Sun 23 Dec 23:53:08 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 1vl5-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl5-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl5-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-4.0-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/1vl5-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-4.0-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 ============================================================ Sun 23 Dec 23:53:23 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/1vl5-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl5-4.0-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 726 and 0 Target number of residues in the AU: 726 Target solvent content: 0.6608 Checking the provided sequence file Detected sequence length: 260 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1040 Adjusted target solvent content: 0.51 Input MTZ file: 1vl5-4.0-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: 4 Cell parameters: 64.006 87.475 105.236 90.000 100.573 90.000 Input sequence file: 1vl5-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 8320 target number of atoms Had to go as low as 0.75 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: 49.849 4.000 Wilson plot Bfac: 85.29 9787 reflections ( 99.93 % complete ) and 0 restraints for refining 9224 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3333 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3269 (Rfree = 0.000) for 9224 atoms. Found 43 (43 requested) and removed 47 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.82 3.77 Search for helices and strands: 0 residues in 0 chains, 9407 seeds are put forward NCS extension: 0 residues added, 9407 seeds are put forward Round 1: 319 peptides, 64 chains. Longest chain 12 peptides. Score 0.277 Round 2: 416 peptides, 71 chains. Longest chain 12 peptides. Score 0.380 Round 3: 476 peptides, 76 chains. Longest chain 16 peptides. Score 0.433 Round 4: 505 peptides, 73 chains. Longest chain 26 peptides. Score 0.488 Round 5: 506 peptides, 75 chains. Longest chain 14 peptides. Score 0.478 Taking the results from Round 4 Chains 74, Residues 432, Estimated correctness of the model 0.0 % 4 chains (49 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 17437 restraints for refining 7509 atoms. 15607 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2681 (Rfree = 0.000) for 7509 atoms. Found 30 (35 requested) and removed 62 (17 requested) atoms. Cycle 2: After refmac, R = 0.2362 (Rfree = 0.000) for 7306 atoms. Found 35 (35 requested) and removed 44 (17 requested) atoms. Cycle 3: After refmac, R = 0.1937 (Rfree = 0.000) for 7219 atoms. Found 16 (34 requested) and removed 40 (17 requested) atoms. Cycle 4: After refmac, R = 0.2130 (Rfree = 0.000) for 7156 atoms. Found 31 (34 requested) and removed 38 (17 requested) atoms. Cycle 5: After refmac, R = 0.2069 (Rfree = 0.000) for 7123 atoms. Found 18 (33 requested) and removed 46 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.70 Search for helices and strands: 0 residues in 0 chains, 7354 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 7376 seeds are put forward Round 1: 402 peptides, 73 chains. Longest chain 13 peptides. Score 0.347 Round 2: 472 peptides, 67 chains. Longest chain 21 peptides. Score 0.480 Round 3: 494 peptides, 71 chains. Longest chain 17 peptides. Score 0.485 Round 4: 505 peptides, 61 chains. Longest chain 22 peptides. Score 0.553 Round 5: 509 peptides, 63 chains. Longest chain 24 peptides. Score 0.547 Taking the results from Round 4 Chains 62, Residues 444, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 16795 restraints for refining 7262 atoms. 15032 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2208 (Rfree = 0.000) for 7262 atoms. Found 21 (34 requested) and removed 54 (17 requested) atoms. Cycle 7: After refmac, R = 0.2086 (Rfree = 0.000) for 7142 atoms. Found 16 (34 requested) and removed 42 (17 requested) atoms. Cycle 8: After refmac, R = 0.2057 (Rfree = 0.000) for 7064 atoms. Found 33 (33 requested) and removed 35 (16 requested) atoms. Cycle 9: After refmac, R = 0.1992 (Rfree = 0.000) for 7015 atoms. Found 20 (33 requested) and removed 40 (16 requested) atoms. Cycle 10: After refmac, R = 0.1858 (Rfree = 0.000) for 6960 atoms. Found 24 (33 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.75 3.70 Search for helices and strands: 0 residues in 0 chains, 7214 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 7232 seeds are put forward Round 1: 429 peptides, 81 chains. Longest chain 14 peptides. Score 0.336 Round 2: 488 peptides, 74 chains. Longest chain 24 peptides. Score 0.460 Round 3: 472 peptides, 71 chains. Longest chain 18 peptides. Score 0.457 Round 4: 489 peptides, 71 chains. Longest chain 18 peptides. Score 0.479 Round 5: 482 peptides, 71 chains. Longest chain 24 peptides. Score 0.470 Taking the results from Round 4 Chains 71, Residues 418, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 16702 restraints for refining 7201 atoms. 15062 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2179 (Rfree = 0.000) for 7201 atoms. Found 25 (34 requested) and removed 57 (17 requested) atoms. Cycle 12: After refmac, R = 0.2023 (Rfree = 0.000) for 7070 atoms. Found 28 (34 requested) and removed 45 (17 requested) atoms. Cycle 13: After refmac, R = 0.2009 (Rfree = 0.000) for 7004 atoms. Found 33 (33 requested) and removed 38 (16 requested) atoms. Cycle 14: After refmac, R = 0.2011 (Rfree = 0.000) for 6956 atoms. Found 33 (33 requested) and removed 33 (16 requested) atoms. Cycle 15: After refmac, R = 0.1600 (Rfree = 0.000) for 6923 atoms. Found 9 (33 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.73 3.68 Search for helices and strands: 0 residues in 0 chains, 7182 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 7207 seeds are put forward Round 1: 395 peptides, 73 chains. Longest chain 17 peptides. Score 0.336 Round 2: 448 peptides, 69 chains. Longest chain 19 peptides. Score 0.437 Round 3: 456 peptides, 68 chains. Longest chain 19 peptides. Score 0.453 Round 4: 478 peptides, 66 chains. Longest chain 23 peptides. Score 0.493 Round 5: 487 peptides, 67 chains. Longest chain 30 peptides. Score 0.499 Taking the results from Round 5 Chains 71, Residues 420, Estimated correctness of the model 0.0 % 5 chains (51 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 15812 restraints for refining 7144 atoms. 14012 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2046 (Rfree = 0.000) for 7144 atoms. Found 18 (33 requested) and removed 53 (16 requested) atoms. Cycle 17: After refmac, R = 0.2004 (Rfree = 0.000) for 7043 atoms. Found 17 (33 requested) and removed 41 (16 requested) atoms. Cycle 18: After refmac, R = 0.1896 (Rfree = 0.000) for 6984 atoms. Found 14 (33 requested) and removed 34 (16 requested) atoms. Cycle 19: After refmac, R = 0.1847 (Rfree = 0.000) for 6933 atoms. Found 21 (33 requested) and removed 37 (16 requested) atoms. Cycle 20: After refmac, R = 0.1891 (Rfree = 0.000) for 6895 atoms. Found 20 (32 requested) and removed 27 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.74 3.69 Search for helices and strands: 0 residues in 0 chains, 7106 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 7126 seeds are put forward Round 1: 373 peptides, 70 chains. Longest chain 14 peptides. Score 0.322 Round 2: 423 peptides, 66 chains. Longest chain 25 peptides. Score 0.421 Round 3: 438 peptides, 65 chains. Longest chain 21 peptides. Score 0.447 Round 4: 449 peptides, 65 chains. Longest chain 23 peptides. Score 0.462 Round 5: 444 peptides, 66 chains. Longest chain 18 peptides. Score 0.449 Taking the results from Round 4 Chains 65, Residues 384, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 16500 restraints for refining 7133 atoms. 15013 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2146 (Rfree = 0.000) for 7133 atoms. Found 24 (33 requested) and removed 46 (16 requested) atoms. Cycle 22: After refmac, R = 0.2077 (Rfree = 0.000) for 7062 atoms. Found 32 (33 requested) and removed 41 (16 requested) atoms. Cycle 23: After refmac, R = 0.2089 (Rfree = 0.000) for 7018 atoms. Found 29 (33 requested) and removed 37 (16 requested) atoms. Cycle 24: After refmac, R = 0.1971 (Rfree = 0.000) for 6986 atoms. Found 26 (33 requested) and removed 32 (16 requested) atoms. Cycle 25: After refmac, R = 0.1622 (Rfree = 0.000) for 6949 atoms. Found 7 (33 requested) and removed 26 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.70 3.65 Search for helices and strands: 0 residues in 0 chains, 7168 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 7185 seeds are put forward Round 1: 376 peptides, 74 chains. Longest chain 15 peptides. Score 0.300 Round 2: 428 peptides, 72 chains. Longest chain 16 peptides. Score 0.391 Round 3: 405 peptides, 66 chains. Longest chain 18 peptides. Score 0.395 Round 4: 399 peptides, 64 chains. Longest chain 18 peptides. Score 0.399 Round 5: 395 peptides, 60 chains. Longest chain 16 peptides. Score 0.419 Taking the results from Round 5 Chains 60, Residues 335, Estimated correctness of the model 0.0 % 5 chains (38 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 16970 restraints for refining 7306 atoms. 15559 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2026 (Rfree = 0.000) for 7306 atoms. Found 26 (34 requested) and removed 56 (17 requested) atoms. Cycle 27: After refmac, R = 0.1992 (Rfree = 0.000) for 7217 atoms. Found 34 (34 requested) and removed 43 (17 requested) atoms. Cycle 28: After refmac, R = 0.1948 (Rfree = 0.000) for 7175 atoms. Found 34 (34 requested) and removed 42 (17 requested) atoms. Cycle 29: After refmac, R = 0.1939 (Rfree = 0.000) for 7139 atoms. Found 29 (34 requested) and removed 43 (17 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1513 (Rfree = 0.000) for 7100 atoms. Found 9 (33 requested) and removed 27 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.70 3.65 Search for helices and strands: 0 residues in 0 chains, 7298 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 7320 seeds are put forward Round 1: 351 peptides, 77 chains. Longest chain 9 peptides. Score 0.240 Round 2: 413 peptides, 78 chains. Longest chain 12 peptides. Score 0.331 Round 3: 401 peptides, 74 chains. Longest chain 18 peptides. Score 0.339 Round 4: 394 peptides, 67 chains. Longest chain 12 peptides. Score 0.373 Round 5: 414 peptides, 71 chains. Longest chain 15 peptides. Score 0.377 Taking the results from Round 5 Chains 74, Residues 343, Estimated correctness of the model 0.0 % 5 chains (35 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 16791 restraints for refining 7272 atoms. 15377 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2053 (Rfree = 0.000) for 7272 atoms. Found 34 (34 requested) and removed 63 (17 requested) atoms. Cycle 32: After refmac, R = 0.1882 (Rfree = 0.000) for 7181 atoms. Found 34 (34 requested) and removed 37 (17 requested) atoms. Cycle 33: After refmac, R = 0.1826 (Rfree = 0.000) for 7145 atoms. Found 31 (34 requested) and removed 30 (17 requested) atoms. Cycle 34: After refmac, R = 0.1856 (Rfree = 0.000) for 7124 atoms. Found 33 (33 requested) and removed 30 (16 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1776 (Rfree = 0.000) for 7095 atoms. Found 21 (33 requested) and removed 25 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 3.65 Search for helices and strands: 0 residues in 0 chains, 7327 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 7339 seeds are put forward Round 1: 341 peptides, 72 chains. Longest chain 8 peptides. Score 0.258 Round 2: 380 peptides, 70 chains. Longest chain 12 peptides. Score 0.333 Round 3: 387 peptides, 66 chains. Longest chain 13 peptides. Score 0.369 Round 4: 407 peptides, 72 chains. Longest chain 17 peptides. Score 0.360 Round 5: 390 peptides, 67 chains. Longest chain 13 peptides. Score 0.367 Taking the results from Round 3 Chains 67, Residues 321, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 16524 restraints for refining 7101 atoms. 15280 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2010 (Rfree = 0.000) for 7101 atoms. Found 33 (33 requested) and removed 64 (16 requested) atoms. Cycle 37: After refmac, R = 0.1918 (Rfree = 0.000) for 7024 atoms. Found 33 (33 requested) and removed 39 (16 requested) atoms. Cycle 38: After refmac, R = 0.1825 (Rfree = 0.000) for 6994 atoms. Found 33 (33 requested) and removed 27 (16 requested) atoms. Cycle 39: After refmac, R = 0.1925 (Rfree = 0.000) for 6980 atoms. Found 33 (33 requested) and removed 31 (16 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1812 (Rfree = 0.000) for 6961 atoms. Found 26 (33 requested) and removed 36 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 3.66 Search for helices and strands: 0 residues in 0 chains, 7154 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 7171 seeds are put forward Round 1: 309 peptides, 67 chains. Longest chain 10 peptides. Score 0.239 Round 2: 363 peptides, 64 chains. Longest chain 11 peptides. Score 0.347 Round 3: 380 peptides, 70 chains. Longest chain 11 peptides. Score 0.333 Round 4: 374 peptides, 59 chains. Longest chain 14 peptides. Score 0.395 Round 5: 359 peptides, 65 chains. Longest chain 11 peptides. Score 0.334 Taking the results from Round 4 Chains 59, Residues 315, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9787 reflections ( 99.93 % complete ) and 16193 restraints for refining 6956 atoms. 14992 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1937 (Rfree = 0.000) for 6956 atoms. Found 33 (33 requested) and removed 47 (16 requested) atoms. Cycle 42: After refmac, R = 0.1913 (Rfree = 0.000) for 6901 atoms. Found 32 (32 requested) and removed 36 (16 requested) atoms. Cycle 43: After refmac, R = 0.1870 (Rfree = 0.000) for 6871 atoms. Found 32 (32 requested) and removed 32 (16 requested) atoms. Cycle 44: After refmac, R = 0.1843 (Rfree = 0.000) for 6858 atoms. Found 32 (32 requested) and removed 25 (16 requested) atoms. Cycle 45: After refmac, R = 0.1867 (Rfree = 0.000) for 6844 atoms. Found 32 (32 requested) and removed 36 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.67 Search for helices and strands: 0 residues in 0 chains, 7077 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 7090 seeds are put forward Round 1: 256 peptides, 54 chains. Longest chain 8 peptides. Score 0.242 Round 2: 316 peptides, 58 chains. Longest chain 13 peptides. Score 0.314 Round 3: 302 peptides, 52 chains. Longest chain 16 peptides. Score 0.334 Round 4: 325 peptides, 57 chains. Longest chain 13 peptides. Score 0.335 Round 5: 330 peptides, 56 chains. Longest chain 13 peptides. Score 0.350 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 56, Residues 274, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vl5-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9787 reflections ( 99.93 % complete ) and 16536 restraints for refining 6996 atoms. 15496 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2023 (Rfree = 0.000) for 6996 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.1938 (Rfree = 0.000) for 6940 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2007 (Rfree = 0.000) for 6889 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.1939 (Rfree = 0.000) for 6847 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Writing output files ... TimeTaking 181.2