Mon 24 Dec 00:02:58 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2hr2-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hr2-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hr2-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.8-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.8-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:03:03 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/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-3.8-parrot-mrncs/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-mrncs.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-mrncs.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 8486 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.3239 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3581 (Rfree = 0.000) for 8486 atoms. Found 46 (46 requested) and removed 47 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.74 3.09 Search for helices and strands: 0 residues in 0 chains, 8814 seeds are put forward NCS extension: 0 residues added, 8814 seeds are put forward Round 1: 419 peptides, 70 chains. Longest chain 12 peptides. Score 0.359 Round 2: 495 peptides, 63 chains. Longest chain 17 peptides. Score 0.482 Round 3: 498 peptides, 55 chains. Longest chain 22 peptides. Score 0.523 Round 4: 505 peptides, 53 chains. Longest chain 23 peptides. Score 0.539 Round 5: 504 peptides, 45 chains. Longest chain 41 peptides. Score 0.575 Taking the results from Round 5 Chains 51, Residues 459, Estimated correctness of the model 0.0 % 6 chains (69 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 14735 restraints for refining 6898 atoms. 12675 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2661 (Rfree = 0.000) for 6898 atoms. Found 37 (37 requested) and removed 54 (18 requested) atoms. Cycle 2: After refmac, R = 0.2457 (Rfree = 0.000) for 6751 atoms. Found 37 (37 requested) and removed 42 (18 requested) atoms. Cycle 3: After refmac, R = 0.2380 (Rfree = 0.000) for 6670 atoms. Found 37 (37 requested) and removed 52 (18 requested) atoms. Cycle 4: After refmac, R = 0.2316 (Rfree = 0.000) for 6592 atoms. Found 36 (36 requested) and removed 41 (18 requested) atoms. Cycle 5: After refmac, R = 0.2274 (Rfree = 0.000) for 6553 atoms. Found 36 (36 requested) and removed 35 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 2.98 Search for helices and strands: 0 residues in 0 chains, 6973 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 6999 seeds are put forward Round 1: 497 peptides, 68 chains. Longest chain 20 peptides. Score 0.459 Round 2: 545 peptides, 56 chains. Longest chain 33 peptides. Score 0.563 Round 3: 533 peptides, 56 chains. Longest chain 31 peptides. Score 0.552 Round 4: 526 peptides, 53 chains. Longest chain 38 peptides. Score 0.559 Round 5: 540 peptides, 57 chains. Longest chain 23 peptides. Score 0.554 Taking the results from Round 2 Chains 61, Residues 489, Estimated correctness of the model 0.0 % 5 chains (59 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 14282 restraints for refining 6778 atoms. 12194 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2516 (Rfree = 0.000) for 6778 atoms. Found 37 (37 requested) and removed 51 (18 requested) atoms. Cycle 7: After refmac, R = 0.2441 (Rfree = 0.000) for 6658 atoms. Found 37 (37 requested) and removed 42 (18 requested) atoms. Cycle 8: After refmac, R = 0.2255 (Rfree = 0.000) for 6591 atoms. Found 36 (36 requested) and removed 39 (18 requested) atoms. Cycle 9: After refmac, R = 0.2268 (Rfree = 0.000) for 6551 atoms. Found 36 (36 requested) and removed 39 (18 requested) atoms. Cycle 10: After refmac, R = 0.2187 (Rfree = 0.000) for 6514 atoms. Found 36 (36 requested) and removed 37 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.62 2.99 Search for helices and strands: 0 residues in 0 chains, 6933 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6952 seeds are put forward Round 1: 507 peptides, 72 chains. Longest chain 15 peptides. Score 0.450 Round 2: 562 peptides, 62 chains. Longest chain 26 peptides. Score 0.553 Round 3: 571 peptides, 60 chains. Longest chain 25 peptides. Score 0.570 Round 4: 554 peptides, 58 chains. Longest chain 24 peptides. Score 0.563 Round 5: 555 peptides, 57 chains. Longest chain 24 peptides. Score 0.568 Taking the results from Round 3 Chains 63, Residues 511, Estimated correctness of the model 0.0 % 5 chains (41 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 14364 restraints for refining 6899 atoms. 12234 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2433 (Rfree = 0.000) for 6899 atoms. Found 37 (37 requested) and removed 67 (18 requested) atoms. Cycle 12: After refmac, R = 0.2403 (Rfree = 0.000) for 6790 atoms. Found 37 (37 requested) and removed 65 (18 requested) atoms. Cycle 13: After refmac, R = 0.2278 (Rfree = 0.000) for 6714 atoms. Found 37 (37 requested) and removed 52 (18 requested) atoms. Cycle 14: After refmac, R = 0.2260 (Rfree = 0.000) for 6668 atoms. Found 36 (36 requested) and removed 55 (18 requested) atoms. Cycle 15: After refmac, R = 0.2211 (Rfree = 0.000) for 6630 atoms. Found 36 (36 requested) and removed 34 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.01 Search for helices and strands: 0 residues in 0 chains, 7101 seeds are put forward NCS extension: 14 residues added (5 deleted due to clashes), 7115 seeds are put forward Round 1: 497 peptides, 78 chains. Longest chain 20 peptides. Score 0.409 Round 2: 553 peptides, 68 chains. Longest chain 27 peptides. Score 0.517 Round 3: 552 peptides, 61 chains. Longest chain 23 peptides. Score 0.548 Round 4: 543 peptides, 62 chains. Longest chain 25 peptides. Score 0.535 Round 5: 550 peptides, 62 chains. Longest chain 24 peptides. Score 0.541 Taking the results from Round 3 Chains 65, Residues 491, Estimated correctness of the model 0.0 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 14557 restraints for refining 6901 atoms. 12543 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2485 (Rfree = 0.000) for 6901 atoms. Found 37 (37 requested) and removed 57 (18 requested) atoms. Cycle 17: After refmac, R = 0.2203 (Rfree = 0.000) for 6829 atoms. Found 37 (37 requested) and removed 41 (18 requested) atoms. Cycle 18: After refmac, R = 0.2224 (Rfree = 0.000) for 6795 atoms. Found 37 (37 requested) and removed 50 (18 requested) atoms. Cycle 19: After refmac, R = 0.2104 (Rfree = 0.000) for 6762 atoms. Found 37 (37 requested) and removed 32 (18 requested) atoms. Cycle 20: After refmac, R = 0.2106 (Rfree = 0.000) for 6744 atoms. Found 37 (37 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 3.02 Search for helices and strands: 0 residues in 0 chains, 7178 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 7193 seeds are put forward Round 1: 467 peptides, 73 chains. Longest chain 23 peptides. Score 0.400 Round 2: 534 peptides, 77 chains. Longest chain 17 peptides. Score 0.455 Round 3: 528 peptides, 62 chains. Longest chain 18 peptides. Score 0.520 Round 4: 538 peptides, 68 chains. Longest chain 24 peptides. Score 0.502 Round 5: 546 peptides, 68 chains. Longest chain 22 peptides. Score 0.510 Taking the results from Round 3 Chains 64, Residues 466, Estimated correctness of the model 0.0 % 6 chains (63 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 14716 restraints for refining 6902 atoms. 12682 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2318 (Rfree = 0.000) for 6902 atoms. Found 37 (37 requested) and removed 43 (18 requested) atoms. Cycle 22: After refmac, R = 0.2260 (Rfree = 0.000) for 6858 atoms. Found 37 (37 requested) and removed 43 (18 requested) atoms. Cycle 23: After refmac, R = 0.2229 (Rfree = 0.000) for 6832 atoms. Found 37 (37 requested) and removed 39 (18 requested) atoms. Cycle 24: After refmac, R = 0.2195 (Rfree = 0.000) for 6809 atoms. Found 37 (37 requested) and removed 36 (18 requested) atoms. Cycle 25: After refmac, R = 0.2190 (Rfree = 0.000) for 6797 atoms. Found 37 (37 requested) and removed 40 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 2.98 Search for helices and strands: 0 residues in 0 chains, 7184 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 7203 seeds are put forward Round 1: 484 peptides, 77 chains. Longest chain 15 peptides. Score 0.399 Round 2: 502 peptides, 65 chains. Longest chain 18 peptides. Score 0.479 Round 3: 497 peptides, 60 chains. Longest chain 21 peptides. Score 0.498 Round 4: 504 peptides, 62 chains. Longest chain 24 peptides. Score 0.496 Round 5: 511 peptides, 58 chains. Longest chain 22 peptides. Score 0.522 Taking the results from Round 5 Chains 61, Residues 453, Estimated correctness of the model 0.0 % 6 chains (54 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 15006 restraints for refining 6902 atoms. 13056 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2496 (Rfree = 0.000) for 6902 atoms. Found 37 (37 requested) and removed 49 (18 requested) atoms. Cycle 27: After refmac, R = 0.2318 (Rfree = 0.000) for 6847 atoms. Found 37 (37 requested) and removed 39 (18 requested) atoms. Cycle 28: After refmac, R = 0.2227 (Rfree = 0.000) for 6802 atoms. Found 37 (37 requested) and removed 31 (18 requested) atoms. Cycle 29: After refmac, R = 0.2166 (Rfree = 0.000) for 6772 atoms. Found 37 (37 requested) and removed 29 (18 requested) atoms. Cycle 30: After refmac, R = 0.1834 (Rfree = 0.000) for 6758 atoms. Found 16 (37 requested) and removed 27 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.61 2.98 Search for helices and strands: 0 residues in 0 chains, 7121 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 7143 seeds are put forward Round 1: 460 peptides, 81 chains. Longest chain 13 peptides. Score 0.350 Round 2: 503 peptides, 67 chains. Longest chain 22 peptides. Score 0.470 Round 3: 506 peptides, 67 chains. Longest chain 17 peptides. Score 0.474 Round 4: 545 peptides, 68 chains. Longest chain 21 peptides. Score 0.509 Round 5: 521 peptides, 69 chains. Longest chain 18 peptides. Score 0.480 Taking the results from Round 4 Chains 69, Residues 477, Estimated correctness of the model 0.0 % 7 chains (73 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 14488 restraints for refining 6901 atoms. 12365 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2378 (Rfree = 0.000) for 6901 atoms. Found 37 (37 requested) and removed 38 (18 requested) atoms. Cycle 32: After refmac, R = 0.2232 (Rfree = 0.000) for 6864 atoms. Found 37 (37 requested) and removed 34 (18 requested) atoms. Cycle 33: After refmac, R = 0.2098 (Rfree = 0.000) for 6838 atoms. Found 22 (37 requested) and removed 34 (18 requested) atoms. Cycle 34: After refmac, R = 0.2046 (Rfree = 0.000) for 6807 atoms. Found 24 (37 requested) and removed 22 (18 requested) atoms. Cycle 35: After refmac, R = 0.2032 (Rfree = 0.000) for 6795 atoms. Found 21 (37 requested) and removed 30 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.62 2.99 Search for helices and strands: 0 residues in 0 chains, 7174 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 7199 seeds are put forward Round 1: 465 peptides, 76 chains. Longest chain 16 peptides. Score 0.382 Round 2: 506 peptides, 71 chains. Longest chain 16 peptides. Score 0.454 Round 3: 508 peptides, 70 chains. Longest chain 17 peptides. Score 0.461 Round 4: 501 peptides, 68 chains. Longest chain 18 peptides. Score 0.463 Round 5: 520 peptides, 63 chains. Longest chain 22 peptides. Score 0.507 Taking the results from Round 5 Chains 68, Residues 457, Estimated correctness of the model 0.0 % 7 chains (65 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 14841 restraints for refining 6901 atoms. 12842 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2527 (Rfree = 0.000) for 6901 atoms. Found 37 (37 requested) and removed 42 (18 requested) atoms. Cycle 37: After refmac, R = 0.2269 (Rfree = 0.000) for 6841 atoms. Found 37 (37 requested) and removed 42 (18 requested) atoms. Cycle 38: After refmac, R = 0.2132 (Rfree = 0.000) for 6790 atoms. Found 31 (37 requested) and removed 30 (18 requested) atoms. Cycle 39: After refmac, R = 0.2046 (Rfree = 0.000) for 6769 atoms. Found 26 (37 requested) and removed 33 (18 requested) atoms. Cycle 40: After refmac, R = 0.1977 (Rfree = 0.000) for 6752 atoms. Found 20 (37 requested) and removed 32 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.00 Search for helices and strands: 0 residues in 0 chains, 7077 seeds are put forward NCS extension: 10 residues added (3 deleted due to clashes), 7087 seeds are put forward Round 1: 437 peptides, 78 chains. Longest chain 13 peptides. Score 0.338 Round 2: 499 peptides, 70 chains. Longest chain 16 peptides. Score 0.451 Round 3: 504 peptides, 69 chains. Longest chain 21 peptides. Score 0.462 Round 4: 509 peptides, 69 chains. Longest chain 21 peptides. Score 0.467 Round 5: 498 peptides, 64 chains. Longest chain 21 peptides. Score 0.480 Taking the results from Round 5 Chains 65, Residues 434, Estimated correctness of the model 0.0 % 7 chains (57 residues) have been docked in sequence ------------------------------------------------------ 14444 reflections ( 98.08 % complete ) and 15031 restraints for refining 6902 atoms. 13163 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2326 (Rfree = 0.000) for 6902 atoms. Found 37 (37 requested) and removed 34 (18 requested) atoms. Cycle 42: After refmac, R = 0.2174 (Rfree = 0.000) for 6868 atoms. Found 37 (37 requested) and removed 30 (18 requested) atoms. Cycle 43: After refmac, R = 0.2121 (Rfree = 0.000) for 6855 atoms. Found 34 (37 requested) and removed 33 (18 requested) atoms. Cycle 44: After refmac, R = 0.2094 (Rfree = 0.000) for 6830 atoms. Found 37 (37 requested) and removed 27 (18 requested) atoms. Cycle 45: After refmac, R = 0.2073 (Rfree = 0.000) for 6824 atoms. Found 37 (37 requested) and removed 27 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.63 3.00 Search for helices and strands: 0 residues in 0 chains, 7199 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 7219 seeds are put forward Round 1: 400 peptides, 72 chains. Longest chain 13 peptides. Score 0.324 Round 2: 462 peptides, 74 chains. Longest chain 15 peptides. Score 0.389 Round 3: 456 peptides, 67 chains. Longest chain 20 peptides. Score 0.419 Round 4: 476 peptides, 74 chains. Longest chain 19 peptides. Score 0.406 Round 5: 455 peptides, 63 chains. Longest chain 20 peptides. Score 0.438 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 63, Residues 392, Estimated correctness of the model 0.0 % 5 chains (27 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2hr2-3_warpNtrace.pdb as input Building loops using Loopy2018 63 chains (392 residues) following loop building 5 chains (27 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14444 reflections ( 98.08 % complete ) and 15680 restraints for refining 6902 atoms. 14089 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2369 (Rfree = 0.000) for 6902 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2279 (Rfree = 0.000) for 6833 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2293 (Rfree = 0.000) for 6796 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2192 (Rfree = 0.000) for 6753 atoms. TimeTaking 85.25