null Mon 24 Dec 08:05:54 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vme-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vme-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vme-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vme-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vme-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vme-3.4-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 08:05:59 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/noncs/ArpWArp/wArpResults/WorkingDir/1vme-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vme-3.4-parrot-noncs/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 623 and 0 Target number of residues in the AU: 623 Target solvent content: 0.6451 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-3.4-parrot-noncs.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-3.4-parrot-noncs.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 3.400 Wilson plot Bfac: 74.80 12971 reflections ( 99.85 % complete ) and 0 restraints for refining 7308 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3174 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2862 (Rfree = 0.000) for 7308 atoms. Found 55 (55 requested) and removed 77 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 7435 seeds are put forward NCS extension: 0 residues added, 7435 seeds are put forward Round 1: 429 peptides, 78 chains. Longest chain 11 peptides. Score 0.385 Round 2: 506 peptides, 72 chains. Longest chain 15 peptides. Score 0.543 Round 3: 519 peptides, 69 chains. Longest chain 20 peptides. Score 0.578 Round 4: 534 peptides, 64 chains. Longest chain 23 peptides. Score 0.625 Round 5: 532 peptides, 65 chains. Longest chain 26 peptides. Score 0.617 Taking the results from Round 4 Chains 64, Residues 470, Estimated correctness of the model 36.6 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 12983 restraints for refining 5962 atoms. 11053 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2566 (Rfree = 0.000) for 5962 atoms. Found 45 (45 requested) and removed 47 (22 requested) atoms. Cycle 2: After refmac, R = 0.2585 (Rfree = 0.000) for 5878 atoms. Found 35 (45 requested) and removed 43 (22 requested) atoms. Cycle 3: After refmac, R = 0.2390 (Rfree = 0.000) for 5844 atoms. Found 20 (44 requested) and removed 35 (22 requested) atoms. Cycle 4: After refmac, R = 0.2365 (Rfree = 0.000) for 5815 atoms. Found 21 (44 requested) and removed 38 (22 requested) atoms. Cycle 5: After refmac, R = 0.2276 (Rfree = 0.000) for 5788 atoms. Found 27 (43 requested) and removed 31 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 5981 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 5999 seeds are put forward Round 1: 454 peptides, 69 chains. Longest chain 23 peptides. Score 0.487 Round 2: 517 peptides, 65 chains. Longest chain 25 peptides. Score 0.599 Round 3: 520 peptides, 68 chains. Longest chain 20 peptides. Score 0.585 Round 4: 524 peptides, 63 chains. Longest chain 25 peptides. Score 0.618 Round 5: 545 peptides, 65 chains. Longest chain 20 peptides. Score 0.633 Taking the results from Round 5 Chains 68, Residues 480, Estimated correctness of the model 39.1 % 6 chains (57 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 12699 restraints for refining 5965 atoms. 10639 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2473 (Rfree = 0.000) for 5965 atoms. Found 44 (45 requested) and removed 42 (22 requested) atoms. Cycle 7: After refmac, R = 0.2321 (Rfree = 0.000) for 5949 atoms. Found 22 (45 requested) and removed 41 (22 requested) atoms. Cycle 8: After refmac, R = 0.2282 (Rfree = 0.000) for 5922 atoms. Found 15 (44 requested) and removed 32 (22 requested) atoms. Cycle 9: After refmac, R = 0.2248 (Rfree = 0.000) for 5901 atoms. Found 24 (44 requested) and removed 28 (22 requested) atoms. Cycle 10: After refmac, R = 0.2221 (Rfree = 0.000) for 5894 atoms. Found 10 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.25 Search for helices and strands: 0 residues in 0 chains, 6100 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6118 seeds are put forward Round 1: 478 peptides, 73 chains. Longest chain 21 peptides. Score 0.497 Round 2: 527 peptides, 63 chains. Longest chain 29 peptides. Score 0.622 Round 3: 533 peptides, 62 chains. Longest chain 30 peptides. Score 0.635 Round 4: 531 peptides, 56 chains. Longest chain 41 peptides. Score 0.664 Round 5: 536 peptides, 63 chains. Longest chain 28 peptides. Score 0.633 Taking the results from Round 4 Chains 64, Residues 475, Estimated correctness of the model 48.2 % 5 chains (82 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 12184 restraints for refining 5964 atoms. 10020 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2402 (Rfree = 0.000) for 5964 atoms. Found 34 (45 requested) and removed 43 (22 requested) atoms. Cycle 12: After refmac, R = 0.2243 (Rfree = 0.000) for 5938 atoms. Found 21 (44 requested) and removed 27 (22 requested) atoms. Cycle 13: After refmac, R = 0.2191 (Rfree = 0.000) for 5926 atoms. Found 14 (44 requested) and removed 28 (22 requested) atoms. Cycle 14: After refmac, R = 0.2188 (Rfree = 0.000) for 5908 atoms. Found 19 (44 requested) and removed 25 (22 requested) atoms. Cycle 15: After refmac, R = 0.2125 (Rfree = 0.000) for 5898 atoms. Found 11 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.26 Search for helices and strands: 0 residues in 0 chains, 6050 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 6074 seeds are put forward Round 1: 481 peptides, 75 chains. Longest chain 32 peptides. Score 0.488 Round 2: 515 peptides, 67 chains. Longest chain 37 peptides. Score 0.585 Round 3: 502 peptides, 69 chains. Longest chain 22 peptides. Score 0.556 Round 4: 533 peptides, 66 chains. Longest chain 22 peptides. Score 0.613 Round 5: 521 peptides, 64 chains. Longest chain 32 peptides. Score 0.609 Taking the results from Round 4 Chains 67, Residues 467, Estimated correctness of the model 32.9 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 12965 restraints for refining 5964 atoms. 11045 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2352 (Rfree = 0.000) for 5964 atoms. Found 37 (45 requested) and removed 36 (22 requested) atoms. Cycle 17: After refmac, R = 0.2218 (Rfree = 0.000) for 5950 atoms. Found 20 (45 requested) and removed 25 (22 requested) atoms. Cycle 18: After refmac, R = 0.2197 (Rfree = 0.000) for 5930 atoms. Found 19 (44 requested) and removed 24 (22 requested) atoms. Cycle 19: After refmac, R = 0.2113 (Rfree = 0.000) for 5909 atoms. Found 18 (44 requested) and removed 22 (22 requested) atoms. Cycle 20: After refmac, R = 0.2109 (Rfree = 0.000) for 5896 atoms. Found 20 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 6046 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 6067 seeds are put forward Round 1: 450 peptides, 71 chains. Longest chain 32 peptides. Score 0.467 Round 2: 490 peptides, 68 chains. Longest chain 23 peptides. Score 0.545 Round 3: 499 peptides, 65 chains. Longest chain 23 peptides. Score 0.576 Round 4: 506 peptides, 64 chains. Longest chain 42 peptides. Score 0.590 Round 5: 493 peptides, 65 chains. Longest chain 20 peptides. Score 0.568 Taking the results from Round 4 Chains 67, Residues 442, Estimated correctness of the model 25.4 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 12889 restraints for refining 5963 atoms. 11047 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2287 (Rfree = 0.000) for 5963 atoms. Found 30 (45 requested) and removed 39 (22 requested) atoms. Cycle 22: After refmac, R = 0.2165 (Rfree = 0.000) for 5940 atoms. Found 18 (44 requested) and removed 29 (22 requested) atoms. Cycle 23: After refmac, R = 0.2090 (Rfree = 0.000) for 5918 atoms. Found 15 (44 requested) and removed 28 (22 requested) atoms. Cycle 24: After refmac, R = 0.2041 (Rfree = 0.000) for 5899 atoms. Found 14 (44 requested) and removed 24 (22 requested) atoms. Cycle 25: After refmac, R = 0.2033 (Rfree = 0.000) for 5881 atoms. Found 14 (44 requested) and removed 24 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 3.20 Search for helices and strands: 0 residues in 0 chains, 6070 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 6094 seeds are put forward Round 1: 425 peptides, 77 chains. Longest chain 26 peptides. Score 0.385 Round 2: 460 peptides, 67 chains. Longest chain 29 peptides. Score 0.509 Round 3: 479 peptides, 62 chains. Longest chain 29 peptides. Score 0.567 Round 4: 477 peptides, 66 chains. Longest chain 30 peptides. Score 0.540 Round 5: 481 peptides, 63 chains. Longest chain 36 peptides. Score 0.563 Taking the results from Round 3 Chains 63, Residues 417, Estimated correctness of the model 17.5 % 9 chains (83 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 12569 restraints for refining 5965 atoms. 10686 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2281 (Rfree = 0.000) for 5965 atoms. Found 26 (45 requested) and removed 44 (22 requested) atoms. Cycle 27: After refmac, R = 0.2150 (Rfree = 0.000) for 5934 atoms. Found 15 (44 requested) and removed 25 (22 requested) atoms. Cycle 28: After refmac, R = 0.2093 (Rfree = 0.000) for 5915 atoms. Found 10 (44 requested) and removed 23 (22 requested) atoms. Cycle 29: After refmac, R = 0.2037 (Rfree = 0.000) for 5891 atoms. Found 4 (44 requested) and removed 22 (22 requested) atoms. Cycle 30: After refmac, R = 0.2006 (Rfree = 0.000) for 5867 atoms. Found 6 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 3.23 Search for helices and strands: 0 residues in 0 chains, 6025 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 6048 seeds are put forward Round 1: 417 peptides, 71 chains. Longest chain 15 peptides. Score 0.415 Round 2: 461 peptides, 64 chains. Longest chain 22 peptides. Score 0.530 Round 3: 445 peptides, 65 chains. Longest chain 22 peptides. Score 0.500 Round 4: 451 peptides, 61 chains. Longest chain 22 peptides. Score 0.534 Round 5: 430 peptides, 61 chains. Longest chain 24 peptides. Score 0.504 Taking the results from Round 4 Chains 63, Residues 390, Estimated correctness of the model 5.7 % 5 chains (49 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 13020 restraints for refining 5965 atoms. 11346 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2313 (Rfree = 0.000) for 5965 atoms. Found 31 (45 requested) and removed 34 (22 requested) atoms. Cycle 32: After refmac, R = 0.2183 (Rfree = 0.000) for 5950 atoms. Found 10 (45 requested) and removed 25 (22 requested) atoms. Cycle 33: After refmac, R = 0.2084 (Rfree = 0.000) for 5931 atoms. Found 6 (44 requested) and removed 22 (22 requested) atoms. Cycle 34: After refmac, R = 0.2069 (Rfree = 0.000) for 5908 atoms. Found 8 (44 requested) and removed 22 (22 requested) atoms. Cycle 35: After refmac, R = 0.2046 (Rfree = 0.000) for 5893 atoms. Found 6 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 6027 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 6054 seeds are put forward Round 1: 384 peptides, 67 chains. Longest chain 24 peptides. Score 0.388 Round 2: 425 peptides, 66 chains. Longest chain 23 peptides. Score 0.462 Round 3: 423 peptides, 56 chains. Longest chain 24 peptides. Score 0.526 Round 4: 433 peptides, 59 chains. Longest chain 22 peptides. Score 0.521 Round 5: 417 peptides, 62 chains. Longest chain 18 peptides. Score 0.477 Taking the results from Round 3 Chains 58, Residues 367, Estimated correctness of the model 2.7 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 13372 restraints for refining 5965 atoms. 11922 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2214 (Rfree = 0.000) for 5965 atoms. Found 27 (45 requested) and removed 25 (22 requested) atoms. Cycle 37: After refmac, R = 0.2141 (Rfree = 0.000) for 5957 atoms. Found 10 (45 requested) and removed 24 (22 requested) atoms. Cycle 38: After refmac, R = 0.2099 (Rfree = 0.000) for 5941 atoms. Found 8 (44 requested) and removed 23 (22 requested) atoms. Cycle 39: After refmac, R = 0.2193 (Rfree = 0.000) for 5918 atoms. Found 25 (44 requested) and removed 22 (22 requested) atoms. Cycle 40: After refmac, R = 0.2028 (Rfree = 0.000) for 5919 atoms. Found 6 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 6064 seeds are put forward NCS extension: 37 residues added (1 deleted due to clashes), 6101 seeds are put forward Round 1: 367 peptides, 66 chains. Longest chain 14 peptides. Score 0.366 Round 2: 399 peptides, 65 chains. Longest chain 21 peptides. Score 0.428 Round 3: 410 peptides, 64 chains. Longest chain 16 peptides. Score 0.453 Round 4: 411 peptides, 64 chains. Longest chain 19 peptides. Score 0.454 Round 5: 406 peptides, 59 chains. Longest chain 17 peptides. Score 0.481 Taking the results from Round 5 Chains 59, Residues 347, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 12971 reflections ( 99.85 % complete ) and 13648 restraints for refining 5965 atoms. 12294 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2307 (Rfree = 0.000) for 5965 atoms. Found 33 (45 requested) and removed 28 (22 requested) atoms. Cycle 42: After refmac, R = 0.2182 (Rfree = 0.000) for 5957 atoms. Found 21 (45 requested) and removed 25 (22 requested) atoms. Cycle 43: After refmac, R = 0.2112 (Rfree = 0.000) for 5953 atoms. Found 18 (44 requested) and removed 23 (22 requested) atoms. Cycle 44: After refmac, R = 0.1999 (Rfree = 0.000) for 5944 atoms. Found 11 (44 requested) and removed 23 (22 requested) atoms. Cycle 45: After refmac, R = 0.1948 (Rfree = 0.000) for 5927 atoms. Found 3 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 3.24 Search for helices and strands: 0 residues in 0 chains, 6070 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 6098 seeds are put forward Round 1: 362 peptides, 70 chains. Longest chain 11 peptides. Score 0.327 Round 2: 405 peptides, 67 chains. Longest chain 20 peptides. Score 0.423 Round 3: 402 peptides, 56 chains. Longest chain 22 peptides. Score 0.495 Round 4: 409 peptides, 61 chains. Longest chain 18 peptides. Score 0.472 Round 5: 401 peptides, 59 chains. Longest chain 19 peptides. Score 0.473 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 57, Residues 346, Estimated correctness of the model 0.0 % 5 chains (28 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 1vme-3_warpNtrace.pdb as input Building loops using Loopy2018 57 chains (346 residues) following loop building 5 chains (28 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12971 reflections ( 99.85 % complete ) and 13479 restraints for refining 5965 atoms. 12056 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2211 (Rfree = 0.000) for 5965 atoms. Found 0 (45 requested) and removed 21 (22 requested) atoms. Cycle 47: After refmac, R = 0.2126 (Rfree = 0.000) for 5938 atoms. Found 0 (44 requested) and removed 9 (22 requested) atoms. Cycle 48: After refmac, R = 0.2046 (Rfree = 0.000) for 5921 atoms. Found 0 (44 requested) and removed 8 (22 requested) atoms. Cycle 49: After refmac, R = 0.2073 (Rfree = 0.000) for 5905 atoms. Found 0 (44 requested) and removed 10 (22 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:11:50 GMT 2018 Job finished. TimeTaking 65.93 Used memory is bytes: 12661120