Mon 24 Dec 01:13:42 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 1vme-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vme-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vme-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vme-3.6-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/1vme-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vme-3.6-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 ============================================================ Mon 24 Dec 01:13:47 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/1vme-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vme-3.6-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 607 and 0 Target number of residues in the AU: 607 Target solvent content: 0.6542 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-3.6-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: 55.242 95.831 90.130 90.000 95.426 90.000 Input sequence file: 1vme-3.6-parrot-mrncs.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 3.600 Wilson plot Bfac: 80.80 10948 reflections ( 99.82 % complete ) and 0 restraints for refining 7240 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3153 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3071 (Rfree = 0.000) for 7240 atoms. Found 46 (46 requested) and removed 52 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.41 Search for helices and strands: 0 residues in 0 chains, 7380 seeds are put forward NCS extension: 0 residues added, 7380 seeds are put forward Round 1: 409 peptides, 74 chains. Longest chain 11 peptides. Score 0.380 Round 2: 474 peptides, 66 chains. Longest chain 18 peptides. Score 0.535 Round 3: 468 peptides, 64 chains. Longest chain 19 peptides. Score 0.539 Round 4: 493 peptides, 63 chains. Longest chain 24 peptides. Score 0.579 Round 5: 504 peptides, 66 chains. Longest chain 25 peptides. Score 0.576 Taking the results from Round 4 Chains 66, Residues 430, Estimated correctness of the model 6.3 % 5 chains (51 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 12835 restraints for refining 5943 atoms. 11000 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2552 (Rfree = 0.000) for 5943 atoms. Found 32 (38 requested) and removed 52 (19 requested) atoms. Cycle 2: After refmac, R = 0.2506 (Rfree = 0.000) for 5842 atoms. Found 34 (37 requested) and removed 40 (18 requested) atoms. Cycle 3: After refmac, R = 0.2395 (Rfree = 0.000) for 5807 atoms. Found 22 (37 requested) and removed 47 (18 requested) atoms. Cycle 4: After refmac, R = 0.2366 (Rfree = 0.000) for 5746 atoms. Found 27 (37 requested) and removed 39 (18 requested) atoms. Cycle 5: After refmac, R = 0.2341 (Rfree = 0.000) for 5715 atoms. Found 27 (36 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 3.47 Search for helices and strands: 0 residues in 0 chains, 5922 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 5940 seeds are put forward Round 1: 433 peptides, 71 chains. Longest chain 14 peptides. Score 0.441 Round 2: 480 peptides, 64 chains. Longest chain 21 peptides. Score 0.556 Round 3: 495 peptides, 68 chains. Longest chain 21 peptides. Score 0.552 Round 4: 493 peptides, 71 chains. Longest chain 26 peptides. Score 0.531 Round 5: 478 peptides, 64 chains. Longest chain 18 peptides. Score 0.553 Taking the results from Round 2 Chains 65, Residues 416, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 13128 restraints for refining 5895 atoms. 11469 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2436 (Rfree = 0.000) for 5895 atoms. Found 29 (37 requested) and removed 56 (18 requested) atoms. Cycle 7: After refmac, R = 0.2317 (Rfree = 0.000) for 5840 atoms. Found 37 (37 requested) and removed 45 (18 requested) atoms. Cycle 8: After refmac, R = 0.2354 (Rfree = 0.000) for 5815 atoms. Found 32 (37 requested) and removed 42 (18 requested) atoms. Cycle 9: After refmac, R = 0.2280 (Rfree = 0.000) for 5789 atoms. Found 37 (37 requested) and removed 40 (18 requested) atoms. Cycle 10: After refmac, R = 0.1983 (Rfree = 0.000) for 5771 atoms. Found 9 (37 requested) and removed 29 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.40 Search for helices and strands: 0 residues in 0 chains, 5972 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 5995 seeds are put forward Round 1: 421 peptides, 68 chains. Longest chain 18 peptides. Score 0.442 Round 2: 474 peptides, 66 chains. Longest chain 16 peptides. Score 0.535 Round 3: 476 peptides, 65 chains. Longest chain 20 peptides. Score 0.544 Round 4: 485 peptides, 64 chains. Longest chain 18 peptides. Score 0.563 Round 5: 478 peptides, 65 chains. Longest chain 18 peptides. Score 0.547 Taking the results from Round 4 Chains 66, Residues 421, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 13126 restraints for refining 5947 atoms. 11421 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2293 (Rfree = 0.000) for 5947 atoms. Found 33 (38 requested) and removed 46 (19 requested) atoms. Cycle 12: After refmac, R = 0.2255 (Rfree = 0.000) for 5909 atoms. Found 29 (38 requested) and removed 36 (19 requested) atoms. Cycle 13: After refmac, R = 0.2207 (Rfree = 0.000) for 5873 atoms. Found 21 (37 requested) and removed 33 (18 requested) atoms. Cycle 14: After refmac, R = 0.1945 (Rfree = 0.000) for 5841 atoms. Found 3 (37 requested) and removed 28 (18 requested) atoms. Cycle 15: After refmac, R = 0.1926 (Rfree = 0.000) for 5805 atoms. Found 5 (37 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.61 3.47 Search for helices and strands: 0 residues in 0 chains, 5974 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5990 seeds are put forward Round 1: 420 peptides, 77 chains. Longest chain 11 peptides. Score 0.377 Round 2: 456 peptides, 65 chains. Longest chain 17 peptides. Score 0.516 Round 3: 474 peptides, 66 chains. Longest chain 15 peptides. Score 0.535 Round 4: 475 peptides, 61 chains. Longest chain 22 peptides. Score 0.568 Round 5: 502 peptides, 71 chains. Longest chain 20 peptides. Score 0.544 Taking the results from Round 4 Chains 63, Residues 414, Estimated correctness of the model 1.7 % 4 chains (44 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 12932 restraints for refining 5946 atoms. 11173 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2392 (Rfree = 0.000) for 5946 atoms. Found 34 (38 requested) and removed 45 (19 requested) atoms. Cycle 17: After refmac, R = 0.2342 (Rfree = 0.000) for 5907 atoms. Found 38 (38 requested) and removed 41 (19 requested) atoms. Cycle 18: After refmac, R = 0.2246 (Rfree = 0.000) for 5887 atoms. Found 35 (37 requested) and removed 32 (18 requested) atoms. Cycle 19: After refmac, R = 0.1952 (Rfree = 0.000) for 5880 atoms. Found 13 (37 requested) and removed 22 (18 requested) atoms. Cycle 20: After refmac, R = 0.1920 (Rfree = 0.000) for 5862 atoms. Found 13 (37 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.42 Search for helices and strands: 0 residues in 0 chains, 6111 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 6131 seeds are put forward Round 1: 394 peptides, 70 chains. Longest chain 13 peptides. Score 0.383 Round 2: 446 peptides, 63 chains. Longest chain 14 peptides. Score 0.514 Round 3: 456 peptides, 61 chains. Longest chain 29 peptides. Score 0.541 Round 4: 442 peptides, 58 chains. Longest chain 29 peptides. Score 0.541 Round 5: 465 peptides, 58 chains. Longest chain 38 peptides. Score 0.572 Taking the results from Round 5 Chains 62, Residues 407, Estimated correctness of the model 3.4 % 5 chains (46 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 12739 restraints for refining 5945 atoms. 11017 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2333 (Rfree = 0.000) for 5945 atoms. Found 33 (38 requested) and removed 45 (19 requested) atoms. Cycle 22: After refmac, R = 0.2186 (Rfree = 0.000) for 5895 atoms. Found 27 (38 requested) and removed 27 (19 requested) atoms. Cycle 23: After refmac, R = 0.2172 (Rfree = 0.000) for 5869 atoms. Found 34 (37 requested) and removed 29 (18 requested) atoms. Cycle 24: After refmac, R = 0.2102 (Rfree = 0.000) for 5858 atoms. Found 27 (37 requested) and removed 30 (18 requested) atoms. Cycle 25: After refmac, R = 0.2063 (Rfree = 0.000) for 5846 atoms. Found 20 (37 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.37 Search for helices and strands: 0 residues in 0 chains, 6012 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6031 seeds are put forward Round 1: 386 peptides, 68 chains. Longest chain 20 peptides. Score 0.384 Round 2: 443 peptides, 69 chains. Longest chain 16 peptides. Score 0.470 Round 3: 429 peptides, 63 chains. Longest chain 17 peptides. Score 0.489 Round 4: 441 peptides, 61 chains. Longest chain 18 peptides. Score 0.520 Round 5: 444 peptides, 58 chains. Longest chain 20 peptides. Score 0.544 Taking the results from Round 5 Chains 60, Residues 386, Estimated correctness of the model 0.0 % 6 chains (55 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 12900 restraints for refining 5946 atoms. 11230 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2477 (Rfree = 0.000) for 5946 atoms. Found 38 (38 requested) and removed 43 (19 requested) atoms. Cycle 27: After refmac, R = 0.2330 (Rfree = 0.000) for 5909 atoms. Found 38 (38 requested) and removed 36 (19 requested) atoms. Cycle 28: After refmac, R = 0.2335 (Rfree = 0.000) for 5886 atoms. Found 37 (37 requested) and removed 37 (18 requested) atoms. Cycle 29: After refmac, R = 0.2270 (Rfree = 0.000) for 5867 atoms. Found 37 (37 requested) and removed 32 (18 requested) atoms. Cycle 30: After refmac, R = 0.2312 (Rfree = 0.000) for 5855 atoms. Found 37 (37 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.43 Search for helices and strands: 0 residues in 0 chains, 6011 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 6035 seeds are put forward Round 1: 331 peptides, 59 chains. Longest chain 12 peptides. Score 0.356 Round 2: 380 peptides, 57 chains. Longest chain 14 peptides. Score 0.454 Round 3: 401 peptides, 59 chains. Longest chain 16 peptides. Score 0.473 Round 4: 414 peptides, 57 chains. Longest chain 16 peptides. Score 0.507 Round 5: 423 peptides, 63 chains. Longest chain 17 peptides. Score 0.480 Taking the results from Round 4 Chains 57, Residues 357, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 13456 restraints for refining 5947 atoms. 12045 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2369 (Rfree = 0.000) for 5947 atoms. Found 32 (38 requested) and removed 32 (19 requested) atoms. Cycle 32: After refmac, R = 0.2384 (Rfree = 0.000) for 5934 atoms. Found 38 (38 requested) and removed 35 (19 requested) atoms. Cycle 33: After refmac, R = 0.2383 (Rfree = 0.000) for 5922 atoms. Found 37 (38 requested) and removed 37 (19 requested) atoms. Cycle 34: After refmac, R = 0.2320 (Rfree = 0.000) for 5903 atoms. Found 37 (37 requested) and removed 27 (18 requested) atoms. Cycle 35: After refmac, R = 0.2355 (Rfree = 0.000) for 5895 atoms. Found 37 (37 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.47 Search for helices and strands: 0 residues in 0 chains, 6063 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 6077 seeds are put forward Round 1: 333 peptides, 67 chains. Longest chain 12 peptides. Score 0.297 Round 2: 355 peptides, 56 chains. Longest chain 18 peptides. Score 0.420 Round 3: 385 peptides, 65 chains. Longest chain 13 peptides. Score 0.404 Round 4: 380 peptides, 58 chains. Longest chain 14 peptides. Score 0.447 Round 5: 401 peptides, 66 chains. Longest chain 12 peptides. Score 0.424 Taking the results from Round 4 Chains 58, Residues 322, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 13522 restraints for refining 5946 atoms. 12216 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2422 (Rfree = 0.000) for 5946 atoms. Found 38 (38 requested) and removed 40 (19 requested) atoms. Cycle 37: After refmac, R = 0.2326 (Rfree = 0.000) for 5933 atoms. Found 37 (38 requested) and removed 32 (19 requested) atoms. Cycle 38: After refmac, R = 0.2233 (Rfree = 0.000) for 5925 atoms. Found 27 (38 requested) and removed 32 (19 requested) atoms. Cycle 39: After refmac, R = 0.1958 (Rfree = 0.000) for 5914 atoms. Found 5 (37 requested) and removed 24 (18 requested) atoms. Cycle 40: After refmac, R = 0.1889 (Rfree = 0.000) for 5889 atoms. Found 7 (37 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.38 Search for helices and strands: 0 residues in 0 chains, 6029 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 6043 seeds are put forward Round 1: 307 peptides, 62 chains. Longest chain 12 peptides. Score 0.287 Round 2: 346 peptides, 60 chains. Longest chain 13 peptides. Score 0.375 Round 3: 360 peptides, 57 chains. Longest chain 17 peptides. Score 0.421 Round 4: 359 peptides, 61 chains. Longest chain 19 peptides. Score 0.390 Round 5: 370 peptides, 61 chains. Longest chain 16 peptides. Score 0.409 Taking the results from Round 3 Chains 57, Residues 303, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 10948 reflections ( 99.82 % complete ) and 13608 restraints for refining 5947 atoms. 12402 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2318 (Rfree = 0.000) for 5947 atoms. Found 31 (38 requested) and removed 29 (19 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2323 (Rfree = 0.000) for 5940 atoms. Found 38 (38 requested) and removed 33 (19 requested) atoms. Cycle 43: After refmac, R = 0.2270 (Rfree = 0.000) for 5934 atoms. Found 38 (38 requested) and removed 29 (19 requested) atoms. Cycle 44: After refmac, R = 0.1965 (Rfree = 0.000) for 5935 atoms. Found 11 (38 requested) and removed 25 (19 requested) atoms. Cycle 45: After refmac, R = 0.1916 (Rfree = 0.000) for 5913 atoms. Found 10 (37 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.40 Search for helices and strands: 0 residues in 0 chains, 6086 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6108 seeds are put forward Round 1: 278 peptides, 62 chains. Longest chain 8 peptides. Score 0.230 Round 2: 306 peptides, 55 chains. Longest chain 12 peptides. Score 0.342 Round 3: 329 peptides, 59 chains. Longest chain 15 peptides. Score 0.352 Round 4: 332 peptides, 52 chains. Longest chain 17 peptides. Score 0.411 Round 5: 331 peptides, 53 chains. Longest chain 16 peptides. Score 0.402 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 53, Residues 280, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vme-3_warpNtrace.pdb as input Building loops using Loopy2018 53 chains (280 residues) following loop building 3 chains (15 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10948 reflections ( 99.82 % complete ) and 13720 restraints for refining 5946 atoms. 12618 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2283 (Rfree = 0.000) for 5946 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2343 (Rfree = 0.000) for 5912 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.2449 (Rfree = 0.000) for 5885 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2312 (Rfree = 0.000) for 5849 atoms. TimeTaking 72.98