Sun 23 Dec 22:22:46 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 1vp4-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vp4-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vp4-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp4-3.2-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/1vp4-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp4-3.2-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 22:22:56 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/1vp4-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp4-3.2-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 716 and 0 Target number of residues in the AU: 716 Target solvent content: 0.6401 Checking the provided sequence file Detected sequence length: 425 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 850 Adjusted target solvent content: 0.57 Input MTZ file: 1vp4-3.2-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: 170 Cell parameters: 164.860 164.860 68.609 90.000 90.000 120.000 Input sequence file: 1vp4-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 6800 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: 142.773 3.200 Wilson plot Bfac: 72.01 17764 reflections ( 99.82 % complete ) and 0 restraints for refining 7515 atoms. Observations/parameters ratio is 0.59 ------------------------------------------------------ Starting model: R = 0.3506 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3299 (Rfree = 0.000) for 7515 atoms. Found 67 (67 requested) and removed 204 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 2.95 Search for helices and strands: 0 residues in 0 chains, 7559 seeds are put forward NCS extension: 0 residues added, 7559 seeds are put forward Round 1: 393 peptides, 79 chains. Longest chain 12 peptides. Score 0.301 Round 2: 501 peptides, 80 chains. Longest chain 16 peptides. Score 0.458 Round 3: 523 peptides, 82 chains. Longest chain 19 peptides. Score 0.476 Round 4: 500 peptides, 76 chains. Longest chain 20 peptides. Score 0.480 Round 5: 531 peptides, 78 chains. Longest chain 22 peptides. Score 0.510 Taking the results from Round 5 Chains 78, Residues 453, Estimated correctness of the model 14.5 % 6 chains (40 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13157 restraints for refining 6208 atoms. 11289 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2918 (Rfree = 0.000) for 6208 atoms. Found 45 (55 requested) and removed 84 (27 requested) atoms. Cycle 2: After refmac, R = 0.2756 (Rfree = 0.000) for 6111 atoms. Found 29 (55 requested) and removed 53 (27 requested) atoms. Cycle 3: After refmac, R = 0.3053 (Rfree = 0.000) for 6056 atoms. Found 54 (54 requested) and removed 42 (27 requested) atoms. Cycle 4: After refmac, R = 0.2683 (Rfree = 0.000) for 6048 atoms. Found 15 (54 requested) and removed 37 (27 requested) atoms. Cycle 5: After refmac, R = 0.2621 (Rfree = 0.000) for 6023 atoms. Found 6 (54 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.29 3.00 Search for helices and strands: 0 residues in 0 chains, 6241 seeds are put forward NCS extension: 11 residues added (4 deleted due to clashes), 6252 seeds are put forward Round 1: 461 peptides, 79 chains. Longest chain 14 peptides. Score 0.407 Round 2: 502 peptides, 69 chains. Longest chain 18 peptides. Score 0.524 Round 3: 516 peptides, 65 chains. Longest chain 20 peptides. Score 0.563 Round 4: 518 peptides, 70 chains. Longest chain 19 peptides. Score 0.538 Round 5: 538 peptides, 71 chains. Longest chain 22 peptides. Score 0.557 Taking the results from Round 3 Chains 66, Residues 451, Estimated correctness of the model 30.7 % 5 chains (36 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13427 restraints for refining 6208 atoms. 11567 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2791 (Rfree = 0.000) for 6208 atoms. Found 55 (55 requested) and removed 42 (27 requested) atoms. Cycle 7: After refmac, R = 0.2702 (Rfree = 0.000) for 6198 atoms. Found 31 (55 requested) and removed 33 (27 requested) atoms. Cycle 8: After refmac, R = 0.2718 (Rfree = 0.000) for 6190 atoms. Found 25 (55 requested) and removed 33 (27 requested) atoms. Cycle 9: After refmac, R = 0.2635 (Rfree = 0.000) for 6163 atoms. Found 20 (55 requested) and removed 35 (27 requested) atoms. Cycle 10: After refmac, R = 0.2852 (Rfree = 0.000) for 6141 atoms. Found 55 (55 requested) and removed 41 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 2.96 Search for helices and strands: 0 residues in 0 chains, 6423 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 6445 seeds are put forward Round 1: 459 peptides, 76 chains. Longest chain 15 peptides. Score 0.423 Round 2: 519 peptides, 72 chains. Longest chain 21 peptides. Score 0.528 Round 3: 506 peptides, 69 chains. Longest chain 24 peptides. Score 0.529 Round 4: 506 peptides, 70 chains. Longest chain 17 peptides. Score 0.523 Round 5: 502 peptides, 67 chains. Longest chain 19 peptides. Score 0.535 Taking the results from Round 5 Chains 69, Residues 435, Estimated correctness of the model 22.4 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13812 restraints for refining 6208 atoms. 12112 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2754 (Rfree = 0.000) for 6208 atoms. Found 45 (55 requested) and removed 35 (27 requested) atoms. Cycle 12: After refmac, R = 0.2968 (Rfree = 0.000) for 6193 atoms. Found 55 (55 requested) and removed 41 (27 requested) atoms. Cycle 13: After refmac, R = 0.2694 (Rfree = 0.000) for 6189 atoms. Found 36 (55 requested) and removed 34 (27 requested) atoms. Cycle 14: After refmac, R = 0.2573 (Rfree = 0.000) for 6177 atoms. Found 18 (55 requested) and removed 35 (27 requested) atoms. Cycle 15: After refmac, R = 0.2586 (Rfree = 0.000) for 6151 atoms. Found 20 (55 requested) and removed 36 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 6379 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 6405 seeds are put forward Round 1: 440 peptides, 74 chains. Longest chain 14 peptides. Score 0.408 Round 2: 497 peptides, 77 chains. Longest chain 24 peptides. Score 0.470 Round 3: 496 peptides, 68 chains. Longest chain 26 peptides. Score 0.522 Round 4: 476 peptides, 66 chains. Longest chain 16 peptides. Score 0.507 Round 5: 511 peptides, 65 chains. Longest chain 38 peptides. Score 0.557 Taking the results from Round 5 Chains 66, Residues 446, Estimated correctness of the model 28.9 % 3 chains (52 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13122 restraints for refining 6208 atoms. 11198 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2708 (Rfree = 0.000) for 6208 atoms. Found 55 (55 requested) and removed 45 (27 requested) atoms. Cycle 17: After refmac, R = 0.2553 (Rfree = 0.000) for 6189 atoms. Found 26 (55 requested) and removed 31 (27 requested) atoms. Cycle 18: After refmac, R = 0.2517 (Rfree = 0.000) for 6171 atoms. Found 18 (55 requested) and removed 39 (27 requested) atoms. Cycle 19: After refmac, R = 0.2474 (Rfree = 0.000) for 6139 atoms. Found 14 (55 requested) and removed 27 (27 requested) atoms. Cycle 20: After refmac, R = 0.2449 (Rfree = 0.000) for 6119 atoms. Found 11 (54 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 6317 seeds are put forward NCS extension: 50 residues added (2 deleted due to clashes), 6367 seeds are put forward Round 1: 421 peptides, 72 chains. Longest chain 18 peptides. Score 0.392 Round 2: 469 peptides, 67 chains. Longest chain 19 peptides. Score 0.492 Round 3: 455 peptides, 63 chains. Longest chain 20 peptides. Score 0.497 Round 4: 460 peptides, 66 chains. Longest chain 19 peptides. Score 0.486 Round 5: 480 peptides, 68 chains. Longest chain 20 peptides. Score 0.501 Taking the results from Round 5 Chains 68, Residues 412, Estimated correctness of the model 11.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13938 restraints for refining 6207 atoms. 12358 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2644 (Rfree = 0.000) for 6207 atoms. Found 53 (55 requested) and removed 37 (27 requested) atoms. Cycle 22: After refmac, R = 0.2532 (Rfree = 0.000) for 6206 atoms. Found 33 (55 requested) and removed 32 (27 requested) atoms. Cycle 23: After refmac, R = 0.2483 (Rfree = 0.000) for 6192 atoms. Found 27 (55 requested) and removed 40 (27 requested) atoms. Cycle 24: After refmac, R = 0.2467 (Rfree = 0.000) for 6164 atoms. Found 28 (55 requested) and removed 28 (27 requested) atoms. Cycle 25: After refmac, R = 0.2439 (Rfree = 0.000) for 6153 atoms. Found 22 (55 requested) and removed 35 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.26 2.97 Search for helices and strands: 0 residues in 0 chains, 6346 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 6384 seeds are put forward Round 1: 405 peptides, 71 chains. Longest chain 12 peptides. Score 0.375 Round 2: 440 peptides, 65 chains. Longest chain 17 peptides. Score 0.465 Round 3: 459 peptides, 63 chains. Longest chain 20 peptides. Score 0.503 Round 4: 442 peptides, 65 chains. Longest chain 18 peptides. Score 0.468 Round 5: 453 peptides, 62 chains. Longest chain 20 peptides. Score 0.501 Taking the results from Round 3 Chains 63, Residues 396, Estimated correctness of the model 12.3 % 6 chains (38 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13723 restraints for refining 6208 atoms. 12100 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2642 (Rfree = 0.000) for 6208 atoms. Found 55 (55 requested) and removed 33 (27 requested) atoms. Cycle 27: After refmac, R = 0.2549 (Rfree = 0.000) for 6221 atoms. Found 34 (55 requested) and removed 33 (27 requested) atoms. Cycle 28: After refmac, R = 0.2496 (Rfree = 0.000) for 6207 atoms. Found 27 (55 requested) and removed 28 (27 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2465 (Rfree = 0.000) for 6197 atoms. Found 16 (55 requested) and removed 29 (27 requested) atoms. Cycle 30: After refmac, R = 0.2466 (Rfree = 0.000) for 6176 atoms. Found 23 (55 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.01 Search for helices and strands: 0 residues in 0 chains, 6412 seeds are put forward NCS extension: 23 residues added (5 deleted due to clashes), 6435 seeds are put forward Round 1: 381 peptides, 67 chains. Longest chain 12 peptides. Score 0.364 Round 2: 430 peptides, 65 chains. Longest chain 15 peptides. Score 0.451 Round 3: 434 peptides, 63 chains. Longest chain 16 peptides. Score 0.469 Round 4: 441 peptides, 60 chains. Longest chain 19 peptides. Score 0.497 Round 5: 444 peptides, 57 chains. Longest chain 19 peptides. Score 0.519 Taking the results from Round 5 Chains 58, Residues 387, Estimated correctness of the model 17.4 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13747 restraints for refining 6208 atoms. 12163 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2565 (Rfree = 0.000) for 6208 atoms. Found 53 (55 requested) and removed 34 (27 requested) atoms. Cycle 32: After refmac, R = 0.2475 (Rfree = 0.000) for 6220 atoms. Found 17 (55 requested) and removed 34 (27 requested) atoms. Cycle 33: After refmac, R = 0.2417 (Rfree = 0.000) for 6199 atoms. Found 18 (55 requested) and removed 27 (27 requested) atoms. Cycle 34: After refmac, R = 0.2421 (Rfree = 0.000) for 6186 atoms. Found 22 (55 requested) and removed 28 (27 requested) atoms. Cycle 35: After refmac, R = 0.2327 (Rfree = 0.000) for 6171 atoms. Found 19 (55 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 6369 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 6384 seeds are put forward Round 1: 400 peptides, 72 chains. Longest chain 16 peptides. Score 0.360 Round 2: 428 peptides, 64 chains. Longest chain 20 peptides. Score 0.454 Round 3: 447 peptides, 67 chains. Longest chain 18 peptides. Score 0.462 Round 4: 438 peptides, 63 chains. Longest chain 21 peptides. Score 0.474 Round 5: 431 peptides, 65 chains. Longest chain 17 peptides. Score 0.452 Taking the results from Round 4 Chains 66, Residues 375, Estimated correctness of the model 2.7 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 13837 restraints for refining 6208 atoms. 12305 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2517 (Rfree = 0.000) for 6208 atoms. Found 52 (55 requested) and removed 45 (27 requested) atoms. Cycle 37: After refmac, R = 0.2465 (Rfree = 0.000) for 6190 atoms. Found 24 (55 requested) and removed 30 (27 requested) atoms. Cycle 38: After refmac, R = 0.2417 (Rfree = 0.000) for 6172 atoms. Found 30 (55 requested) and removed 28 (27 requested) atoms. Cycle 39: After refmac, R = 0.2397 (Rfree = 0.000) for 6166 atoms. Found 25 (55 requested) and removed 27 (27 requested) atoms. Cycle 40: After refmac, R = 0.2362 (Rfree = 0.000) for 6155 atoms. Found 23 (55 requested) and removed 29 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 6366 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6384 seeds are put forward Round 1: 364 peptides, 69 chains. Longest chain 11 peptides. Score 0.323 Round 2: 407 peptides, 65 chains. Longest chain 17 peptides. Score 0.417 Round 3: 396 peptides, 62 chains. Longest chain 23 peptides. Score 0.421 Round 4: 401 peptides, 62 chains. Longest chain 17 peptides. Score 0.428 Round 5: 397 peptides, 60 chains. Longest chain 14 peptides. Score 0.435 Taking the results from Round 5 Chains 61, Residues 337, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 17764 reflections ( 99.82 % complete ) and 14223 restraints for refining 6205 atoms. 12851 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2523 (Rfree = 0.000) for 6205 atoms. Found 55 (55 requested) and removed 33 (27 requested) atoms. Cycle 42: After refmac, R = 0.2424 (Rfree = 0.000) for 6219 atoms. Found 18 (55 requested) and removed 28 (27 requested) atoms. Cycle 43: After refmac, R = 0.2645 (Rfree = 0.000) for 6206 atoms. Found 53 (55 requested) and removed 28 (27 requested) atoms. Cycle 44: After refmac, R = 0.2350 (Rfree = 0.000) for 6220 atoms. Found 23 (55 requested) and removed 28 (27 requested) atoms. Cycle 45: After refmac, R = 0.2591 (Rfree = 0.000) for 6192 atoms. Found 55 (55 requested) and removed 29 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 2.95 Search for helices and strands: 0 residues in 0 chains, 6465 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 6482 seeds are put forward Round 1: 309 peptides, 62 chains. Longest chain 11 peptides. Score 0.280 Round 2: 359 peptides, 60 chains. Longest chain 17 peptides. Score 0.377 Round 3: 383 peptides, 64 chains. Longest chain 13 peptides. Score 0.388 Round 4: 422 peptides, 71 chains. Longest chain 12 peptides. Score 0.400 Round 5: 417 peptides, 70 chains. Longest chain 12 peptides. Score 0.400 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 70, Residues 347, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vp4-3_warpNtrace.pdb as input Building loops using Loopy2018 70 chains (347 residues) following loop building 3 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17764 reflections ( 99.82 % complete ) and 14016 restraints for refining 6208 atoms. 12668 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2448 (Rfree = 0.000) for 6208 atoms. Found 0 (55 requested) and removed 20 (27 requested) atoms. Cycle 47: After refmac, R = 0.2473 (Rfree = 0.000) for 6171 atoms. Found 0 (55 requested) and removed 7 (27 requested) atoms. Cycle 48: After refmac, R = 0.2468 (Rfree = 0.000) for 6160 atoms. Found 0 (55 requested) and removed 8 (27 requested) atoms. Cycle 49: After refmac, R = 0.2842 (Rfree = 0.000) for 6148 atoms. TimeTaking 89.22