0.000) for 5003 atoms. Found 26 (27 requested) and removed 42 (13 requested) atoms. Cycle 3: After refmac, R = 0.2420 (Rfree = 0.000) for 4966 atoms. Found 21 (27 requested) and removed 29 (13 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2359 (Rfree = 0.000) for 4941 atoms. Found 14 (27 requested) and removed 28 (13 requested) atoms. Cycle 5: After refmac, R = 0.2297 (Rfree = 0.000) for 4916 atoms. Found 15 (27 requested) and removed 26 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 2.55 Search for helices and strands: 0 residues in 0 chains, 5100 seeds are put forward NCS extension: 34 residues added (9 deleted due to clashes), 5134 seeds are put forward Round 1: 441 peptides, 61 chains. Longest chain 18 peptides. Score 0.472 Round 2: 461 peptides, 51 chains. Longest chain 25 peptides. Score 0.553 Round 3: 460 peptides, 49 chains. Longest chain 25 peptides. Score 0.562 Round 4: 470 peptides, 51 chains. Longest chain 24 peptides. Score 0.563 Round 5: 466 peptides, 54 chains. Longest chain 29 peptides. Score 0.542 Taking the results from Round 4 Chains 54, Residues 419, Estimated correctness of the model 0.0 % 7 chains (67 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12351 reflections ( 99.65 % complete ) and 10318 restraints for refining 5065 atoms. 8477 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2730 (Rfree = 0.000) for 5065 atoms. Found 27 (27 requested) and removed 26 (13 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2456 (Rfree = 0.000) for 5024 atoms. Found 18 (27 requested) and removed 26 (13 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2359 (Rfree = 0.000) for 4996 atoms. Found 20 (27 requested) and removed 32 (13 requested) atoms. Cycle 9: After refmac, R = 0.2293 (Rfree = 0.000) for 4974 atoms. Found 13 (27 requested) and removed 29 (13 requested) atoms. Cycle 10: After refmac, R = 0.2244 (Rfree = 0.000) for 4953 atoms. Found 11 (27 requested) and removed 28 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 2.54 Search for helices and strands: 0 residues in 0 chains, 5124 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 5150 seeds are put forward Round 1: 459 peptides, 61 chains. Longest chain 23 peptides. Score 0.495 Round 2: 468 peptides, 52 chains. Longest chain 26 peptides. Score 0.555 Round 3: 467 peptides, 54 chains. Longest chain 26 peptides. Score 0.543 Round 4: 473 peptides, 47 chains. Longest chain 42 peptides. Score 0.587 Round 5: 484 peptides, 47 chains. Longest chain 43 peptides. Score 0.599 Taking the results from Round 5 Chains 51, Residues 437, Estimated correctness of the model 0.0 % 7 chains (68 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 9967 restraints for refining 5066 atoms. 7990 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2885 (Rfree = 0.000) for 5066 atoms. Found 27 (27 requested) and removed 36 (13 requested) atoms. Cycle 12: After refmac, R = 0.2586 (Rfree = 0.000) for 5019 atoms. Found 18 (27 requested) and removed 34 (13 requested) atoms. Cycle 13: After refmac, R = 0.2515 (Rfree = 0.000) for 4978 atoms. Found 13 (27 requested) and removed 27 (13 requested) atoms. Cycle 14: After refmac, R = 0.2464 (Rfree = 0.000) for 4949 atoms. Found 10 (27 requested) and removed 24 (13 requested) atoms. Cycle 15: After refmac, R = 0.2477 (Rfree = 0.000) for 4927 atoms. Found 15 (27 requested) and removed 30 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.29 2.56 Search for helices and strands: 0 residues in 0 chains, 5117 seeds are put forward NCS extension: 22 residues added (8 deleted due to clashes), 5139 seeds are put forward Round 1: 440 peptides, 62 chains. Longest chain 20 peptides. Score 0.465 Round 2: 479 peptides, 52 chains. Longest chain 29 peptides. Score 0.568 Round 3: 479 peptides, 52 chains. Longest chain 29 peptides. Score 0.568 Round 4: 457 peptides, 46 chains. Longest chain 27 peptides. Score 0.575 Round 5: 463 peptides, 46 chains. Longest chain 28 peptides. Score 0.581 Taking the results from Round 5 Chains 47, Residues 417, Estimated correctness of the model 0.0 % 2 chains (41 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10513 restraints for refining 5065 atoms. 8718 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2970 (Rfree = 0.000) for 5065 atoms. Found 27 (27 requested) and removed 33 (13 requested) atoms. Cycle 17: After refmac, R = 0.2584 (Rfree = 0.000) for 5031 atoms. Found 22 (27 requested) and removed 31 (13 requested) atoms. Cycle 18: After refmac, R = 0.2509 (Rfree = 0.000) for 5000 atoms. Found 23 (27 requested) and removed 33 (13 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2482 (Rfree = 0.000) for 4978 atoms. Found 15 (27 requested) and removed 31 (13 requested) atoms. Cycle 20: After refmac, R = 0.2491 (Rfree = 0.000) for 4948 atoms. Found 27 (27 requested) and removed 32 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 2.52 Search for helices and strands: 0 residues in 0 chains, 5118 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 5147 seeds are put forward Round 1: 417 peptides, 61 chains. Longest chain 23 peptides. Score 0.441 Round 2: 443 peptides, 53 chains. Longest chain 23 peptides. Score 0.520 Round 3: 460 peptides, 55 chains. Longest chain 27 peptides. Score 0.530 Round 4: 450 peptides, 49 chains. Longest chain 32 peptides. Score 0.551 Round 5: 459 peptides, 57 chains. Longest chain 20 peptides. Score 0.517 Taking the results from Round 4 Chains 49, Residues 401, Estimated correctness of the model 0.0 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10866 restraints for refining 5066 atoms. 9246 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2813 (Rfree = 0.000) for 5066 atoms. Found 27 (27 requested) and removed 37 (13 requested) atoms. Cycle 22: After refmac, R = 0.2511 (Rfree = 0.000) for 5028 atoms. Found 12 (27 requested) and removed 29 (13 requested) atoms. Cycle 23: After refmac, R = 0.2459 (Rfree = 0.000) for 5000 atoms. Found 7 (27 requested) and removed 24 (13 requested) atoms. Cycle 24: After refmac, R = 0.2412 (Rfree = 0.000) for 4978 atoms. Found 9 (27 requested) and removed 23 (13 requested) atoms. Cycle 25: After refmac, R = 0.2364 (Rfree = 0.000) for 4959 atoms. Found 10 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 2.58 Search for helices and strands: 0 residues in 0 chains, 5144 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 5169 seeds are put forward Round 1: 397 peptides, 60 chains. Longest chain 15 peptides. Score 0.419 Round 2: 453 peptides, 56 chains. Longest chain 22 peptides. Score 0.516 Round 3: 447 peptides, 56 chains. Longest chain 24 peptides. Score 0.508 Round 4: 445 peptides, 49 chains. Longest chain 26 peptides. Score 0.545 Round 5: 441 peptides, 53 chains. Longest chain 20 peptides. Score 0.518 Taking the results from Round 4 Chains 55, Residues 396, Estimated correctness of the model 0.0 % 6 chains (72 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10350 restraints for refining 5066 atoms. 8518 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2734 (Rfree = 0.000) for 5066 atoms. Found 27 (27 requested) and removed 37 (13 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2540 (Rfree = 0.000) for 5035 atoms. Found 13 (27 requested) and removed 26 (13 requested) atoms. Cycle 28: After refmac, R = 0.2452 (Rfree = 0.000) for 5008 atoms. Found 10 (27 requested) and removed 25 (13 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2408 (Rfree = 0.000) for 4986 atoms. Found 9 (27 requested) and removed 22 (13 requested) atoms. Cycle 30: After refmac, R = 0.2372 (Rfree = 0.000) for 4962 atoms. Found 9 (27 requested) and removed 26 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 2.61 Search for helices and strands: 0 residues in 0 chains, 5148 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 5175 seeds are put forward Round 1: 411 peptides, 66 chains. Longest chain 15 peptides. Score 0.402 Round 2: 439 peptides, 54 chains. Longest chain 21 peptides. Score 0.510 Round 3: 441 peptides, 58 chains. Longest chain 19 peptides. Score 0.489 Round 4: 450 peptides, 53 chains. Longest chain 29 peptides. Score 0.529 Round 5: 451 peptides, 54 chains. Longest chain 22 peptides. Score 0.524 Taking the results from Round 4 Chains 56, Residues 397, Estimated correctness of the model 0.0 % 5 chains (48 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10613 restraints for refining 5066 atoms. 8910 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2769 (Rfree = 0.000) for 5066 atoms. Found 27 (27 requested) and removed 27 (13 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2594 (Rfree = 0.000) for 5029 atoms. Found 10 (27 requested) and removed 27 (13 requested) atoms. Cycle 33: After refmac, R = 0.2492 (Rfree = 0.000) for 5003 atoms. Found 15 (27 requested) and removed 29 (13 requested) atoms. Cycle 34: After refmac, R = 0.2449 (Rfree = 0.000) for 4978 atoms. Found 12 (27 requested) and removed 29 (13 requested) atoms. Cycle 35: After refmac, R = 0.2419 (Rfree = 0.000) for 4954 atoms. Found 9 (27 requested) and removed 28 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 2.58 Search for helices and strands: 0 residues in 0 chains, 5101 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5118 seeds are put forward Round 1: 414 peptides, 65 chains. Longest chain 17 peptides. Score 0.412 Round 2: 436 peptides, 59 chains. Longest chain 24 peptides. Score 0.477 Round 3: 439 peptides, 55 chains. Longest chain 20 peptides. Score 0.504 Round 4: 439 peptides, 52 chains. Longest chain 19 peptides. Score 0.521 Round 5: 445 peptides, 57 chains. Longest chain 22 peptides. Score 0.500 Taking the results from Round 4 Chains 55, Residues 387, Estimated correctness of the model 0.0 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10848 restraints for refining 5065 atoms. 9218 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2845 (Rfree = 0.000) for 5065 atoms. Found 27 (27 requested) and removed 30 (13 requested) atoms. Cycle 37: After refmac, R = 0.2682 (Rfree = 0.000) for 5036 atoms. Found 19 (27 requested) and removed 24 (13 requested) atoms. Cycle 38: After refmac, R = 0.2584 (Rfree = 0.000) for 5016 atoms. Found 16 (27 requested) and removed 25 (13 requested) atoms. Cycle 39: After refmac, R = 0.2522 (Rfree = 0.000) for 4998 atoms. Found 12 (27 requested) and removed 26 (13 requested) atoms. Cycle 40: After refmac, R = 0.2482 (Rfree = 0.000) for 4979 atoms. Found 9 (27 requested) and removed 23 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 2.59 Search for helices and strands: 0 residues in 0 chains, 5170 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 5184 seeds are put forward Round 1: 380 peptides, 60 chains. Longest chain 23 peptides. Score 0.396 Round 2: 418 peptides, 46 chains. Longest chain 24 peptides. Score 0.530 Round 3: 418 peptides, 50 chains. Longest chain 26 peptides. Score 0.507 Round 4: 413 peptides, 48 chains. Longest chain 27 peptides. Score 0.512 Round 5: 425 peptides, 48 chains. Longest chain 23 peptides. Score 0.527 Taking the results from Round 2 Chains 48, Residues 372, Estimated correctness of the model 0.0 % 5 chains (35 residues) have been docked in sequence ------------------------------------------------------ 12351 reflections ( 99.65 % complete ) and 10790 restraints for refining 5066 atoms. 9247 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2896 (Rfree = 0.000) for 5066 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. Cycle 42: After refmac, R = 0.2696 (Rfree = 0.000) for 5066 atoms. Found 21 (27 requested) and removed 21 (13 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2605 (Rfree = 0.000) for 5056 atoms. Found 9 (27 requested) and removed 15 (13 requested) atoms. Cycle 44: After refmac, R = 0.2557 (Rfree = 0.000) for 5041 atoms. Found 7 (27 requested) and removed 19 (13 requested) atoms. Cycle 45: After refmac, R = 0.2511 (Rfree = 0.000) for 5023 atoms. Found 7 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.34 2.60 Search for helices and strands: 0 residues in 0 chains, 5222 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 5234 seeds are put forward Round 1: 370 peptides, 57 chains. Longest chain 17 peptides. Score 0.401 Round 2: 408 peptides, 60 chains. Longest chain 16 peptides. Score 0.435 Round 3: 438 peptides, 53 chains. Longest chain 27 peptides. Score 0.514 Round 4: 404 peptides, 50 chains. Longest chain 25 peptides. Score 0.489 Round 5: 422 peptides, 49 chains. Longest chain 21 peptides. Score 0.518 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 53, Residues 373, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2g0t-3_warpNtrace.pdb as input Building loops using Loopy2018 53 chains (373 residues) following loop building 3 chains (27 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB ---> Final restrained refinement block. No atom update. 12351 reflections ( 99.65 % complete ) and 10909 restraints for refining 5066 atoms. 9373 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3248 (Rfree = 0.000) for 5066 atoms. Found 0 (27 requested) and removed 10 (13 requested) atoms. Cycle 47: After refmac, R = 0.2873 (Rfree = 0.000) for 5044 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2736 (Rfree = 0.000) for 5016 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2665 (Rfree = 0.000) for 4991 atoms. Found 0 (27 requested) and removed 7 (13 requested) atoms. Writing output files ... Failed to save intermediate PDBFailed to save intermediate PDB TimeTaking 191.6