Sun 23 Dec 22:23:08 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 1vkz-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkz-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkz-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-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/1vkz-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-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 22:23:15 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/1vkz-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-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 652 and 0 Target number of residues in the AU: 652 Target solvent content: 0.5834 Checking the provided sequence file Detected sequence length: 412 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 824 Adjusted target solvent content: 0.47 Input MTZ file: 1vkz-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: 63.745 78.443 85.018 90.000 95.062 90.000 Input sequence file: 1vkz-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 6592 target number of atoms Had to go as low as 0.55 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: 19.959 3.600 Wilson plot Bfac: 46.03 9503 reflections ( 96.69 % complete ) and 0 restraints for refining 7253 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.2876 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2892 (Rfree = 0.000) for 7253 atoms. Found 46 (46 requested) and removed 69 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.04 3.16 Search for helices and strands: 0 residues in 0 chains, 7359 seeds are put forward NCS extension: 0 residues added, 7359 seeds are put forward Round 1: 315 peptides, 62 chains. Longest chain 9 peptides. Score 0.314 Round 2: 415 peptides, 72 chains. Longest chain 13 peptides. Score 0.425 Round 3: 446 peptides, 71 chains. Longest chain 18 peptides. Score 0.487 Round 4: 459 peptides, 73 chains. Longest chain 18 peptides. Score 0.494 Round 5: 482 peptides, 69 chains. Longest chain 25 peptides. Score 0.558 Taking the results from Round 5 Chains 72, Residues 413, Estimated correctness of the model 0.0 % 8 chains (46 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 9503 reflections ( 96.69 % complete ) and 13081 restraints for refining 5974 atoms. 11353 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2405 (Rfree = 0.000) for 5974 atoms. Found 38 (38 requested) and removed 66 (19 requested) atoms. Cycle 2: After refmac, R = 0.2296 (Rfree = 0.000) for 5801 atoms. Found 38 (38 requested) and removed 42 (19 requested) atoms. Cycle 3: After refmac, R = 0.2016 (Rfree = 0.000) for 5732 atoms. Found 32 (37 requested) and removed 27 (18 requested) atoms. Cycle 4: After refmac, R = 0.1833 (Rfree = 0.000) for 5708 atoms. Found 16 (36 requested) and removed 31 (18 requested) atoms. Cycle 5: After refmac, R = 0.1762 (Rfree = 0.000) for 5673 atoms. Found 9 (36 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.04 3.16 Search for helices and strands: 0 residues in 0 chains, 5822 seeds are put forward NCS extension: 37 residues added (3 deleted due to clashes), 5859 seeds are put forward Round 1: 430 peptides, 81 chains. Longest chain 18 peptides. Score 0.383 Round 2: 481 peptides, 73 chains. Longest chain 17 peptides. Score 0.529 Round 3: 508 peptides, 77 chains. Longest chain 16 peptides. Score 0.544 Round 4: 508 peptides, 73 chains. Longest chain 25 peptides. Score 0.570 Round 5: 504 peptides, 71 chains. Longest chain 21 peptides. Score 0.577 Taking the results from Round 5 Chains 72, Residues 433, Estimated correctness of the model 5.5 % 5 chains (42 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 12761 restraints for refining 5940 atoms. 10939 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2367 (Rfree = 0.000) for 5940 atoms. Found 38 (38 requested) and removed 73 (19 requested) atoms. Cycle 7: After refmac, R = 0.2084 (Rfree = 0.000) for 5826 atoms. Found 37 (37 requested) and removed 43 (18 requested) atoms. Cycle 8: After refmac, R = 0.1971 (Rfree = 0.000) for 5784 atoms. Found 28 (37 requested) and removed 41 (18 requested) atoms. Cycle 9: After refmac, R = 0.1885 (Rfree = 0.000) for 5753 atoms. Found 30 (37 requested) and removed 27 (18 requested) atoms. Cycle 10: After refmac, R = 0.1825 (Rfree = 0.000) for 5740 atoms. Found 18 (36 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 3.20 Search for helices and strands: 0 residues in 0 chains, 5920 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 5943 seeds are put forward Round 1: 432 peptides, 82 chains. Longest chain 17 peptides. Score 0.379 Round 2: 473 peptides, 77 chains. Longest chain 15 peptides. Score 0.489 Round 3: 468 peptides, 68 chains. Longest chain 18 peptides. Score 0.543 Round 4: 476 peptides, 69 chains. Longest chain 16 peptides. Score 0.549 Round 5: 492 peptides, 72 chains. Longest chain 23 peptides. Score 0.553 Taking the results from Round 5 Chains 78, Residues 420, Estimated correctness of the model 0.0 % 7 chains (56 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 12989 restraints for refining 5976 atoms. 11208 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2320 (Rfree = 0.000) for 5976 atoms. Found 38 (38 requested) and removed 64 (19 requested) atoms. Cycle 12: After refmac, R = 0.2117 (Rfree = 0.000) for 5877 atoms. Found 37 (38 requested) and removed 47 (19 requested) atoms. Cycle 13: After refmac, R = 0.1937 (Rfree = 0.000) for 5840 atoms. Found 29 (37 requested) and removed 32 (18 requested) atoms. Cycle 14: After refmac, R = 0.1828 (Rfree = 0.000) for 5814 atoms. Found 28 (37 requested) and removed 30 (18 requested) atoms. Cycle 15: After refmac, R = 0.1774 (Rfree = 0.000) for 5801 atoms. Found 31 (37 requested) and removed 30 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.08 3.21 Search for helices and strands: 0 residues in 0 chains, 5991 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 6003 seeds are put forward Round 1: 401 peptides, 72 chains. Longest chain 15 peptides. Score 0.400 Round 2: 459 peptides, 73 chains. Longest chain 16 peptides. Score 0.494 Round 3: 453 peptides, 71 chains. Longest chain 28 peptides. Score 0.498 Round 4: 447 peptides, 64 chains. Longest chain 25 peptides. Score 0.538 Round 5: 469 peptides, 66 chains. Longest chain 21 peptides. Score 0.558 Taking the results from Round 5 Chains 67, Residues 403, Estimated correctness of the model 0.0 % 6 chains (32 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13408 restraints for refining 5976 atoms. 11789 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2252 (Rfree = 0.000) for 5976 atoms. Found 38 (38 requested) and removed 52 (19 requested) atoms. Cycle 17: After refmac, R = 0.2021 (Rfree = 0.000) for 5915 atoms. Found 38 (38 requested) and removed 44 (19 requested) atoms. Cycle 18: After refmac, R = 0.1859 (Rfree = 0.000) for 5882 atoms. Found 26 (37 requested) and removed 26 (18 requested) atoms. Cycle 19: After refmac, R = 0.1812 (Rfree = 0.000) for 5871 atoms. Found 27 (37 requested) and removed 26 (18 requested) atoms. Cycle 20: After refmac, R = 0.1733 (Rfree = 0.000) for 5863 atoms. Found 17 (37 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.07 3.20 Search for helices and strands: 0 residues in 0 chains, 6032 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6054 seeds are put forward Round 1: 389 peptides, 74 chains. Longest chain 11 peptides. Score 0.361 Round 2: 427 peptides, 64 chains. Longest chain 20 peptides. Score 0.506 Round 3: 444 peptides, 69 chains. Longest chain 18 peptides. Score 0.498 Round 4: 442 peptides, 67 chains. Longest chain 14 peptides. Score 0.509 Round 5: 444 peptides, 62 chains. Longest chain 17 peptides. Score 0.547 Taking the results from Round 5 Chains 65, Residues 382, Estimated correctness of the model 0.0 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13399 restraints for refining 5976 atoms. 11813 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2286 (Rfree = 0.000) for 5976 atoms. Found 38 (38 requested) and removed 43 (19 requested) atoms. Cycle 22: After refmac, R = 0.2058 (Rfree = 0.000) for 5919 atoms. Found 37 (38 requested) and removed 37 (19 requested) atoms. Cycle 23: After refmac, R = 0.2038 (Rfree = 0.000) for 5894 atoms. Found 37 (37 requested) and removed 32 (18 requested) atoms. Cycle 24: After refmac, R = 0.1901 (Rfree = 0.000) for 5883 atoms. Found 36 (37 requested) and removed 28 (18 requested) atoms. Cycle 25: After refmac, R = 0.1900 (Rfree = 0.000) for 5876 atoms. Found 25 (37 requested) and removed 32 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.09 3.22 Search for helices and strands: 0 residues in 0 chains, 6031 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 6044 seeds are put forward Round 1: 375 peptides, 70 chains. Longest chain 12 peptides. Score 0.367 Round 2: 404 peptides, 62 chains. Longest chain 19 peptides. Score 0.482 Round 3: 410 peptides, 68 chains. Longest chain 15 peptides. Score 0.447 Round 4: 439 peptides, 64 chains. Longest chain 16 peptides. Score 0.525 Round 5: 417 peptides, 64 chains. Longest chain 16 peptides. Score 0.489 Taking the results from Round 4 Chains 67, Residues 375, Estimated correctness of the model 0.0 % 7 chains (51 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13283 restraints for refining 5974 atoms. 11673 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2155 (Rfree = 0.000) for 5974 atoms. Found 38 (38 requested) and removed 46 (19 requested) atoms. Cycle 27: After refmac, R = 0.1960 (Rfree = 0.000) for 5919 atoms. Found 34 (38 requested) and removed 32 (19 requested) atoms. Cycle 28: After refmac, R = 0.1880 (Rfree = 0.000) for 5902 atoms. Found 32 (37 requested) and removed 30 (18 requested) atoms. Cycle 29: After refmac, R = 0.1787 (Rfree = 0.000) for 5892 atoms. Found 19 (37 requested) and removed 28 (18 requested) atoms. Cycle 30: After refmac, R = 0.1760 (Rfree = 0.000) for 5876 atoms. Found 22 (37 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.07 3.20 Search for helices and strands: 0 residues in 0 chains, 6027 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 6038 seeds are put forward Round 1: 343 peptides, 67 chains. Longest chain 14 peptides. Score 0.328 Round 2: 382 peptides, 60 chains. Longest chain 15 peptides. Score 0.459 Round 3: 402 peptides, 64 chains. Longest chain 15 peptides. Score 0.464 Round 4: 401 peptides, 58 chains. Longest chain 19 peptides. Score 0.506 Round 5: 396 peptides, 55 chains. Longest chain 20 peptides. Score 0.520 Taking the results from Round 5 Chains 60, Residues 341, Estimated correctness of the model 0.0 % 11 chains (71 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13173 restraints for refining 5976 atoms. 11626 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2085 (Rfree = 0.000) for 5976 atoms. Found 38 (38 requested) and removed 43 (19 requested) atoms. Cycle 32: After refmac, R = 0.1853 (Rfree = 0.000) for 5935 atoms. Found 25 (38 requested) and removed 36 (19 requested) atoms. Cycle 33: After refmac, R = 0.1819 (Rfree = 0.000) for 5903 atoms. Found 29 (38 requested) and removed 26 (19 requested) atoms. Cycle 34: After refmac, R = 0.1753 (Rfree = 0.000) for 5895 atoms. Found 22 (37 requested) and removed 24 (18 requested) atoms. Cycle 35: After refmac, R = 0.1726 (Rfree = 0.000) for 5879 atoms. Found 23 (37 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 3.25 Search for helices and strands: 0 residues in 0 chains, 6052 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 6078 seeds are put forward Round 1: 333 peptides, 64 chains. Longest chain 11 peptides. Score 0.334 Round 2: 399 peptides, 64 chains. Longest chain 18 peptides. Score 0.458 Round 3: 381 peptides, 60 chains. Longest chain 17 peptides. Score 0.457 Round 4: 376 peptides, 56 chains. Longest chain 16 peptides. Score 0.479 Round 5: 371 peptides, 56 chains. Longest chain 13 peptides. Score 0.471 Taking the results from Round 4 Chains 59, Residues 320, Estimated correctness of the model 0.0 % 4 chains (28 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13596 restraints for refining 5975 atoms. 12268 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1963 (Rfree = 0.000) for 5975 atoms. Found 29 (38 requested) and removed 33 (19 requested) atoms. Cycle 37: After refmac, R = 0.1785 (Rfree = 0.000) for 5948 atoms. Found 28 (38 requested) and removed 27 (19 requested) atoms. Cycle 38: After refmac, R = 0.1709 (Rfree = 0.000) for 5936 atoms. Found 23 (38 requested) and removed 31 (19 requested) atoms. Cycle 39: After refmac, R = 0.1682 (Rfree = 0.000) for 5920 atoms. Found 18 (38 requested) and removed 22 (19 requested) atoms. Cycle 40: After refmac, R = 0.1676 (Rfree = 0.000) for 5912 atoms. Found 22 (37 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.09 3.22 Search for helices and strands: 0 residues in 0 chains, 6055 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 6075 seeds are put forward Round 1: 278 peptides, 52 chains. Longest chain 11 peptides. Score 0.326 Round 2: 292 peptides, 49 chains. Longest chain 12 peptides. Score 0.381 Round 3: 310 peptides, 50 chains. Longest chain 19 peptides. Score 0.407 Round 4: 336 peptides, 52 chains. Longest chain 13 peptides. Score 0.439 Round 5: 332 peptides, 53 chains. Longest chain 15 peptides. Score 0.424 Taking the results from Round 4 Chains 52, Residues 284, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 9503 reflections ( 96.69 % complete ) and 13802 restraints for refining 5976 atoms. 12647 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1990 (Rfree = 0.000) for 5976 atoms. Found 37 (38 requested) and removed 36 (19 requested) atoms. Cycle 42: After refmac, R = 0.1902 (Rfree = 0.000) for 5951 atoms. Found 36 (38 requested) and removed 27 (19 requested) atoms. Cycle 43: After refmac, R = 0.1761 (Rfree = 0.000) for 5945 atoms. Found 20 (38 requested) and removed 28 (19 requested) atoms. Cycle 44: After refmac, R = 0.1705 (Rfree = 0.000) for 5924 atoms. Found 28 (38 requested) and removed 28 (19 requested) atoms. Cycle 45: After refmac, R = 0.1488 (Rfree = 0.000) for 5915 atoms. Found 8 (38 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 3.22 Search for helices and strands: 0 residues in 0 chains, 6024 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6037 seeds are put forward Round 1: 266 peptides, 53 chains. Longest chain 11 peptides. Score 0.291 Round 2: 298 peptides, 51 chains. Longest chain 21 peptides. Score 0.375 Round 3: 309 peptides, 54 chains. Longest chain 13 peptides. Score 0.371 Round 4: 315 peptides, 49 chains. Longest chain 21 peptides. Score 0.425 Round 5: 301 peptides, 50 chains. Longest chain 15 peptides. Score 0.390 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 266, Estimated correctness of the model 0.0 % 4 chains (26 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 1vkz-3_warpNtrace.pdb as input Building loops using Loopy2018 49 chains (266 residues) following loop building 4 chains (26 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9503 reflections ( 96.69 % complete ) and 13716 restraints for refining 5976 atoms. 12618 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2073 (Rfree = 0.000) for 5976 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.1957 (Rfree = 0.000) for 5927 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.1794 (Rfree = 0.000) for 5897 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.1805 (Rfree = 0.000) for 5862 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Writing output files ... TimeTaking 73.88