Tue 25 Dec 19:27:55 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 1vrb-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vrb-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vrb-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vrb-3.4-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/1vrb-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vrb-3.4-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 ============================================================ Tue 25 Dec 19:28:05 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/1vrb-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vrb-3.4-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 927 and 0 Target number of residues in the AU: 927 Target solvent content: 0.6462 Checking the provided sequence file Detected sequence length: 342 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1368 Adjusted target solvent content: 0.48 Input MTZ file: 1vrb-3.4-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: 47.576 104.273 285.843 90.000 90.000 90.000 Input sequence file: 1vrb-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 10944 target number of atoms Had to go as low as 0.60 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: 48.979 3.400 Wilson plot Bfac: 75.79 20098 reflections ( 98.18 % complete ) and 0 restraints for refining 12133 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3368 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3035 (Rfree = 0.000) for 12133 atoms. Found 91 (91 requested) and removed 182 (45 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 12275 seeds are put forward NCS extension: 0 residues added, 12275 seeds are put forward Round 1: 472 peptides, 94 chains. Longest chain 15 peptides. Score 0.297 Round 2: 591 peptides, 101 chains. Longest chain 17 peptides. Score 0.404 Round 3: 648 peptides, 108 chains. Longest chain 22 peptides. Score 0.433 Round 4: 652 peptides, 107 chains. Longest chain 20 peptides. Score 0.442 Round 5: 669 peptides, 104 chains. Longest chain 15 peptides. Score 0.474 Taking the results from Round 5 Chains 104, Residues 565, Estimated correctness of the model 0.0 % 8 chains (33 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 20098 reflections ( 98.18 % complete ) and 23483 restraints for refining 9948 atoms. 21250 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2580 (Rfree = 0.000) for 9948 atoms. Found 44 (75 requested) and removed 79 (37 requested) atoms. Cycle 2: After refmac, R = 0.2528 (Rfree = 0.000) for 9806 atoms. Found 29 (74 requested) and removed 65 (37 requested) atoms. Cycle 3: After refmac, R = 0.2301 (Rfree = 0.000) for 9696 atoms. Found 27 (73 requested) and removed 52 (36 requested) atoms. Cycle 4: After refmac, R = 0.2238 (Rfree = 0.000) for 9625 atoms. Found 22 (73 requested) and removed 48 (36 requested) atoms. Cycle 5: After refmac, R = 0.2224 (Rfree = 0.000) for 9572 atoms. Found 18 (72 requested) and removed 48 (36 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 9901 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 9918 seeds are put forward Round 1: 551 peptides, 107 chains. Longest chain 11 peptides. Score 0.327 Round 2: 621 peptides, 101 chains. Longest chain 14 peptides. Score 0.437 Round 3: 664 peptides, 102 chains. Longest chain 20 peptides. Score 0.477 Round 4: 656 peptides, 98 chains. Longest chain 18 peptides. Score 0.487 Round 5: 678 peptides, 105 chains. Longest chain 18 peptides. Score 0.478 Taking the results from Round 4 Chains 98, Residues 558, Estimated correctness of the model 0.0 % 5 chains (23 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 22910 restraints for refining 9877 atoms. 20719 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2559 (Rfree = 0.000) for 9877 atoms. Found 68 (74 requested) and removed 80 (37 requested) atoms. Cycle 7: After refmac, R = 0.2351 (Rfree = 0.000) for 9818 atoms. Found 23 (74 requested) and removed 55 (37 requested) atoms. Cycle 8: After refmac, R = 0.2400 (Rfree = 0.000) for 9753 atoms. Found 37 (73 requested) and removed 57 (36 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2196 (Rfree = 0.000) for 9705 atoms. Found 22 (73 requested) and removed 57 (36 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2160 (Rfree = 0.000) for 9653 atoms. Found 11 (73 requested) and removed 52 (36 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.42 Search for helices and strands: 0 residues in 0 chains, 9963 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 9982 seeds are put forward Round 1: 576 peptides, 114 chains. Longest chain 12 peptides. Score 0.321 Round 2: 638 peptides, 104 chains. Longest chain 26 peptides. Score 0.441 Round 3: 634 peptides, 100 chains. Longest chain 17 peptides. Score 0.455 Round 4: 661 peptides, 100 chains. Longest chain 17 peptides. Score 0.483 Round 5: 667 peptides, 101 chains. Longest chain 20 peptides. Score 0.485 Taking the results from Round 5 Chains 103, Residues 566, Estimated correctness of the model 0.0 % 8 chains (57 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 22774 restraints for refining 9951 atoms. 20438 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2526 (Rfree = 0.000) for 9951 atoms. Found 68 (75 requested) and removed 69 (37 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2306 (Rfree = 0.000) for 9900 atoms. Found 21 (75 requested) and removed 59 (37 requested) atoms. Cycle 13: After refmac, R = 0.2373 (Rfree = 0.000) for 9834 atoms. Found 40 (74 requested) and removed 52 (37 requested) atoms. Cycle 14: After refmac, R = 0.2254 (Rfree = 0.000) for 9801 atoms. Found 35 (74 requested) and removed 52 (37 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2069 (Rfree = 0.000) for 9763 atoms. Found 17 (73 requested) and removed 42 (36 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 10029 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 10043 seeds are put forward Round 1: 562 peptides, 107 chains. Longest chain 17 peptides. Score 0.340 Round 2: 640 peptides, 109 chains. Longest chain 17 peptides. Score 0.420 Round 3: 636 peptides, 106 chains. Longest chain 19 peptides. Score 0.429 Round 4: 672 peptides, 108 chains. Longest chain 20 peptides. Score 0.459 Round 5: 670 peptides, 103 chains. Longest chain 20 peptides. Score 0.479 Taking the results from Round 5 Chains 106, Residues 567, Estimated correctness of the model 0.0 % 9 chains (57 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 22801 restraints for refining 9949 atoms. 20485 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2475 (Rfree = 0.000) for 9949 atoms. Found 69 (75 requested) and removed 60 (37 requested) atoms. Cycle 17: After refmac, R = 0.2294 (Rfree = 0.000) for 9931 atoms. Found 33 (75 requested) and removed 47 (37 requested) atoms. Cycle 18: After refmac, R = 0.2245 (Rfree = 0.000) for 9892 atoms. Found 34 (74 requested) and removed 54 (37 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2108 (Rfree = 0.000) for 9847 atoms. Found 23 (74 requested) and removed 48 (37 requested) atoms. Cycle 20: After refmac, R = 0.2111 (Rfree = 0.000) for 9801 atoms. Found 36 (74 requested) and removed 48 (37 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 3.44 Search for helices and strands: 0 residues in 0 chains, 10077 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 10098 seeds are put forward Round 1: 536 peptides, 102 chains. Longest chain 14 peptides. Score 0.334 Round 2: 617 peptides, 99 chains. Longest chain 15 peptides. Score 0.442 Round 3: 610 peptides, 98 chains. Longest chain 17 peptides. Score 0.439 Round 4: 630 peptides, 98 chains. Longest chain 20 peptides. Score 0.460 Round 5: 601 peptides, 91 chains. Longest chain 21 peptides. Score 0.462 Taking the results from Round 5 Chains 93, Residues 510, Estimated correctness of the model 0.0 % 6 chains (34 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 23241 restraints for refining 9951 atoms. 21204 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2409 (Rfree = 0.000) for 9951 atoms. Found 67 (75 requested) and removed 53 (37 requested) atoms. Cycle 22: After refmac, R = 0.2319 (Rfree = 0.000) for 9935 atoms. Found 55 (75 requested) and removed 56 (37 requested) atoms. Cycle 23: After refmac, R = 0.2044 (Rfree = 0.000) for 9892 atoms. Found 27 (75 requested) and removed 47 (37 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1977 (Rfree = 0.000) for 9844 atoms. Found 21 (74 requested) and removed 46 (37 requested) atoms. Cycle 25: After refmac, R = 0.1964 (Rfree = 0.000) for 9803 atoms. Found 17 (74 requested) and removed 44 (37 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.43 Search for helices and strands: 0 residues in 0 chains, 10059 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 10080 seeds are put forward Round 1: 490 peptides, 97 chains. Longest chain 12 peptides. Score 0.304 Round 2: 602 peptides, 100 chains. Longest chain 18 peptides. Score 0.421 Round 3: 615 peptides, 98 chains. Longest chain 17 peptides. Score 0.444 Round 4: 592 peptides, 92 chains. Longest chain 18 peptides. Score 0.448 Round 5: 581 peptides, 94 chains. Longest chain 13 peptides. Score 0.426 Taking the results from Round 4 Chains 92, Residues 500, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 23226 restraints for refining 9950 atoms. 21294 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2317 (Rfree = 0.000) for 9950 atoms. Found 75 (75 requested) and removed 49 (37 requested) atoms. Cycle 27: After refmac, R = 0.2137 (Rfree = 0.000) for 9925 atoms. Found 48 (75 requested) and removed 55 (37 requested) atoms. Cycle 28: After refmac, R = 0.1997 (Rfree = 0.000) for 9900 atoms. Found 21 (74 requested) and removed 44 (37 requested) atoms. Cycle 29: After refmac, R = 0.1986 (Rfree = 0.000) for 9869 atoms. Found 22 (74 requested) and removed 41 (37 requested) atoms. Cycle 30: After refmac, R = 0.1986 (Rfree = 0.000) for 9835 atoms. Found 24 (74 requested) and removed 46 (37 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 10062 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 10081 seeds are put forward Round 1: 451 peptides, 93 chains. Longest chain 13 peptides. Score 0.275 Round 2: 529 peptides, 91 chains. Longest chain 14 peptides. Score 0.382 Round 3: 538 peptides, 89 chains. Longest chain 18 peptides. Score 0.403 Round 4: 581 peptides, 93 chains. Longest chain 17 peptides. Score 0.431 Round 5: 569 peptides, 89 chains. Longest chain 18 peptides. Score 0.437 Taking the results from Round 5 Chains 89, Residues 480, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 23335 restraints for refining 9950 atoms. 21504 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2192 (Rfree = 0.000) for 9950 atoms. Found 69 (75 requested) and removed 65 (37 requested) atoms. Cycle 32: After refmac, R = 0.2019 (Rfree = 0.000) for 9933 atoms. Found 31 (75 requested) and removed 50 (37 requested) atoms. Cycle 33: After refmac, R = 0.1992 (Rfree = 0.000) for 9891 atoms. Found 12 (74 requested) and removed 49 (37 requested) atoms. Cycle 34: After refmac, R = 0.1923 (Rfree = 0.000) for 9839 atoms. Found 27 (74 requested) and removed 45 (37 requested) atoms. Cycle 35: After refmac, R = 0.1924 (Rfree = 0.000) for 9812 atoms. Found 21 (74 requested) and removed 49 (37 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 3.42 Search for helices and strands: 0 residues in 0 chains, 10016 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 10046 seeds are put forward Round 1: 432 peptides, 90 chains. Longest chain 19 peptides. Score 0.267 Round 2: 511 peptides, 92 chains. Longest chain 15 peptides. Score 0.356 Round 3: 558 peptides, 93 chains. Longest chain 21 peptides. Score 0.405 Round 4: 559 peptides, 90 chains. Longest chain 16 peptides. Score 0.421 Round 5: 556 peptides, 89 chains. Longest chain 19 peptides. Score 0.423 Taking the results from Round 5 Chains 90, Residues 467, Estimated correctness of the model 0.0 % 7 chains (41 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 22911 restraints for refining 9951 atoms. 21004 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2287 (Rfree = 0.000) for 9951 atoms. Found 64 (75 requested) and removed 49 (37 requested) atoms. Cycle 37: After refmac, R = 0.2152 (Rfree = 0.000) for 9938 atoms. Found 63 (75 requested) and removed 48 (37 requested) atoms. Cycle 38: After refmac, R = 0.2124 (Rfree = 0.000) for 9926 atoms. Found 59 (75 requested) and removed 46 (37 requested) atoms. Cycle 39: After refmac, R = 0.2051 (Rfree = 0.000) for 9917 atoms. Found 34 (75 requested) and removed 48 (37 requested) atoms. Cycle 40: After refmac, R = 0.2045 (Rfree = 0.000) for 9891 atoms. Found 44 (74 requested) and removed 42 (37 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 10150 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 10163 seeds are put forward Round 1: 406 peptides, 85 chains. Longest chain 9 peptides. Score 0.260 Round 2: 453 peptides, 83 chains. Longest chain 15 peptides. Score 0.332 Round 3: 471 peptides, 86 chains. Longest chain 16 peptides. Score 0.338 Round 4: 465 peptides, 80 chains. Longest chain 17 peptides. Score 0.363 Round 5: 460 peptides, 80 chains. Longest chain 18 peptides. Score 0.357 Taking the results from Round 4 Chains 82, Residues 385, Estimated correctness of the model 0.0 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ 20098 reflections ( 98.18 % complete ) and 23553 restraints for refining 9950 atoms. 22000 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2145 (Rfree = 0.000) for 9950 atoms. Found 66 (75 requested) and removed 44 (37 requested) atoms. Cycle 42: After refmac, R = 0.2007 (Rfree = 0.000) for 9952 atoms. Found 37 (75 requested) and removed 42 (37 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2018 (Rfree = 0.000) for 9937 atoms. Found 37 (75 requested) and removed 42 (37 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1933 (Rfree = 0.000) for 9920 atoms. Found 33 (74 requested) and removed 42 (37 requested) atoms. Cycle 45: After refmac, R = 0.1900 (Rfree = 0.000) for 9897 atoms. Found 22 (74 requested) and removed 39 (37 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.39 Search for helices and strands: 0 residues in 0 chains, 10129 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 10143 seeds are put forward Round 1: 377 peptides, 77 chains. Longest chain 10 peptides. Score 0.267 Round 2: 396 peptides, 71 chains. Longest chain 12 peptides. Score 0.326 Round 3: 420 peptides, 71 chains. Longest chain 13 peptides. Score 0.356 Round 4: 423 peptides, 69 chains. Longest chain 19 peptides. Score 0.371 Round 5: 435 peptides, 73 chains. Longest chain 16 peptides. Score 0.364 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 69, Residues 354, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 1vrb-3_warpNtrace.pdb as input Building loops using Loopy2018 69 chains (354 residues) following loop building 2 chains (15 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20098 reflections ( 98.18 % complete ) and 23764 restraints for refining 9951 atoms. 22370 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2080 (Rfree = 0.000) for 9951 atoms. Found 0 (75 requested) and removed 37 (37 requested) atoms. Cycle 47: After refmac, R = 0.1964 (Rfree = 0.000) for 9899 atoms. Found 0 (74 requested) and removed 37 (37 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 48: After refmac, R = 0.1949 (Rfree = 0.000) for 9854 atoms. Found 0 (74 requested) and removed 36 (37 requested) atoms. Cycle 49: After refmac, R = 0.1919 (Rfree = 0.000) for 9812 atoms. Found 0 (74 requested) and removed 20 (37 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 21:41:17 GMT 2018 Job finished. Failed to save intermediate PDB TimeTaking 133.36