Mon 24 Dec 00:26:55 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 2fqp-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fqp-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fqp-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.8-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/2fqp-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.8-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 00:27:00 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/2fqp-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.8-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 225 and 0 Target number of residues in the AU: 225 Target solvent content: 0.6404 Checking the provided sequence file Detected sequence length: 97 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 388 Adjusted target solvent content: 0.38 Input MTZ file: 2fqp-3.8-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: 35.909 92.640 53.056 90.000 106.409 90.000 Input sequence file: 2fqp-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3104 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: 50.895 3.801 Wilson plot Bfac: 71.89 2715 reflections ( 81.65 % complete ) and 0 restraints for refining 3442 atoms. Observations/parameters ratio is 0.20 ------------------------------------------------------ Starting model: R = 0.3224 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2829 (Rfree = 0.000) for 3442 atoms. Found 18 (18 requested) and removed 243 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.97 Search for helices and strands: 0 residues in 0 chains, 3264 seeds are put forward NCS extension: 0 residues added, 3264 seeds are put forward Round 1: 88 peptides, 20 chains. Longest chain 6 peptides. Score 0.216 Round 2: 110 peptides, 23 chains. Longest chain 7 peptides. Score 0.270 Round 3: 133 peptides, 26 chains. Longest chain 9 peptides. Score 0.324 Round 4: 131 peptides, 26 chains. Longest chain 9 peptides. Score 0.314 Round 5: 128 peptides, 25 chains. Longest chain 9 peptides. Score 0.320 Taking the results from Round 3 Chains 26, Residues 107, Estimated correctness of the model 0.0 % 4 chains (15 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 6609 restraints for refining 2782 atoms. 6175 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2061 (Rfree = 0.000) for 2782 atoms. Found 9 (15 requested) and removed 27 (7 requested) atoms. Cycle 2: After refmac, R = 0.2086 (Rfree = 0.000) for 2721 atoms. Found 12 (15 requested) and removed 19 (7 requested) atoms. Cycle 3: After refmac, R = 0.1466 (Rfree = 0.000) for 2692 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. Cycle 4: After refmac, R = 0.1400 (Rfree = 0.000) for 2678 atoms. Found 4 (14 requested) and removed 8 (7 requested) atoms. Cycle 5: After refmac, R = 0.1383 (Rfree = 0.000) for 2663 atoms. Found 1 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.99 Search for helices and strands: 0 residues in 0 chains, 2709 seeds are put forward NCS extension: 0 residues added, 2709 seeds are put forward Round 1: 90 peptides, 21 chains. Longest chain 6 peptides. Score 0.203 Round 2: 125 peptides, 27 chains. Longest chain 6 peptides. Score 0.261 Round 3: 129 peptides, 26 chains. Longest chain 7 peptides. Score 0.304 Round 4: 128 peptides, 23 chains. Longest chain 11 peptides. Score 0.363 Round 5: 141 peptides, 27 chains. Longest chain 9 peptides. Score 0.343 Taking the results from Round 4 Chains 24, Residues 105, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 5390 restraints for refining 2412 atoms. 4959 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1712 (Rfree = 0.000) for 2412 atoms. Found 8 (13 requested) and removed 10 (6 requested) atoms. Cycle 7: After refmac, R = 0.1932 (Rfree = 0.000) for 2400 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 8: After refmac, R = 0.1418 (Rfree = 0.000) for 2391 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 9: After refmac, R = 0.1253 (Rfree = 0.000) for 2384 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. Cycle 10: After refmac, R = 0.1225 (Rfree = 0.000) for 2377 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 4.03 Search for helices and strands: 0 residues in 0 chains, 2413 seeds are put forward NCS extension: 0 residues added, 2413 seeds are put forward Round 1: 119 peptides, 28 chains. Longest chain 6 peptides. Score 0.206 Round 2: 136 peptides, 27 chains. Longest chain 8 peptides. Score 0.318 Round 3: 138 peptides, 25 chains. Longest chain 10 peptides. Score 0.370 Round 4: 151 peptides, 29 chains. Longest chain 11 peptides. Score 0.351 Round 5: 150 peptides, 28 chains. Longest chain 12 peptides. Score 0.367 Taking the results from Round 3 Chains 25, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 5355 restraints for refining 2369 atoms. 4928 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1843 (Rfree = 0.000) for 2369 atoms. Found 11 (13 requested) and removed 9 (6 requested) atoms. Cycle 12: After refmac, R = 0.1508 (Rfree = 0.000) for 2365 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. Cycle 13: After refmac, R = 0.1423 (Rfree = 0.000) for 2362 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 14: After refmac, R = 0.1415 (Rfree = 0.000) for 2353 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.1420 (Rfree = 0.000) for 2347 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 4.00 Search for helices and strands: 0 residues in 0 chains, 2381 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2384 seeds are put forward Round 1: 131 peptides, 30 chains. Longest chain 7 peptides. Score 0.227 Round 2: 133 peptides, 27 chains. Longest chain 9 peptides. Score 0.303 Round 3: 149 peptides, 27 chains. Longest chain 15 peptides. Score 0.382 Round 4: 142 peptides, 25 chains. Longest chain 11 peptides. Score 0.390 Round 5: 143 peptides, 25 chains. Longest chain 12 peptides. Score 0.394 Taking the results from Round 5 Chains 25, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 5556 restraints for refining 2433 atoms. 5109 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1696 (Rfree = 0.000) for 2433 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 17: After refmac, R = 0.1764 (Rfree = 0.000) for 2422 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 18: After refmac, R = 0.1727 (Rfree = 0.000) for 2419 atoms. Found 11 (13 requested) and removed 11 (6 requested) atoms. Cycle 19: After refmac, R = 0.1244 (Rfree = 0.000) for 2416 atoms. Found 7 (13 requested) and removed 8 (6 requested) atoms. Cycle 20: After refmac, R = 0.1163 (Rfree = 0.000) for 2413 atoms. Found 3 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.99 Search for helices and strands: 0 residues in 0 chains, 2467 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2479 seeds are put forward Round 1: 112 peptides, 25 chains. Longest chain 8 peptides. Score 0.235 Round 2: 127 peptides, 24 chains. Longest chain 13 peptides. Score 0.337 Round 3: 137 peptides, 28 chains. Longest chain 13 peptides. Score 0.302 Round 4: 129 peptides, 23 chains. Longest chain 12 peptides. Score 0.368 Round 5: 142 peptides, 24 chains. Longest chain 13 peptides. Score 0.410 Taking the results from Round 5 Chains 24, Residues 118, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 5432 restraints for refining 2422 atoms. 4984 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1817 (Rfree = 0.000) for 2422 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 22: After refmac, R = 0.1531 (Rfree = 0.000) for 2408 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Cycle 23: After refmac, R = 0.1086 (Rfree = 0.000) for 2397 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. Cycle 24: After refmac, R = 0.0941 (Rfree = 0.000) for 2389 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 25: After refmac, R = 0.0917 (Rfree = 0.000) for 2383 atoms. Found 4 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 4.03 Search for helices and strands: 0 residues in 0 chains, 2432 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 2450 seeds are put forward Round 1: 95 peptides, 21 chains. Longest chain 8 peptides. Score 0.232 Round 2: 129 peptides, 25 chains. Longest chain 10 peptides. Score 0.326 Round 3: 130 peptides, 22 chains. Longest chain 10 peptides. Score 0.394 Round 4: 124 peptides, 19 chains. Longest chain 11 peptides. Score 0.428 Round 5: 125 peptides, 20 chains. Longest chain 15 peptides. Score 0.412 Taking the results from Round 4 Chains 19, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 5431 restraints for refining 2386 atoms. 5030 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1466 (Rfree = 0.000) for 2386 atoms. Found 10 (13 requested) and removed 12 (6 requested) atoms. Cycle 27: After refmac, R = 0.1539 (Rfree = 0.000) for 2379 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Cycle 28: After refmac, R = 0.1506 (Rfree = 0.000) for 2381 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.1555 (Rfree = 0.000) for 2382 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. Cycle 30: After refmac, R = 0.1892 (Rfree = 0.000) for 2382 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.90 Search for helices and strands: 0 residues in 0 chains, 2424 seeds are put forward NCS extension: 0 residues added, 2424 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 8 peptides. Score 0.244 Round 2: 111 peptides, 20 chains. Longest chain 10 peptides. Score 0.343 Round 3: 119 peptides, 21 chains. Longest chain 10 peptides. Score 0.361 Round 4: 131 peptides, 21 chains. Longest chain 11 peptides. Score 0.420 Round 5: 119 peptides, 20 chains. Longest chain 10 peptides. Score 0.383 Taking the results from Round 4 Chains 21, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 5254 restraints for refining 2350 atoms. 4835 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1662 (Rfree = 0.000) for 2350 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 32: After refmac, R = 0.1711 (Rfree = 0.000) for 2342 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 33: After refmac, R = 0.1484 (Rfree = 0.000) for 2342 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 34: After refmac, R = 0.1036 (Rfree = 0.000) for 2345 atoms. Found 6 (12 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.1150 (Rfree = 0.000) for 2342 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.43 4.04 Search for helices and strands: 0 residues in 0 chains, 2396 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2408 seeds are put forward Round 1: 104 peptides, 24 chains. Longest chain 8 peptides. Score 0.213 Round 2: 121 peptides, 23 chains. Longest chain 9 peptides. Score 0.328 Round 3: 113 peptides, 20 chains. Longest chain 11 peptides. Score 0.353 Round 4: 121 peptides, 20 chains. Longest chain 13 peptides. Score 0.393 Round 5: 123 peptides, 20 chains. Longest chain 13 peptides. Score 0.403 Taking the results from Round 5 Chains 20, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 5519 restraints for refining 2409 atoms. 5127 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1468 (Rfree = 0.000) for 2409 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 37: After refmac, R = 0.1606 (Rfree = 0.000) for 2404 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1441 (Rfree = 0.000) for 2406 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 39: After refmac, R = 0.1511 (Rfree = 0.000) for 2405 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 40: After refmac, R = 0.0888 (Rfree = 0.000) for 2401 atoms. Found 5 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 4.07 Search for helices and strands: 0 residues in 0 chains, 2454 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 2466 seeds are put forward Round 1: 110 peptides, 23 chains. Longest chain 9 peptides. Score 0.270 Round 2: 109 peptides, 21 chains. Longest chain 9 peptides. Score 0.310 Round 3: 111 peptides, 22 chains. Longest chain 9 peptides. Score 0.298 Round 4: 112 peptides, 17 chains. Longest chain 13 peptides. Score 0.414 Round 5: 110 peptides, 17 chains. Longest chain 15 peptides. Score 0.404 Taking the results from Round 4 Chains 17, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2715 reflections ( 81.65 % complete ) and 5637 restraints for refining 2436 atoms. 5274 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1409 (Rfree = 0.000) for 2436 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 42: After refmac, R = 0.1446 (Rfree = 0.000) for 2433 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 43: After refmac, R = 0.1528 (Rfree = 0.000) for 2434 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 44: After refmac, R = 0.0924 (Rfree = 0.000) for 2437 atoms. Found 5 (13 requested) and removed 6 (6 requested) atoms. Cycle 45: After refmac, R = 0.0816 (Rfree = 0.000) for 2433 atoms. Found 8 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 4.06 Search for helices and strands: 0 residues in 0 chains, 2503 seeds are put forward NCS extension: 10 residues added (0 deleted due to clashes), 2513 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 7 peptides. Score 0.230 Round 2: 103 peptides, 18 chains. Longest chain 11 peptides. Score 0.346 Round 3: 103 peptides, 19 chains. Longest chain 15 peptides. Score 0.324 Round 4: 91 peptides, 14 chains. Longest chain 16 peptides. Score 0.377 Round 5: 92 peptides, 16 chains. Longest chain 11 peptides. Score 0.335 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 77, 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 2fqp-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2715 reflections ( 81.65 % complete ) and 5826 restraints for refining 2457 atoms. 5532 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1594 (Rfree = 0.000) for 2457 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1586 (Rfree = 0.000) for 2450 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1732 (Rfree = 0.000) for 2438 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1359 (Rfree = 0.000) for 2430 atoms. TimeTaking 35.78