Sun 23 Dec 22:23:10 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 1vme-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vme-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vme-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-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/1vme-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-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 ============================================================ Sun 23 Dec 22:23:19 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/1vme-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-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 607 and 0 Target number of residues in the AU: 607 Target solvent content: 0.6542 Checking the provided sequence file Detected sequence length: 410 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 820 Adjusted target solvent content: 0.53 Input MTZ file: 1vme-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: 4 Cell parameters: 55.242 95.831 90.130 90.000 95.426 90.000 Input sequence file: 1vme-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 6560 target number of atoms Had to go as low as 0.70 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: 48.998 3.600 Wilson plot Bfac: 80.80 10948 reflections ( 99.82 % complete ) and 0 restraints for refining 7237 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3208 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3091 (Rfree = 0.000) for 7237 atoms. Found 46 (46 requested) and removed 61 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.41 Search for helices and strands: 0 residues in 0 chains, 7389 seeds are put forward NCS extension: 0 residues added, 7389 seeds are put forward Round 1: 394 peptides, 70 chains. Longest chain 13 peptides. Score 0.383 Round 2: 490 peptides, 73 chains. Longest chain 16 peptides. Score 0.514 Round 3: 499 peptides, 67 chains. Longest chain 21 peptides. Score 0.564 Round 4: 531 peptides, 65 chains. Longest chain 22 peptides. Score 0.616 Round 5: 518 peptides, 65 chains. Longest chain 20 peptides. Score 0.600 Taking the results from Round 4 Chains 65, Residues 466, Estimated correctness of the model 20.8 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 12928 restraints for refining 5944 atoms. 11053 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2554 (Rfree = 0.000) for 5944 atoms. Found 26 (38 requested) and removed 41 (19 requested) atoms. Cycle 2: After refmac, R = 0.2575 (Rfree = 0.000) for 5848 atoms. Found 35 (38 requested) and removed 39 (19 requested) atoms. Cycle 3: After refmac, R = 0.2451 (Rfree = 0.000) for 5792 atoms. Found 26 (37 requested) and removed 49 (18 requested) atoms. Cycle 4: After refmac, R = 0.2454 (Rfree = 0.000) for 5735 atoms. Found 29 (37 requested) and removed 33 (18 requested) atoms. Cycle 5: After refmac, R = 0.2436 (Rfree = 0.000) for 5717 atoms. Found 36 (36 requested) and removed 34 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 5935 seeds are put forward NCS extension: 13 residues added (4 deleted due to clashes), 5948 seeds are put forward Round 1: 460 peptides, 76 chains. Longest chain 15 peptides. Score 0.449 Round 2: 483 peptides, 64 chains. Longest chain 20 peptides. Score 0.560 Round 3: 503 peptides, 63 chains. Longest chain 24 peptides. Score 0.592 Round 4: 502 peptides, 61 chains. Longest chain 21 peptides. Score 0.603 Round 5: 509 peptides, 64 chains. Longest chain 24 peptides. Score 0.594 Taking the results from Round 4 Chains 65, Residues 441, Estimated correctness of the model 15.8 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 12968 restraints for refining 5947 atoms. 11164 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2553 (Rfree = 0.000) for 5947 atoms. Found 34 (38 requested) and removed 64 (19 requested) atoms. Cycle 7: After refmac, R = 0.2454 (Rfree = 0.000) for 5880 atoms. Found 37 (37 requested) and removed 44 (18 requested) atoms. Cycle 8: After refmac, R = 0.2433 (Rfree = 0.000) for 5848 atoms. Found 37 (37 requested) and removed 47 (18 requested) atoms. Cycle 9: After refmac, R = 0.2359 (Rfree = 0.000) for 5823 atoms. Found 31 (37 requested) and removed 31 (18 requested) atoms. Cycle 10: After refmac, R = 0.2394 (Rfree = 0.000) for 5815 atoms. Found 37 (37 requested) and removed 38 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 5999 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 6015 seeds are put forward Round 1: 417 peptides, 74 chains. Longest chain 13 peptides. Score 0.393 Round 2: 468 peptides, 68 chains. Longest chain 16 peptides. Score 0.514 Round 3: 473 peptides, 66 chains. Longest chain 16 peptides. Score 0.534 Round 4: 507 peptides, 63 chains. Longest chain 26 peptides. Score 0.597 Round 5: 517 peptides, 61 chains. Longest chain 24 peptides. Score 0.621 Taking the results from Round 5 Chains 64, Residues 456, Estimated correctness of the model 22.7 % 6 chains (49 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 12485 restraints for refining 5945 atoms. 10562 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2526 (Rfree = 0.000) for 5945 atoms. Found 31 (38 requested) and removed 51 (19 requested) atoms. Cycle 12: After refmac, R = 0.2436 (Rfree = 0.000) for 5891 atoms. Found 33 (38 requested) and removed 47 (19 requested) atoms. Cycle 13: After refmac, R = 0.2301 (Rfree = 0.000) for 5861 atoms. Found 19 (37 requested) and removed 37 (18 requested) atoms. Cycle 14: After refmac, R = 0.2326 (Rfree = 0.000) for 5830 atoms. Found 25 (37 requested) and removed 32 (18 requested) atoms. Cycle 15: After refmac, R = 0.2233 (Rfree = 0.000) for 5814 atoms. Found 27 (37 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 3.47 Search for helices and strands: 0 residues in 0 chains, 6014 seeds are put forward NCS extension: 39 residues added (1 deleted due to clashes), 6053 seeds are put forward Round 1: 419 peptides, 73 chains. Longest chain 15 peptides. Score 0.404 Round 2: 443 peptides, 60 chains. Longest chain 17 peptides. Score 0.529 Round 3: 453 peptides, 67 chains. Longest chain 25 peptides. Score 0.499 Round 4: 448 peptides, 58 chains. Longest chain 25 peptides. Score 0.549 Round 5: 473 peptides, 62 chains. Longest chain 22 peptides. Score 0.559 Taking the results from Round 5 Chains 64, Residues 411, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 13346 restraints for refining 5947 atoms. 11702 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2599 (Rfree = 0.000) for 5947 atoms. Found 38 (38 requested) and removed 48 (19 requested) atoms. Cycle 17: After refmac, R = 0.2488 (Rfree = 0.000) for 5908 atoms. Found 38 (38 requested) and removed 37 (19 requested) atoms. Cycle 18: After refmac, R = 0.2411 (Rfree = 0.000) for 5884 atoms. Found 37 (37 requested) and removed 33 (18 requested) atoms. Cycle 19: After refmac, R = 0.2406 (Rfree = 0.000) for 5870 atoms. Found 37 (37 requested) and removed 33 (18 requested) atoms. Cycle 20: After refmac, R = 0.2157 (Rfree = 0.000) for 5868 atoms. Found 12 (37 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 3.43 Search for helices and strands: 0 residues in 0 chains, 6013 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 6031 seeds are put forward Round 1: 404 peptides, 73 chains. Longest chain 15 peptides. Score 0.378 Round 2: 449 peptides, 65 chains. Longest chain 18 peptides. Score 0.506 Round 3: 446 peptides, 63 chains. Longest chain 16 peptides. Score 0.514 Round 4: 469 peptides, 63 chains. Longest chain 18 peptides. Score 0.547 Round 5: 455 peptides, 62 chains. Longest chain 17 peptides. Score 0.534 Taking the results from Round 4 Chains 63, Residues 406, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 13247 restraints for refining 5947 atoms. 11609 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2692 (Rfree = 0.000) for 5947 atoms. Found 38 (38 requested) and removed 35 (19 requested) atoms. Cycle 22: After refmac, R = 0.2653 (Rfree = 0.000) for 5921 atoms. Found 38 (38 requested) and removed 38 (19 requested) atoms. Cycle 23: After refmac, R = 0.2583 (Rfree = 0.000) for 5899 atoms. Found 37 (37 requested) and removed 37 (18 requested) atoms. Cycle 24: After refmac, R = 0.2470 (Rfree = 0.000) for 5884 atoms. Found 37 (37 requested) and removed 34 (18 requested) atoms. Cycle 25: After refmac, R = 0.2424 (Rfree = 0.000) for 5870 atoms. Found 37 (37 requested) and removed 28 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.62 3.48 Search for helices and strands: 0 residues in 0 chains, 6087 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 6106 seeds are put forward Round 1: 371 peptides, 68 chains. Longest chain 16 peptides. Score 0.358 Round 2: 426 peptides, 69 chains. Longest chain 17 peptides. Score 0.443 Round 3: 447 peptides, 66 chains. Longest chain 15 peptides. Score 0.496 Round 4: 465 peptides, 73 chains. Longest chain 14 peptides. Score 0.477 Round 5: 458 peptides, 65 chains. Longest chain 16 peptides. Score 0.519 Taking the results from Round 5 Chains 65, Residues 393, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 13660 restraints for refining 5945 atoms. 12153 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2566 (Rfree = 0.000) for 5945 atoms. Found 38 (38 requested) and removed 27 (19 requested) atoms. Cycle 27: After refmac, R = 0.2587 (Rfree = 0.000) for 5907 atoms. Found 38 (38 requested) and removed 39 (19 requested) atoms. Cycle 28: After refmac, R = 0.2522 (Rfree = 0.000) for 5877 atoms. Found 37 (37 requested) and removed 34 (18 requested) atoms. Cycle 29: After refmac, R = 0.2481 (Rfree = 0.000) for 5855 atoms. Found 37 (37 requested) and removed 25 (18 requested) atoms. Cycle 30: After refmac, R = 0.2475 (Rfree = 0.000) for 5845 atoms. Found 37 (37 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.60 3.46 Search for helices and strands: 0 residues in 0 chains, 6032 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 6055 seeds are put forward Round 1: 379 peptides, 72 chains. Longest chain 12 peptides. Score 0.342 Round 2: 415 peptides, 69 chains. Longest chain 16 peptides. Score 0.425 Round 3: 412 peptides, 63 chains. Longest chain 15 peptides. Score 0.463 Round 4: 426 peptides, 63 chains. Longest chain 15 peptides. Score 0.484 Round 5: 414 peptides, 62 chains. Longest chain 17 peptides. Score 0.473 Taking the results from Round 4 Chains 64, Residues 363, Estimated correctness of the model 0.0 % 6 chains (35 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 13389 restraints for refining 5947 atoms. 11920 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2618 (Rfree = 0.000) for 5947 atoms. Found 38 (38 requested) and removed 53 (19 requested) atoms. Cycle 32: After refmac, R = 0.2486 (Rfree = 0.000) for 5895 atoms. Found 33 (38 requested) and removed 35 (19 requested) atoms. Cycle 33: After refmac, R = 0.2481 (Rfree = 0.000) for 5878 atoms. Found 37 (37 requested) and removed 32 (18 requested) atoms. Cycle 34: After refmac, R = 0.2449 (Rfree = 0.000) for 5867 atoms. Found 37 (37 requested) and removed 29 (18 requested) atoms. Cycle 35: After refmac, R = 0.2385 (Rfree = 0.000) for 5868 atoms. Found 37 (37 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 3.41 Search for helices and strands: 0 residues in 0 chains, 6044 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 6060 seeds are put forward Round 1: 322 peptides, 64 chains. Longest chain 13 peptides. Score 0.300 Round 2: 363 peptides, 65 chains. Longest chain 13 peptides. Score 0.367 Round 3: 383 peptides, 66 chains. Longest chain 15 peptides. Score 0.394 Round 4: 384 peptides, 61 chains. Longest chain 15 peptides. Score 0.432 Round 5: 381 peptides, 64 chains. Longest chain 13 peptides. Score 0.405 Taking the results from Round 4 Chains 61, Residues 323, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 13716 restraints for refining 5946 atoms. 12461 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2485 (Rfree = 0.000) for 5946 atoms. Found 28 (38 requested) and removed 33 (19 requested) atoms. Cycle 37: After refmac, R = 0.2416 (Rfree = 0.000) for 5913 atoms. Found 38 (38 requested) and removed 27 (19 requested) atoms. Cycle 38: After refmac, R = 0.2385 (Rfree = 0.000) for 5909 atoms. Found 38 (38 requested) and removed 25 (19 requested) atoms. Cycle 39: After refmac, R = 0.2321 (Rfree = 0.000) for 5912 atoms. Found 37 (37 requested) and removed 23 (18 requested) atoms. Cycle 40: After refmac, R = 0.2322 (Rfree = 0.000) for 5914 atoms. Found 32 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 3.47 Search for helices and strands: 0 residues in 0 chains, 6082 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6095 seeds are put forward Round 1: 313 peptides, 62 chains. Longest chain 12 peptides. Score 0.299 Round 2: 356 peptides, 57 chains. Longest chain 13 peptides. Score 0.414 Round 3: 374 peptides, 63 chains. Longest chain 14 peptides. Score 0.401 Round 4: 379 peptides, 62 chains. Longest chain 13 peptides. Score 0.416 Round 5: 387 peptides, 61 chains. Longest chain 12 peptides. Score 0.437 Taking the results from Round 5 Chains 61, Residues 326, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 13742 restraints for refining 5947 atoms. 12427 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2471 (Rfree = 0.000) for 5947 atoms. Found 38 (38 requested) and removed 36 (19 requested) atoms. Cycle 42: After refmac, R = 0.2427 (Rfree = 0.000) for 5920 atoms. Found 28 (38 requested) and removed 33 (19 requested) atoms. Cycle 43: After refmac, R = 0.2365 (Rfree = 0.000) for 5902 atoms. Found 37 (37 requested) and removed 22 (18 requested) atoms. Cycle 44: After refmac, R = 0.2347 (Rfree = 0.000) for 5901 atoms. Found 30 (37 requested) and removed 25 (18 requested) atoms. Cycle 45: After refmac, R = 0.2303 (Rfree = 0.000) for 5892 atoms. Found 23 (37 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.60 3.46 Search for helices and strands: 0 residues in 0 chains, 6039 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6052 seeds are put forward Round 1: 283 peptides, 58 chains. Longest chain 12 peptides. Score 0.273 Round 2: 317 peptides, 53 chains. Longest chain 14 peptides. Score 0.377 Round 3: 332 peptides, 56 chains. Longest chain 15 peptides. Score 0.381 Round 4: 330 peptides, 55 chains. Longest chain 13 peptides. Score 0.385 Round 5: 329 peptides, 50 chains. Longest chain 14 peptides. Score 0.421 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 51, Residues 279, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vme-3_warpNtrace.pdb as input Building loops using Loopy2018 51 chains (279 residues) following loop building 2 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10948 reflections ( 99.82 % complete ) and 14188 restraints for refining 5947 atoms. 13090 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2446 (Rfree = 0.000) for 5947 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2366 (Rfree = 0.000) for 5917 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.2389 (Rfree = 0.000) for 5889 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2300 (Rfree = 0.000) for 5857 atoms. TimeTaking 77.88