Mon 24 Dec 07:36:42 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 2f4l-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2f4l-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2f4l-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.8-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/2f4l-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.8-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 07:36:47 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/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.8-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 842 and 0 Target number of residues in the AU: 842 Target solvent content: 0.6470 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1188 Adjusted target solvent content: 0.50 Input MTZ file: 2f4l-3.8-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: 19 Cell parameters: 80.030 103.980 155.130 90.000 90.000 90.000 Input sequence file: 2f4l-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 9504 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: 86.372 3.800 Wilson plot Bfac: 76.13 13249 reflections ( 99.60 % complete ) and 0 restraints for refining 10469 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3392 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3259 (Rfree = 0.000) for 10469 atoms. Found 57 (57 requested) and removed 120 (28 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.52 Search for helices and strands: 0 residues in 0 chains, 10512 seeds are put forward NCS extension: 0 residues added, 10512 seeds are put forward Round 1: 415 peptides, 82 chains. Longest chain 10 peptides. Score 0.298 Round 2: 570 peptides, 97 chains. Longest chain 14 peptides. Score 0.416 Round 3: 609 peptides, 93 chains. Longest chain 20 peptides. Score 0.482 Round 4: 633 peptides, 88 chains. Longest chain 18 peptides. Score 0.532 Round 5: 630 peptides, 93 chains. Longest chain 19 peptides. Score 0.505 Taking the results from Round 4 Chains 93, Residues 545, Estimated correctness of the model 0.0 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 19514 restraints for refining 8589 atoms. 17329 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2947 (Rfree = 0.000) for 8589 atoms. Found 44 (47 requested) and removed 76 (23 requested) atoms. Cycle 2: After refmac, R = 0.2784 (Rfree = 0.000) for 8358 atoms. Found 43 (47 requested) and removed 63 (23 requested) atoms. Cycle 3: After refmac, R = 0.2718 (Rfree = 0.000) for 8187 atoms. Found 45 (45 requested) and removed 61 (22 requested) atoms. Cycle 4: After refmac, R = 0.2668 (Rfree = 0.000) for 8077 atoms. Found 37 (44 requested) and removed 58 (22 requested) atoms. Cycle 5: After refmac, R = 0.2443 (Rfree = 0.000) for 7989 atoms. Found 38 (44 requested) and removed 33 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.58 Search for helices and strands: 0 residues in 0 chains, 8177 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 8191 seeds are put forward Round 1: 512 peptides, 94 chains. Longest chain 12 peptides. Score 0.359 Round 2: 578 peptides, 86 chains. Longest chain 26 peptides. Score 0.482 Round 3: 576 peptides, 83 chains. Longest chain 22 peptides. Score 0.494 Round 4: 613 peptides, 84 chains. Longest chain 31 peptides. Score 0.529 Round 5: 612 peptides, 92 chains. Longest chain 18 peptides. Score 0.490 Taking the results from Round 4 Chains 86, Residues 529, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 18354 restraints for refining 8160 atoms. 16266 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2617 (Rfree = 0.000) for 8160 atoms. Found 44 (44 requested) and removed 105 (22 requested) atoms. Cycle 7: After refmac, R = 0.2322 (Rfree = 0.000) for 8026 atoms. Found 36 (44 requested) and removed 56 (22 requested) atoms. Cycle 8: After refmac, R = 0.2201 (Rfree = 0.000) for 7961 atoms. Found 44 (44 requested) and removed 51 (22 requested) atoms. Cycle 9: After refmac, R = 0.1832 (Rfree = 0.000) for 7929 atoms. Found 13 (43 requested) and removed 29 (21 requested) atoms. Cycle 10: After refmac, R = 0.1955 (Rfree = 0.000) for 7896 atoms. Found 30 (43 requested) and removed 37 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.57 3.57 Search for helices and strands: 0 residues in 0 chains, 8066 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 8090 seeds are put forward Round 1: 552 peptides, 100 chains. Longest chain 17 peptides. Score 0.378 Round 2: 616 peptides, 93 chains. Longest chain 18 peptides. Score 0.490 Round 3: 610 peptides, 86 chains. Longest chain 24 peptides. Score 0.517 Round 4: 599 peptides, 83 chains. Longest chain 23 peptides. Score 0.519 Round 5: 613 peptides, 87 chains. Longest chain 21 peptides. Score 0.515 Taking the results from Round 4 Chains 83, Residues 516, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 19765 restraints for refining 8473 atoms. 17722 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2256 (Rfree = 0.000) for 8473 atoms. Found 46 (46 requested) and removed 63 (23 requested) atoms. Cycle 12: After refmac, R = 0.2131 (Rfree = 0.000) for 8401 atoms. Found 46 (46 requested) and removed 47 (23 requested) atoms. Cycle 13: After refmac, R = 0.1983 (Rfree = 0.000) for 8330 atoms. Found 46 (46 requested) and removed 38 (23 requested) atoms. Cycle 14: After refmac, R = 0.1629 (Rfree = 0.000) for 8315 atoms. Found 19 (45 requested) and removed 26 (22 requested) atoms. Cycle 15: After refmac, R = 0.1548 (Rfree = 0.000) for 8289 atoms. Found 11 (45 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.59 Search for helices and strands: 0 residues in 0 chains, 8451 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 8478 seeds are put forward Round 1: 526 peptides, 100 chains. Longest chain 13 peptides. Score 0.344 Round 2: 576 peptides, 88 chains. Longest chain 21 peptides. Score 0.469 Round 3: 582 peptides, 88 chains. Longest chain 21 peptides. Score 0.476 Round 4: 593 peptides, 87 chains. Longest chain 21 peptides. Score 0.493 Round 5: 610 peptides, 83 chains. Longest chain 19 peptides. Score 0.531 Taking the results from Round 5 Chains 83, Residues 527, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 19839 restraints for refining 8595 atoms. 17743 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2395 (Rfree = 0.000) for 8595 atoms. Found 47 (47 requested) and removed 60 (23 requested) atoms. Cycle 17: After refmac, R = 0.2231 (Rfree = 0.000) for 8496 atoms. Found 47 (47 requested) and removed 51 (23 requested) atoms. Cycle 18: After refmac, R = 0.2159 (Rfree = 0.000) for 8437 atoms. Found 46 (46 requested) and removed 48 (23 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2092 (Rfree = 0.000) for 8390 atoms. Found 46 (46 requested) and removed 36 (23 requested) atoms. Cycle 20: After refmac, R = 0.2093 (Rfree = 0.000) for 8367 atoms. Found 46 (46 requested) and removed 32 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.60 3.60 Search for helices and strands: 0 residues in 0 chains, 8581 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 8601 seeds are put forward Round 1: 477 peptides, 91 chains. Longest chain 12 peptides. Score 0.330 Round 2: 550 peptides, 88 chains. Longest chain 21 peptides. Score 0.439 Round 3: 555 peptides, 84 chains. Longest chain 21 peptides. Score 0.465 Round 4: 566 peptides, 83 chains. Longest chain 22 peptides. Score 0.483 Round 5: 573 peptides, 87 chains. Longest chain 22 peptides. Score 0.471 Taking the results from Round 4 Chains 83, Residues 483, Estimated correctness of the model 0.0 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 19860 restraints for refining 8595 atoms. 17929 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2468 (Rfree = 0.000) for 8595 atoms. Found 47 (47 requested) and removed 54 (23 requested) atoms. Cycle 22: After refmac, R = 0.2191 (Rfree = 0.000) for 8501 atoms. Found 47 (47 requested) and removed 38 (23 requested) atoms. Cycle 23: After refmac, R = 0.2151 (Rfree = 0.000) for 8457 atoms. Found 46 (46 requested) and removed 41 (23 requested) atoms. Cycle 24: After refmac, R = 0.2094 (Rfree = 0.000) for 8430 atoms. Found 46 (46 requested) and removed 32 (23 requested) atoms. Cycle 25: After refmac, R = 0.2095 (Rfree = 0.000) for 8409 atoms. Found 46 (46 requested) and removed 37 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 3.61 Search for helices and strands: 0 residues in 0 chains, 8596 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 8614 seeds are put forward Round 1: 455 peptides, 95 chains. Longest chain 14 peptides. Score 0.277 Round 2: 528 peptides, 93 chains. Longest chain 15 peptides. Score 0.385 Round 3: 545 peptides, 92 chains. Longest chain 15 peptides. Score 0.412 Round 4: 548 peptides, 87 chains. Longest chain 20 peptides. Score 0.442 Round 5: 543 peptides, 85 chains. Longest chain 17 peptides. Score 0.446 Taking the results from Round 5 Chains 85, Residues 458, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 20390 restraints for refining 8596 atoms. 18643 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2483 (Rfree = 0.000) for 8596 atoms. Found 47 (47 requested) and removed 52 (23 requested) atoms. Cycle 27: After refmac, R = 0.2453 (Rfree = 0.000) for 8530 atoms. Found 47 (47 requested) and removed 43 (23 requested) atoms. Cycle 28: After refmac, R = 0.2315 (Rfree = 0.000) for 8469 atoms. Found 46 (46 requested) and removed 34 (23 requested) atoms. Cycle 29: After refmac, R = 0.2329 (Rfree = 0.000) for 8443 atoms. Found 46 (46 requested) and removed 36 (23 requested) atoms. Cycle 30: After refmac, R = 0.2247 (Rfree = 0.000) for 8418 atoms. Found 46 (46 requested) and removed 40 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.62 Search for helices and strands: 0 residues in 0 chains, 8590 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 8610 seeds are put forward Round 1: 371 peptides, 77 chains. Longest chain 9 peptides. Score 0.265 Round 2: 452 peptides, 80 chains. Longest chain 13 peptides. Score 0.360 Round 3: 476 peptides, 83 chains. Longest chain 14 peptides. Score 0.374 Round 4: 489 peptides, 81 chains. Longest chain 19 peptides. Score 0.402 Round 5: 473 peptides, 76 chains. Longest chain 16 peptides. Score 0.409 Taking the results from Round 5 Chains 76, Residues 397, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 20438 restraints for refining 8475 atoms. 18904 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2365 (Rfree = 0.000) for 8475 atoms. Found 46 (46 requested) and removed 58 (23 requested) atoms. Cycle 32: After refmac, R = 0.2254 (Rfree = 0.000) for 8409 atoms. Found 46 (46 requested) and removed 47 (23 requested) atoms. Cycle 33: After refmac, R = 0.1884 (Rfree = 0.000) for 8373 atoms. Found 27 (46 requested) and removed 31 (23 requested) atoms. Cycle 34: After refmac, R = 0.1736 (Rfree = 0.000) for 8345 atoms. Found 21 (46 requested) and removed 27 (23 requested) atoms. Cycle 35: After refmac, R = 0.1710 (Rfree = 0.000) for 8329 atoms. Found 17 (45 requested) and removed 28 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.62 3.62 Search for helices and strands: 0 residues in 0 chains, 8467 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 8480 seeds are put forward Round 1: 387 peptides, 80 chains. Longest chain 11 peptides. Score 0.270 Round 2: 438 peptides, 76 chains. Longest chain 14 peptides. Score 0.364 Round 3: 463 peptides, 75 chains. Longest chain 13 peptides. Score 0.402 Round 4: 468 peptides, 78 chains. Longest chain 15 peptides. Score 0.392 Round 5: 452 peptides, 72 chains. Longest chain 24 peptides. Score 0.405 Taking the results from Round 5 Chains 74, Residues 380, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 20606 restraints for refining 8595 atoms. 19096 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2380 (Rfree = 0.000) for 8595 atoms. Found 47 (47 requested) and removed 67 (23 requested) atoms. Cycle 37: After refmac, R = 0.2230 (Rfree = 0.000) for 8513 atoms. Found 47 (47 requested) and removed 45 (23 requested) atoms. Cycle 38: After refmac, R = 0.2264 (Rfree = 0.000) for 8474 atoms. Found 46 (46 requested) and removed 44 (23 requested) atoms. Cycle 39: After refmac, R = 0.2193 (Rfree = 0.000) for 8442 atoms. Found 46 (46 requested) and removed 35 (23 requested) atoms. Cycle 40: After refmac, R = 0.2180 (Rfree = 0.000) for 8417 atoms. Found 46 (46 requested) and removed 36 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.56 3.56 Search for helices and strands: 0 residues in 0 chains, 8599 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 8614 seeds are put forward Round 1: 370 peptides, 78 chains. Longest chain 9 peptides. Score 0.257 Round 2: 457 peptides, 81 chains. Longest chain 25 peptides. Score 0.360 Round 3: 470 peptides, 79 chains. Longest chain 12 peptides. Score 0.389 Round 4: 464 peptides, 76 chains. Longest chain 22 peptides. Score 0.398 Round 5: 458 peptides, 70 chains. Longest chain 26 peptides. Score 0.423 Taking the results from Round 5 Chains 71, Residues 388, Estimated correctness of the model 0.0 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 13249 reflections ( 99.60 % complete ) and 19989 restraints for refining 8509 atoms. 18388 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2344 (Rfree = 0.000) for 8509 atoms. Found 46 (46 requested) and removed 67 (23 requested) atoms. Cycle 42: After refmac, R = 0.2256 (Rfree = 0.000) for 8434 atoms. Found 46 (46 requested) and removed 44 (23 requested) atoms. Cycle 43: After refmac, R = 0.2025 (Rfree = 0.000) for 8412 atoms. Found 46 (46 requested) and removed 35 (23 requested) atoms. Cycle 44: After refmac, R = 0.1722 (Rfree = 0.000) for 8405 atoms. Found 20 (46 requested) and removed 52 (23 requested) atoms. Cycle 45: After refmac, R = 0.1940 (Rfree = 0.000) for 8357 atoms. Found 46 (46 requested) and removed 30 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.58 Search for helices and strands: 0 residues in 0 chains, 8509 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 8529 seeds are put forward Round 1: 370 peptides, 80 chains. Longest chain 10 peptides. Score 0.245 Round 2: 411 peptides, 75 chains. Longest chain 12 peptides. Score 0.334 Round 3: 438 peptides, 79 chains. Longest chain 12 peptides. Score 0.347 Round 4: 439 peptides, 75 chains. Longest chain 18 peptides. Score 0.371 Round 5: 438 peptides, 74 chains. Longest chain 14 peptides. Score 0.376 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 74, Residues 364, 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 2f4l-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13249 reflections ( 99.60 % complete ) and 20655 restraints for refining 8570 atoms. 19273 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2304 (Rfree = 0.000) for 8570 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 47: After refmac, R = 0.2368 (Rfree = 0.000) for 8502 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 48: After refmac, R = 0.2261 (Rfree = 0.000) for 8447 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.2272 (Rfree = 0.000) for 8399 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Writing output files ... TimeTaking 87.22