Sun 23 Dec 22:22:56 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 2aml-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2aml-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2aml-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aml-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/2aml-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aml-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 22:23:05 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/2aml-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2aml-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 492 and 0 Target number of residues in the AU: 492 Target solvent content: 0.6119 Checking the provided sequence file Detected sequence length: 373 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 746 Adjusted target solvent content: 0.41 Input MTZ file: 2aml-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: 19 Cell parameters: 56.315 101.397 120.151 90.000 90.000 90.000 Input sequence file: 2aml-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 5968 target number of atoms Had to go as low as 0.65 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: 77.491 3.200 Wilson plot Bfac: 57.53 11884 reflections ( 99.82 % complete ) and 0 restraints for refining 6654 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3055 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2693 (Rfree = 0.000) for 6654 atoms. Found 59 (59 requested) and removed 66 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.12 3.52 Search for helices and strands: 0 residues in 0 chains, 6808 seeds are put forward NCS extension: 0 residues added, 6808 seeds are put forward Round 1: 355 peptides, 69 chains. Longest chain 12 peptides. Score 0.366 Round 2: 391 peptides, 59 chains. Longest chain 18 peptides. Score 0.533 Round 3: 420 peptides, 63 chains. Longest chain 18 peptides. Score 0.555 Round 4: 453 peptides, 59 chains. Longest chain 29 peptides. Score 0.641 Round 5: 494 peptides, 57 chains. Longest chain 24 peptides. Score 0.711 Taking the results from Round 5 Chains 63, Residues 437, Estimated correctness of the model 67.5 % 8 chains (91 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 208 A and 217 A 61 chains (442 residues) following loop building 7 chains (99 residues) in sequence following loop building ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 10676 restraints for refining 5447 atoms. 8581 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2476 (Rfree = 0.000) for 5447 atoms. Found 44 (48 requested) and removed 43 (24 requested) atoms. Cycle 2: After refmac, R = 0.2305 (Rfree = 0.000) for 5386 atoms. Found 32 (47 requested) and removed 32 (24 requested) atoms. Cycle 3: After refmac, R = 0.2183 (Rfree = 0.000) for 5366 atoms. Found 24 (46 requested) and removed 28 (24 requested) atoms. Cycle 4: After refmac, R = 0.2107 (Rfree = 0.000) for 5345 atoms. Found 12 (45 requested) and removed 25 (24 requested) atoms. Cycle 5: After refmac, R = 0.2045 (Rfree = 0.000) for 5325 atoms. Found 9 (43 requested) and removed 24 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.10 3.50 Search for helices and strands: 0 residues in 0 chains, 5556 seeds are put forward NCS extension: 30 residues added (12 deleted due to clashes), 5586 seeds are put forward Round 1: 444 peptides, 68 chains. Longest chain 20 peptides. Score 0.559 Round 2: 481 peptides, 59 chains. Longest chain 33 peptides. Score 0.682 Round 3: 490 peptides, 55 chains. Longest chain 27 peptides. Score 0.718 Round 4: 480 peptides, 53 chains. Longest chain 45 peptides. Score 0.717 Round 5: 464 peptides, 52 chains. Longest chain 27 peptides. Score 0.702 Taking the results from Round 3 Chains 59, Residues 435, Estimated correctness of the model 68.9 % 5 chains (47 residues) have been docked in sequence Building loops using Loopy2018 59 chains (435 residues) following loop building 5 chains (47 residues) in sequence following loop building ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 11574 restraints for refining 5448 atoms. 9714 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2247 (Rfree = 0.000) for 5448 atoms. Found 32 (43 requested) and removed 39 (24 requested) atoms. Cycle 7: After refmac, R = 0.1976 (Rfree = 0.000) for 5427 atoms. Found 20 (42 requested) and removed 27 (24 requested) atoms. Cycle 8: After refmac, R = 0.1894 (Rfree = 0.000) for 5408 atoms. Found 9 (41 requested) and removed 25 (24 requested) atoms. Cycle 9: After refmac, R = 0.1857 (Rfree = 0.000) for 5389 atoms. Found 17 (40 requested) and removed 24 (24 requested) atoms. Cycle 10: After refmac, R = 0.1807 (Rfree = 0.000) for 5382 atoms. Found 9 (39 requested) and removed 27 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 3.47 Search for helices and strands: 0 residues in 0 chains, 5555 seeds are put forward NCS extension: 14 residues added (9 deleted due to clashes), 5569 seeds are put forward Round 1: 436 peptides, 64 chains. Longest chain 16 peptides. Score 0.576 Round 2: 492 peptides, 57 chains. Longest chain 23 peptides. Score 0.709 Round 3: 501 peptides, 55 chains. Longest chain 25 peptides. Score 0.731 Round 4: 499 peptides, 54 chains. Longest chain 27 peptides. Score 0.735 Round 5: 482 peptides, 51 chains. Longest chain 47 peptides. Score 0.731 Taking the results from Round 4 Chains 60, Residues 445, Estimated correctness of the model 72.3 % 5 chains (84 residues) have been docked in sequence Building loops using Loopy2018 60 chains (445 residues) following loop building 5 chains (84 residues) in sequence following loop building ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 11045 restraints for refining 5448 atoms. 8999 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2170 (Rfree = 0.000) for 5448 atoms. Found 38 (38 requested) and removed 39 (24 requested) atoms. Cycle 12: After refmac, R = 0.1963 (Rfree = 0.000) for 5427 atoms. Found 18 (37 requested) and removed 27 (24 requested) atoms. Cycle 13: After refmac, R = 0.1929 (Rfree = 0.000) for 5410 atoms. Found 23 (36 requested) and removed 25 (24 requested) atoms. Cycle 14: After refmac, R = 0.1855 (Rfree = 0.000) for 5396 atoms. Found 19 (36 requested) and removed 25 (24 requested) atoms. Cycle 15: After refmac, R = 0.1790 (Rfree = 0.000) for 5385 atoms. Found 15 (35 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.10 3.50 Search for helices and strands: 0 residues in 0 chains, 5584 seeds are put forward NCS extension: 14 residues added (7 deleted due to clashes), 5598 seeds are put forward Round 1: 433 peptides, 60 chains. Longest chain 21 peptides. Score 0.601 Round 2: 449 peptides, 48 chains. Longest chain 43 peptides. Score 0.707 Round 3: 467 peptides, 55 chains. Longest chain 40 peptides. Score 0.688 Round 4: 482 peptides, 52 chains. Longest chain 26 peptides. Score 0.725 Round 5: 465 peptides, 52 chains. Longest chain 41 peptides. Score 0.704 Taking the results from Round 4 Chains 54, Residues 430, Estimated correctness of the model 70.3 % 3 chains (32 residues) have been docked in sequence Building loops using Loopy2018 54 chains (430 residues) following loop building 3 chains (32 residues) in sequence following loop building ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 11770 restraints for refining 5448 atoms. 9986 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2053 (Rfree = 0.000) for 5448 atoms. Found 27 (34 requested) and removed 28 (24 requested) atoms. Cycle 17: After refmac, R = 0.1897 (Rfree = 0.000) for 5437 atoms. Found 17 (33 requested) and removed 26 (24 requested) atoms. Cycle 18: After refmac, R = 0.1827 (Rfree = 0.000) for 5420 atoms. Found 13 (32 requested) and removed 25 (24 requested) atoms. Cycle 19: After refmac, R = 0.1795 (Rfree = 0.000) for 5401 atoms. Found 11 (31 requested) and removed 24 (24 requested) atoms. Cycle 20: After refmac, R = 0.1753 (Rfree = 0.000) for 5388 atoms. Found 16 (30 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.09 3.49 Search for helices and strands: 0 residues in 0 chains, 5589 seeds are put forward NCS extension: 13 residues added (5 deleted due to clashes), 5602 seeds are put forward Round 1: 429 peptides, 60 chains. Longest chain 28 peptides. Score 0.595 Round 2: 475 peptides, 51 chains. Longest chain 44 peptides. Score 0.722 Round 3: 452 peptides, 53 chains. Longest chain 26 peptides. Score 0.679 Round 4: 469 peptides, 45 chains. Longest chain 40 peptides. Score 0.749 Round 5: 448 peptides, 55 chains. Longest chain 23 peptides. Score 0.661 Taking the results from Round 4 Chains 49, Residues 424, Estimated correctness of the model 74.9 % 3 chains (65 residues) have been docked in sequence Building loops using Loopy2018 49 chains (424 residues) following loop building 3 chains (65 residues) in sequence following loop building ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 11227 restraints for refining 5447 atoms. 9341 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2091 (Rfree = 0.000) for 5447 atoms. Found 29 (29 requested) and removed 32 (24 requested) atoms. Cycle 22: After refmac, R = 0.1907 (Rfree = 0.000) for 5427 atoms. Found 26 (28 requested) and removed 24 (24 requested) atoms. Cycle 23: After refmac, R = 0.1857 (Rfree = 0.000) for 5425 atoms. Found 14 (27 requested) and removed 24 (24 requested) atoms. Cycle 24: After refmac, R = 0.1795 (Rfree = 0.000) for 5406 atoms. Found 17 (26 requested) and removed 25 (24 requested) atoms. Cycle 25: After refmac, R = 0.1768 (Rfree = 0.000) for 5398 atoms. Found 11 (25 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.08 3.48 Search for helices and strands: 0 residues in 0 chains, 5571 seeds are put forward NCS extension: 34 residues added (12 deleted due to clashes), 5605 seeds are put forward Round 1: 409 peptides, 58 chains. Longest chain 19 peptides. Score 0.575 Round 2: 453 peptides, 50 chains. Longest chain 31 peptides. Score 0.700 Round 3: 445 peptides, 48 chains. Longest chain 25 peptides. Score 0.702 Round 4: 436 peptides, 48 chains. Longest chain 41 peptides. Score 0.689 Round 5: 432 peptides, 50 chains. Longest chain 22 peptides. Score 0.670 Taking the results from Round 3 Chains 51, Residues 397, Estimated correctness of the model 65.6 % 5 chains (62 residues) have been docked in sequence Building loops using Loopy2018 51 chains (397 residues) following loop building 5 chains (62 residues) in sequence following loop building ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 11506 restraints for refining 5448 atoms. 9746 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1975 (Rfree = 0.000) for 5448 atoms. Found 24 (24 requested) and removed 35 (24 requested) atoms. Cycle 27: After refmac, R = 0.1778 (Rfree = 0.000) for 5427 atoms. Found 19 (24 requested) and removed 24 (24 requested) atoms. Cycle 28: After refmac, R = 0.1721 (Rfree = 0.000) for 5421 atoms. Found 8 (24 requested) and removed 25 (24 requested) atoms. Cycle 29: After refmac, R = 0.1670 (Rfree = 0.000) for 5402 atoms. Found 11 (24 requested) and removed 24 (24 requested) atoms. Cycle 30: After refmac, R = 0.1703 (Rfree = 0.000) for 5386 atoms. Found 15 (24 requested) and removed 25 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.06 3.45 Search for helices and strands: 0 residues in 0 chains, 5549 seeds are put forward NCS extension: 13 residues added (6 deleted due to clashes), 5562 seeds are put forward Round 1: 420 peptides, 59 chains. Longest chain 25 peptides. Score 0.587 Round 2: 447 peptides, 56 chains. Longest chain 40 peptides. Score 0.652 Round 3: 445 peptides, 49 chains. Longest chain 41 peptides. Score 0.695 Round 4: 436 peptides, 51 chains. Longest chain 25 peptides. Score 0.670 Round 5: 439 peptides, 51 chains. Longest chain 40 peptides. Score 0.674 Taking the results from Round 3 Chains 53, Residues 396, Estimated correctness of the model 64.1 % 5 chains (74 residues) have been docked in sequence ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 11187 restraints for refining 5448 atoms. 9382 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1949 (Rfree = 0.000) for 5448 atoms. Found 24 (24 requested) and removed 37 (24 requested) atoms. Cycle 32: After refmac, R = 0.1822 (Rfree = 0.000) for 5424 atoms. Found 24 (24 requested) and removed 24 (24 requested) atoms. Cycle 33: After refmac, R = 0.1722 (Rfree = 0.000) for 5419 atoms. Found 11 (24 requested) and removed 25 (24 requested) atoms. Cycle 34: After refmac, R = 0.1709 (Rfree = 0.000) for 5404 atoms. Found 16 (24 requested) and removed 24 (24 requested) atoms. Cycle 35: After refmac, R = 0.1667 (Rfree = 0.000) for 5394 atoms. Found 8 (24 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.06 3.45 Search for helices and strands: 0 residues in 0 chains, 5587 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 5609 seeds are put forward Round 1: 373 peptides, 55 chains. Longest chain 18 peptides. Score 0.532 Round 2: 421 peptides, 54 chains. Longest chain 19 peptides. Score 0.626 Round 3: 424 peptides, 50 chains. Longest chain 29 peptides. Score 0.659 Round 4: 413 peptides, 49 chains. Longest chain 24 peptides. Score 0.649 Round 5: 399 peptides, 49 chains. Longest chain 25 peptides. Score 0.626 Taking the results from Round 3 Chains 51, Residues 374, Estimated correctness of the model 56.0 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 11876 restraints for refining 5448 atoms. 10269 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1956 (Rfree = 0.000) for 5448 atoms. Found 24 (24 requested) and removed 27 (24 requested) atoms. Cycle 37: After refmac, R = 0.1834 (Rfree = 0.000) for 5435 atoms. Found 23 (24 requested) and removed 25 (24 requested) atoms. Cycle 38: After refmac, R = 0.1816 (Rfree = 0.000) for 5428 atoms. Found 19 (24 requested) and removed 25 (24 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1737 (Rfree = 0.000) for 5420 atoms. Found 15 (24 requested) and removed 24 (24 requested) atoms. Cycle 40: After refmac, R = 0.1700 (Rfree = 0.000) for 5407 atoms. Found 18 (24 requested) and removed 26 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.05 3.44 Search for helices and strands: 0 residues in 0 chains, 5597 seeds are put forward NCS extension: 20 residues added (8 deleted due to clashes), 5617 seeds are put forward Round 1: 388 peptides, 59 chains. Longest chain 18 peptides. Score 0.528 Round 2: 419 peptides, 54 chains. Longest chain 24 peptides. Score 0.622 Round 3: 431 peptides, 57 chains. Longest chain 24 peptides. Score 0.620 Round 4: 422 peptides, 54 chains. Longest chain 21 peptides. Score 0.627 Round 5: 404 peptides, 50 chains. Longest chain 22 peptides. Score 0.627 Taking the results from Round 5 Chains 52, Residues 354, Estimated correctness of the model 48.1 % 3 chains (34 residues) have been docked in sequence ------------------------------------------------------ 11884 reflections ( 99.82 % complete ) and 11946 restraints for refining 5448 atoms. 10451 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1978 (Rfree = 0.000) for 5448 atoms. Found 24 (24 requested) and removed 26 (24 requested) atoms. Cycle 42: After refmac, R = 0.1829 (Rfree = 0.000) for 5440 atoms. Found 24 (24 requested) and removed 25 (24 requested) atoms. Cycle 43: After refmac, R = 0.1745 (Rfree = 0.000) for 5436 atoms. Found 24 (24 requested) and removed 24 (24 requested) atoms. Cycle 44: After refmac, R = 0.1684 (Rfree = 0.000) for 5434 atoms. Found 20 (24 requested) and removed 25 (24 requested) atoms. Cycle 45: After refmac, R = 0.1574 (Rfree = 0.000) for 5426 atoms. Found 15 (24 requested) and removed 25 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.07 3.47 Search for helices and strands: 0 residues in 0 chains, 5603 seeds are put forward NCS extension: 17 residues added (7 deleted due to clashes), 5620 seeds are put forward Round 1: 338 peptides, 56 chains. Longest chain 18 peptides. Score 0.451 Round 2: 387 peptides, 49 chains. Longest chain 19 peptides. Score 0.606 Round 3: 398 peptides, 51 chains. Longest chain 20 peptides. Score 0.610 Round 4: 393 peptides, 56 chains. Longest chain 19 peptides. Score 0.562 Round 5: 396 peptides, 54 chains. Longest chain 19 peptides. Score 0.583 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 53, Residues 347, Estimated correctness of the model 43.7 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2aml-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11884 reflections ( 99.82 % complete ) and 12211 restraints for refining 5447 atoms. 10846 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1768 (Rfree = 0.000) for 5447 atoms. Found 0 (24 requested) and removed 9 (24 requested) atoms. Cycle 47: After refmac, R = 0.1730 (Rfree = 0.000) for 5436 atoms. Found 0 (24 requested) and removed 6 (24 requested) atoms. Cycle 48: After refmac, R = 0.1753 (Rfree = 0.000) for 5427 atoms. Found 0 (24 requested) and removed 4 (24 requested) atoms. Cycle 49: After refmac, R = 0.1715 (Rfree = 0.000) for 5420 atoms. TimeTaking 75.48