Mon 24 Dec 07:31:55 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 2fqp-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fqp-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fqp-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-4.0-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/2fqp-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-4.0-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 07:32:00 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/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-4.0-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 222 and 0 Target number of residues in the AU: 222 Target solvent content: 0.6452 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-4.0-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: 35.909 92.640 53.056 90.000 106.409 90.000 Input sequence file: 2fqp-4.0-parrot-noncs.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 4.000 Wilson plot Bfac: 74.98 2328 reflections ( 81.71 % complete ) and 0 restraints for refining 3440 atoms. Observations/parameters ratio is 0.17 ------------------------------------------------------ Starting model: R = 0.3262 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2784 (Rfree = 0.000) for 3440 atoms. Found 16 (16 requested) and removed 38 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 4.16 Search for helices and strands: 0 residues in 0 chains, 3456 seeds are put forward NCS extension: 0 residues added, 3456 seeds are put forward Round 1: 83 peptides, 19 chains. Longest chain 7 peptides. Score 0.210 Round 2: 98 peptides, 19 chains. Longest chain 9 peptides. Score 0.297 Round 3: 118 peptides, 22 chains. Longest chain 10 peptides. Score 0.335 Round 4: 121 peptides, 23 chains. Longest chain 9 peptides. Score 0.328 Round 5: 115 peptides, 20 chains. Longest chain 10 peptides. Score 0.363 Taking the results from Round 5 Chains 20, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 6982 restraints for refining 2803 atoms. 6622 conditional restraints added. Observations/parameters ratio is 0.21 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2010 (Rfree = 0.000) for 2803 atoms. Found 9 (13 requested) and removed 235 (6 requested) atoms. Cycle 2: After refmac, R = 0.1751 (Rfree = 0.000) for 2543 atoms. Found 9 (12 requested) and removed 12 (6 requested) atoms. Cycle 3: After refmac, R = 0.1624 (Rfree = 0.000) for 2519 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. Cycle 4: After refmac, R = 0.1546 (Rfree = 0.000) for 2507 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. Cycle 5: After refmac, R = 0.1369 (Rfree = 0.000) for 2496 atoms. Found 6 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 4.20 Search for helices and strands: 0 residues in 0 chains, 2571 seeds are put forward NCS extension: 0 residues added, 2571 seeds are put forward Round 1: 83 peptides, 19 chains. Longest chain 7 peptides. Score 0.210 Round 2: 110 peptides, 23 chains. Longest chain 8 peptides. Score 0.270 Round 3: 132 peptides, 26 chains. Longest chain 8 peptides. Score 0.319 Round 4: 127 peptides, 24 chains. Longest chain 11 peptides. Score 0.337 Round 5: 117 peptides, 22 chains. Longest chain 9 peptides. Score 0.329 Taking the results from Round 4 Chains 24, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5533 restraints for refining 2372 atoms. 5145 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1684 (Rfree = 0.000) for 2372 atoms. Found 5 (11 requested) and removed 11 (5 requested) atoms. Cycle 7: After refmac, R = 0.1576 (Rfree = 0.000) for 2345 atoms. Found 3 (11 requested) and removed 7 (5 requested) atoms. Cycle 8: After refmac, R = 0.1233 (Rfree = 0.000) for 2324 atoms. Found 4 (11 requested) and removed 5 (5 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1154 (Rfree = 0.000) for 2320 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 10: After refmac, R = 0.1287 (Rfree = 0.000) for 2313 atoms. Found 2 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.62 4.26 Search for helices and strands: 0 residues in 0 chains, 2371 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2374 seeds are put forward Round 1: 113 peptides, 24 chains. Longest chain 8 peptides. Score 0.263 Round 2: 116 peptides, 22 chains. Longest chain 8 peptides. Score 0.324 Round 3: 118 peptides, 22 chains. Longest chain 9 peptides. Score 0.335 Round 4: 122 peptides, 24 chains. Longest chain 8 peptides. Score 0.311 Round 5: 137 peptides, 26 chains. Longest chain 9 peptides. Score 0.344 Taking the results from Round 5 Chains 26, Residues 111, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5177 restraints for refining 2299 atoms. 4759 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1553 (Rfree = 0.000) for 2299 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 12: After refmac, R = 0.1346 (Rfree = 0.000) for 2283 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. Cycle 13: After refmac, R = 0.1389 (Rfree = 0.000) for 2270 atoms. Found 5 (10 requested) and removed 8 (5 requested) atoms. Cycle 14: After refmac, R = 0.1181 (Rfree = 0.000) for 2263 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. Cycle 15: After refmac, R = 0.1225 (Rfree = 0.000) for 2256 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 4.21 Search for helices and strands: 0 residues in 0 chains, 2323 seeds are put forward NCS extension: 0 residues added, 2323 seeds are put forward Round 1: 110 peptides, 23 chains. Longest chain 8 peptides. Score 0.270 Round 2: 137 peptides, 26 chains. Longest chain 9 peptides. Score 0.344 Round 3: 128 peptides, 23 chains. Longest chain 11 peptides. Score 0.363 Round 4: 131 peptides, 23 chains. Longest chain 10 peptides. Score 0.378 Round 5: 121 peptides, 20 chains. Longest chain 20 peptides. Score 0.393 Taking the results from Round 5 Chains 20, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5465 restraints for refining 2338 atoms. 5081 conditional restraints added. Observations/parameters ratio is 0.25 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1529 (Rfree = 0.000) for 2338 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 17: After refmac, R = 0.1398 (Rfree = 0.000) for 2329 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 18: After refmac, R = 0.1371 (Rfree = 0.000) for 2330 atoms. Found 6 (11 requested) and removed 6 (5 requested) atoms. Cycle 19: After refmac, R = 0.1169 (Rfree = 0.000) for 2326 atoms. Found 0 (11 requested) and removed 7 (5 requested) atoms. Cycle 20: After refmac, R = 0.1334 (Rfree = 0.000) for 2316 atoms. Found 1 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 4.13 Search for helices and strands: 0 residues in 0 chains, 2360 seeds are put forward NCS extension: 0 residues added, 2360 seeds are put forward Round 1: 122 peptides, 28 chains. Longest chain 6 peptides. Score 0.223 Round 2: 135 peptides, 26 chains. Longest chain 10 peptides. Score 0.334 Round 3: 139 peptides, 27 chains. Longest chain 13 peptides. Score 0.333 Round 4: 140 peptides, 26 chains. Longest chain 14 peptides. Score 0.359 Round 5: 145 peptides, 25 chains. Longest chain 16 peptides. Score 0.404 Taking the results from Round 5 Chains 27, Residues 120, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5687 restraints for refining 2486 atoms. 5191 conditional restraints added. Observations/parameters ratio is 0.23 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1482 (Rfree = 0.000) for 2486 atoms. Found 8 (11 requested) and removed 23 (5 requested) atoms. Cycle 22: After refmac, R = 0.1570 (Rfree = 0.000) for 2461 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. Cycle 23: After refmac, R = 0.1553 (Rfree = 0.000) for 2452 atoms. Found 9 (11 requested) and removed 7 (5 requested) atoms. Cycle 24: After refmac, R = 0.1348 (Rfree = 0.000) for 2447 atoms. Found 5 (11 requested) and removed 8 (5 requested) atoms. Cycle 25: After refmac, R = 0.1125 (Rfree = 0.000) for 2434 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 4.12 Search for helices and strands: 0 residues in 0 chains, 2503 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 2526 seeds are put forward Round 1: 82 peptides, 18 chains. Longest chain 7 peptides. Score 0.229 Round 2: 108 peptides, 22 chains. Longest chain 9 peptides. Score 0.282 Round 3: 111 peptides, 20 chains. Longest chain 10 peptides. Score 0.343 Round 4: 119 peptides, 21 chains. Longest chain 11 peptides. Score 0.361 Round 5: 110 peptides, 19 chains. Longest chain 11 peptides. Score 0.360 Taking the results from Round 4 Chains 21, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5777 restraints for refining 2436 atoms. 5406 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1617 (Rfree = 0.000) for 2436 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 27: After refmac, R = 0.1457 (Rfree = 0.000) for 2419 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 28: After refmac, R = 0.1342 (Rfree = 0.000) for 2418 atoms. Found 9 (11 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.1201 (Rfree = 0.000) for 2416 atoms. Found 8 (11 requested) and removed 6 (5 requested) atoms. Cycle 30: After refmac, R = 0.1274 (Rfree = 0.000) for 2413 atoms. Found 7 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 4.17 Search for helices and strands: 0 residues in 0 chains, 2450 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2465 seeds are put forward Round 1: 85 peptides, 19 chains. Longest chain 6 peptides. Score 0.222 Round 2: 105 peptides, 21 chains. Longest chain 9 peptides. Score 0.288 Round 3: 122 peptides, 23 chains. Longest chain 10 peptides. Score 0.333 Round 4: 130 peptides, 23 chains. Longest chain 17 peptides. Score 0.373 Round 5: 127 peptides, 25 chains. Longest chain 9 peptides. Score 0.315 Taking the results from Round 4 Chains 23, Residues 107, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5578 restraints for refining 2433 atoms. 5150 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1687 (Rfree = 0.000) for 2433 atoms. Found 11 (11 requested) and removed 53 (5 requested) atoms. Cycle 32: After refmac, R = 0.2494 (Rfree = 0.000) for 2378 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 33: After refmac, R = 0.1704 (Rfree = 0.000) for 2362 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 34: After refmac, R = 0.1583 (Rfree = 0.000) for 2363 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.1548 (Rfree = 0.000) for 2359 atoms. Found 7 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 4.10 Search for helices and strands: 0 residues in 0 chains, 2416 seeds are put forward NCS extension: 0 residues added, 2416 seeds are put forward Round 1: 76 peptides, 18 chains. Longest chain 6 peptides. Score 0.192 Round 2: 104 peptides, 21 chains. Longest chain 7 peptides. Score 0.283 Round 3: 104 peptides, 20 chains. Longest chain 10 peptides. Score 0.306 Round 4: 108 peptides, 22 chains. Longest chain 9 peptides. Score 0.282 Round 5: 118 peptides, 22 chains. Longest chain 11 peptides. Score 0.335 Taking the results from Round 5 Chains 22, Residues 96, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5821 restraints for refining 2441 atoms. 5459 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1538 (Rfree = 0.000) for 2441 atoms. Found 10 (11 requested) and removed 29 (5 requested) atoms. Cycle 37: After refmac, R = 0.1400 (Rfree = 0.000) for 2413 atoms. Found 8 (11 requested) and removed 5 (5 requested) atoms. Cycle 38: After refmac, R = 0.1222 (Rfree = 0.000) for 2413 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. Cycle 39: After refmac, R = 0.1219 (Rfree = 0.000) for 2407 atoms. Found 3 (11 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.1380 (Rfree = 0.000) for 2396 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 4.18 Search for helices and strands: 0 residues in 0 chains, 2450 seeds are put forward NCS extension: 0 residues added, 2450 seeds are put forward Round 1: 74 peptides, 18 chains. Longest chain 6 peptides. Score 0.180 Round 2: 91 peptides, 16 chains. Longest chain 11 peptides. Score 0.329 Round 3: 87 peptides, 18 chains. Longest chain 9 peptides. Score 0.259 Round 4: 95 peptides, 18 chains. Longest chain 9 peptides. Score 0.304 Round 5: 106 peptides, 19 chains. Longest chain 10 peptides. Score 0.339 Taking the results from Round 5 Chains 19, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2328 reflections ( 81.71 % complete ) and 5830 restraints for refining 2430 atoms. 5501 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1533 (Rfree = 0.000) for 2430 atoms. Found 7 (11 requested) and removed 6 (5 requested) atoms. Cycle 42: After refmac, R = 0.1375 (Rfree = 0.000) for 2428 atoms. Found 5 (11 requested) and removed 5 (5 requested) atoms. Cycle 43: After refmac, R = 0.1300 (Rfree = 0.000) for 2426 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. Cycle 44: After refmac, R = 0.1282 (Rfree = 0.000) for 2420 atoms. Found 4 (11 requested) and removed 6 (5 requested) atoms. Cycle 45: After refmac, R = 0.1359 (Rfree = 0.000) for 2415 atoms. Found 5 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 4.17 Search for helices and strands: 0 residues in 0 chains, 2459 seeds are put forward NCS extension: 0 residues added, 2459 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 6 peptides. Score 0.200 Round 2: 72 peptides, 15 chains. Longest chain 8 peptides. Score 0.245 Round 3: 84 peptides, 17 chains. Longest chain 7 peptides. Score 0.266 Round 4: 73 peptides, 16 chains. Longest chain 6 peptides. Score 0.225 Round 5: 78 peptides, 16 chains. Longest chain 7 peptides. Score 0.256 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 67, 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-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2328 reflections ( 81.71 % complete ) and 5851 restraints for refining 2396 atoms. 5600 conditional restraints added. Observations/parameters ratio is 0.24 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1578 (Rfree = 0.000) for 2396 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1691 (Rfree = 0.000) for 2385 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1423 (Rfree = 0.000) for 2377 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1365 (Rfree = 0.000) for 2366 atoms. TimeTaking 31.38