Tue 25 Dec 19:27:57 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 2hr2-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hr2-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hr2-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hr2-3.8-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/2hr2-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hr2-3.8-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 19:28:07 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/2hr2-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hr2-3.8-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 901 and 0 Target number of residues in the AU: 901 Target solvent content: 0.6596 Checking the provided sequence file Detected sequence length: 159 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 954 Adjusted target solvent content: 0.64 Input MTZ file: 2hr2-3.8-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: 19 Cell parameters: 89.090 91.280 176.170 90.000 90.000 90.000 Input sequence file: 2hr2-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 7632 target number of atoms Had to go as low as 0.80 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: 88.085 3.800 Wilson plot Bfac: 84.55 14444 reflections ( 98.08 % complete ) and 0 restraints for refining 8409 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3251 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3509 (Rfree = 0.000) for 8409 atoms. Found 46 (46 requested) and removed 33 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.76 3.10 Search for helices and strands: 0 residues in 0 chains, 8742 seeds are put forward NCS extension: 0 residues added, 8742 seeds are put forward Round 1: 408 peptides, 67 chains. Longest chain 14 peptides. Score 0.362 Round 2: 490 peptides, 58 chains. Longest chain 21 peptides. Score 0.501 Round 3: 502 peptides, 52 chains. Longest chain 23 peptides. Score 0.541 Round 4: 489 peptides, 55 chains. Longest chain 19 peptides. Score 0.514 Round 5: 502 peptides, 51 chains. Longest chain 20 peptides. Score 0.545 Taking the results from Round 5 Chains 58, Residues 451, Estimated correctness of the model 0.0 % 7 chains (67 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 15188 restraints for refining 6897 atoms. 13183 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2592 (Rfree = 0.000) for 6897 atoms. Found 37 (37 requested) and removed 58 (18 requested) atoms. Cycle 2: After refmac, R = 0.2402 (Rfree = 0.000) for 6711 atoms. Found 37 (37 requested) and removed 52 (18 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2253 (Rfree = 0.000) for 6625 atoms. Found 29 (36 requested) and removed 43 (18 requested) atoms. Cycle 4: After refmac, R = 0.2233 (Rfree = 0.000) for 6573 atoms. Found 36 (36 requested) and removed 34 (18 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2088 (Rfree = 0.000) for 6541 atoms. Found 29 (36 requested) and removed 38 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 3.04 Search for helices and strands: 0 residues in 0 chains, 6962 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 6981 seeds are put forward Round 1: 485 peptides, 63 chains. Longest chain 22 peptides. Score 0.471 Round 2: 524 peptides, 54 chains. Longest chain 30 peptides. Score 0.553 Round 3: 527 peptides, 57 chains. Longest chain 32 peptides. Score 0.542 Round 4: 536 peptides, 54 chains. Longest chain 28 peptides. Score 0.564 Round 5: 541 peptides, 56 chains. Longest chain 34 peptides. Score 0.560 Taking the results from Round 4 Chains 61, Residues 482, Estimated correctness of the model 0.0 % 9 chains (97 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 14444 reflections ( 98.08 % complete ) and 14389 restraints for refining 6902 atoms. 12195 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2500 (Rfree = 0.000) for 6902 atoms. Found 37 (37 requested) and removed 54 (18 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2374 (Rfree = 0.000) for 6775 atoms. Found 37 (37 requested) and removed 49 (18 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2274 (Rfree = 0.000) for 6697 atoms. Found 36 (37 requested) and removed 36 (18 requested) atoms. Cycle 9: After refmac, R = 0.2218 (Rfree = 0.000) for 6645 atoms. Found 36 (36 requested) and removed 30 (18 requested) atoms. Cycle 10: After refmac, R = 0.2187 (Rfree = 0.000) for 6604 atoms. Found 36 (36 requested) and removed 39 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 3.01 Search for helices and strands: 0 residues in 0 chains, 6975 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 6996 seeds are put forward Round 1: 492 peptides, 73 chains. Longest chain 16 peptides. Score 0.429 Round 2: 558 peptides, 65 chains. Longest chain 27 peptides. Score 0.536 Round 3: 527 peptides, 66 chains. Longest chain 18 peptides. Score 0.500 Round 4: 534 peptides, 66 chains. Longest chain 18 peptides. Score 0.507 Round 5: 540 peptides, 58 chains. Longest chain 25 peptides. Score 0.550 Taking the results from Round 5 Chains 60, Residues 482, Estimated correctness of the model 0.0 % 6 chains (89 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 14060 restraints for refining 6901 atoms. 11826 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2603 (Rfree = 0.000) for 6901 atoms. Found 37 (37 requested) and removed 62 (18 requested) atoms. Cycle 12: After refmac, R = 0.2374 (Rfree = 0.000) for 6802 atoms. Found 37 (37 requested) and removed 52 (18 requested) atoms. Cycle 13: After refmac, R = 0.2248 (Rfree = 0.000) for 6731 atoms. Found 35 (37 requested) and removed 31 (18 requested) atoms. Cycle 14: After refmac, R = 0.2155 (Rfree = 0.000) for 6681 atoms. Found 32 (37 requested) and removed 31 (18 requested) atoms. Cycle 15: After refmac, R = 0.2123 (Rfree = 0.000) for 6642 atoms. Found 30 (36 requested) and removed 38 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.01 Search for helices and strands: 0 residues in 0 chains, 7019 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 7041 seeds are put forward Round 1: 482 peptides, 77 chains. Longest chain 15 peptides. Score 0.397 Round 2: 521 peptides, 68 chains. Longest chain 18 peptides. Score 0.485 Round 3: 535 peptides, 68 chains. Longest chain 19 peptides. Score 0.499 Round 4: 527 peptides, 61 chains. Longest chain 27 peptides. Score 0.524 Round 5: 532 peptides, 62 chains. Longest chain 23 peptides. Score 0.524 Taking the results from Round 5 Chains 65, Residues 470, Estimated correctness of the model 0.0 % 7 chains (55 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 14741 restraints for refining 6902 atoms. 12742 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2634 (Rfree = 0.000) for 6902 atoms. Found 37 (37 requested) and removed 40 (18 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2480 (Rfree = 0.000) for 6813 atoms. Found 37 (37 requested) and removed 39 (18 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2338 (Rfree = 0.000) for 6766 atoms. Found 37 (37 requested) and removed 58 (18 requested) atoms. Cycle 19: After refmac, R = 0.2259 (Rfree = 0.000) for 6721 atoms. Found 37 (37 requested) and removed 32 (18 requested) atoms. Cycle 20: After refmac, R = 0.1951 (Rfree = 0.000) for 6695 atoms. Found 13 (36 requested) and removed 45 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 2.99 Search for helices and strands: 0 residues in 0 chains, 7042 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 7070 seeds are put forward Round 1: 485 peptides, 81 chains. Longest chain 14 peptides. Score 0.380 Round 2: 518 peptides, 70 chains. Longest chain 16 peptides. Score 0.472 Round 3: 519 peptides, 69 chains. Longest chain 17 peptides. Score 0.478 Round 4: 543 peptides, 65 chains. Longest chain 31 peptides. Score 0.521 Round 5: 550 peptides, 68 chains. Longest chain 25 peptides. Score 0.514 Taking the results from Round 4 Chains 67, Residues 478, Estimated correctness of the model 0.0 % 5 chains (39 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 14747 restraints for refining 6902 atoms. 12779 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2587 (Rfree = 0.000) for 6902 atoms. Found 37 (37 requested) and removed 39 (18 requested) atoms. Cycle 22: After refmac, R = 0.2469 (Rfree = 0.000) for 6837 atoms. Found 37 (37 requested) and removed 46 (18 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2400 (Rfree = 0.000) for 6776 atoms. Found 37 (37 requested) and removed 28 (18 requested) atoms. Cycle 24: After refmac, R = 0.2297 (Rfree = 0.000) for 6748 atoms. Found 37 (37 requested) and removed 29 (18 requested) atoms. Cycle 25: After refmac, R = 0.2269 (Rfree = 0.000) for 6731 atoms. Found 37 (37 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.62 2.99 Search for helices and strands: 0 residues in 0 chains, 7062 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 7085 seeds are put forward Round 1: 473 peptides, 81 chains. Longest chain 12 peptides. Score 0.366 Round 2: 503 peptides, 68 chains. Longest chain 19 peptides. Score 0.466 Round 3: 538 peptides, 68 chains. Longest chain 29 peptides. Score 0.502 Round 4: 522 peptides, 69 chains. Longest chain 17 peptides. Score 0.481 Round 5: 506 peptides, 66 chains. Longest chain 22 peptides. Score 0.478 Taking the results from Round 3 Chains 73, Residues 470, Estimated correctness of the model 0.0 % 5 chains (44 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 14755 restraints for refining 6902 atoms. 12804 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2457 (Rfree = 0.000) for 6902 atoms. Found 37 (37 requested) and removed 38 (18 requested) atoms. Cycle 27: After refmac, R = 0.2301 (Rfree = 0.000) for 6838 atoms. Found 37 (37 requested) and removed 31 (18 requested) atoms. Cycle 28: After refmac, R = 0.2233 (Rfree = 0.000) for 6802 atoms. Found 37 (37 requested) and removed 35 (18 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2189 (Rfree = 0.000) for 6775 atoms. Found 37 (37 requested) and removed 34 (18 requested) atoms. Cycle 30: After refmac, R = 0.1870 (Rfree = 0.000) for 6753 atoms. Found 10 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 3.00 Search for helices and strands: 0 residues in 0 chains, 7090 seeds are put forward NCS extension: 37 residues added (3 deleted due to clashes), 7127 seeds are put forward Round 1: 446 peptides, 78 chains. Longest chain 15 peptides. Score 0.349 Round 2: 514 peptides, 76 chains. Longest chain 13 peptides. Score 0.438 Round 3: 513 peptides, 73 chains. Longest chain 20 peptides. Score 0.452 Round 4: 522 peptides, 69 chains. Longest chain 17 peptides. Score 0.481 Round 5: 512 peptides, 73 chains. Longest chain 14 peptides. Score 0.451 Taking the results from Round 4 Chains 69, Residues 453, Estimated correctness of the model 0.0 % 5 chains (46 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 14752 restraints for refining 6898 atoms. 12824 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2448 (Rfree = 0.000) for 6898 atoms. Found 37 (37 requested) and removed 40 (18 requested) atoms. Cycle 32: After refmac, R = 0.2193 (Rfree = 0.000) for 6816 atoms. Found 37 (37 requested) and removed 34 (18 requested) atoms. Cycle 33: After refmac, R = 0.2107 (Rfree = 0.000) for 6775 atoms. Found 37 (37 requested) and removed 34 (18 requested) atoms. Cycle 34: After refmac, R = 0.2046 (Rfree = 0.000) for 6760 atoms. Found 36 (37 requested) and removed 32 (18 requested) atoms. Cycle 35: After refmac, R = 0.1963 (Rfree = 0.000) for 6750 atoms. Found 31 (37 requested) and removed 27 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 2.98 Search for helices and strands: 0 residues in 0 chains, 7075 seeds are put forward NCS extension: 13 residues added (5 deleted due to clashes), 7088 seeds are put forward Round 1: 434 peptides, 77 chains. Longest chain 12 peptides. Score 0.340 Round 2: 462 peptides, 72 chains. Longest chain 15 peptides. Score 0.400 Round 3: 488 peptides, 73 chains. Longest chain 14 peptides. Score 0.424 Round 4: 497 peptides, 74 chains. Longest chain 18 peptides. Score 0.429 Round 5: 471 peptides, 69 chains. Longest chain 15 peptides. Score 0.425 Taking the results from Round 4 Chains 77, Residues 423, Estimated correctness of the model 0.0 % 6 chains (54 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 14444 reflections ( 98.08 % complete ) and 15003 restraints for refining 6903 atoms. 13197 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2376 (Rfree = 0.000) for 6903 atoms. Found 37 (37 requested) and removed 47 (18 requested) atoms. Cycle 37: After refmac, R = 0.2137 (Rfree = 0.000) for 6825 atoms. Found 35 (37 requested) and removed 34 (18 requested) atoms. Cycle 38: After refmac, R = 0.2002 (Rfree = 0.000) for 6790 atoms. Found 37 (37 requested) and removed 27 (18 requested) atoms. Cycle 39: After refmac, R = 0.1914 (Rfree = 0.000) for 6785 atoms. Found 26 (37 requested) and removed 27 (18 requested) atoms. Cycle 40: After refmac, R = 0.1947 (Rfree = 0.000) for 6768 atoms. Found 37 (37 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.00 Search for helices and strands: 0 residues in 0 chains, 7126 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 7140 seeds are put forward Round 1: 449 peptides, 81 chains. Longest chain 15 peptides. Score 0.337 Round 2: 493 peptides, 80 chains. Longest chain 21 peptides. Score 0.395 Round 3: 499 peptides, 79 chains. Longest chain 13 peptides. Score 0.407 Round 4: 471 peptides, 75 chains. Longest chain 15 peptides. Score 0.395 Round 5: 489 peptides, 77 chains. Longest chain 16 peptides. Score 0.405 Taking the results from Round 3 Chains 80, Residues 420, Estimated correctness of the model 0.0 % 6 chains (39 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 15252 restraints for refining 6903 atoms. 13548 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2275 (Rfree = 0.000) for 6903 atoms. Found 37 (37 requested) and removed 33 (18 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2155 (Rfree = 0.000) for 6858 atoms. Found 37 (37 requested) and removed 35 (18 requested) atoms. Cycle 43: After refmac, R = 0.2186 (Rfree = 0.000) for 6839 atoms. Found 37 (37 requested) and removed 29 (18 requested) atoms. Cycle 44: After refmac, R = 0.2060 (Rfree = 0.000) for 6815 atoms. Found 37 (37 requested) and removed 32 (18 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.2107 (Rfree = 0.000) for 6804 atoms. Found 37 (37 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 3.01 Search for helices and strands: 0 residues in 0 chains, 7164 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 7178 seeds are put forward Round 1: 389 peptides, 75 chains. Longest chain 9 peptides. Score 0.293 Round 2: 452 peptides, 76 chains. Longest chain 17 peptides. Score 0.367 Round 3: 461 peptides, 70 chains. Longest chain 15 peptides. Score 0.409 Round 4: 455 peptides, 73 chains. Longest chain 13 peptides. Score 0.386 Round 5: 466 peptides, 74 chains. Longest chain 13 peptides. Score 0.394 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 70, Residues 391, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2hr2-3_warpNtrace.pdb as input Building loops using Loopy2018 70 chains (391 residues) following loop building 4 chains (21 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14444 reflections ( 98.08 % complete ) and 15335 restraints for refining 6901 atoms. 13779 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2320 (Rfree = 0.000) for 6901 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2219 (Rfree = 0.000) for 6845 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2165 (Rfree = 0.000) for 6794 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2186 (Rfree = 0.000) for 6748 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:07:21 GMT 2018 Job finished. Failed to save intermediate PDB TimeTaking 99.41