Mon 24 Dec 08:07:02 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 2pgc-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pgc-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pgc-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pgc-3.6-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/2pgc-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pgc-3.6-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 08:07:06 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/2pgc-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pgc-3.6-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 742 and 0 Target number of residues in the AU: 742 Target solvent content: 0.6561 Checking the provided sequence file Detected sequence length: 207 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 1035 Adjusted target solvent content: 0.52 Input MTZ file: 2pgc-3.6-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: 18 Cell parameters: 137.477 139.862 60.737 90.000 90.000 90.000 Input sequence file: 2pgc-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 8280 target number of atoms Had to go as low as 0.75 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: 98.043 3.600 Wilson plot Bfac: 82.18 14118 reflections ( 99.56 % complete ) and 0 restraints for refining 9144 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3449 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3262 (Rfree = 0.000) for 9144 atoms. Found 58 (58 requested) and removed 39 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.52 Search for helices and strands: 0 residues in 0 chains, 9328 seeds are put forward NCS extension: 0 residues added, 9328 seeds are put forward Round 1: 331 peptides, 69 chains. Longest chain 10 peptides. Score 0.262 Round 2: 478 peptides, 85 chains. Longest chain 16 peptides. Score 0.381 Round 3: 515 peptides, 82 chains. Longest chain 18 peptides. Score 0.448 Round 4: 568 peptides, 78 chains. Longest chain 21 peptides. Score 0.535 Round 5: 562 peptides, 81 chains. Longest chain 21 peptides. Score 0.512 Taking the results from Round 4 Chains 81, Residues 490, Estimated correctness of the model 0.0 % 5 chains (39 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 16735 restraints for refining 7505 atoms. 14727 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3197 (Rfree = 0.000) for 7505 atoms. Found 43 (48 requested) and removed 60 (24 requested) atoms. Cycle 2: After refmac, R = 0.3074 (Rfree = 0.000) for 7348 atoms. Found 35 (48 requested) and removed 51 (24 requested) atoms. Cycle 3: After refmac, R = 0.3029 (Rfree = 0.000) for 7191 atoms. Found 33 (47 requested) and removed 47 (23 requested) atoms. Cycle 4: After refmac, R = 0.3023 (Rfree = 0.000) for 7070 atoms. Found 31 (46 requested) and removed 46 (23 requested) atoms. Cycle 5: After refmac, R = 0.3036 (Rfree = 0.000) for 6966 atoms. Found 40 (45 requested) and removed 37 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.63 3.53 Search for helices and strands: 0 residues in 0 chains, 7218 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 7234 seeds are put forward Round 1: 416 peptides, 84 chains. Longest chain 16 peptides. Score 0.296 Round 2: 514 peptides, 83 chains. Longest chain 21 peptides. Score 0.441 Round 3: 548 peptides, 80 chains. Longest chain 19 peptides. Score 0.501 Round 4: 556 peptides, 82 chains. Longest chain 24 peptides. Score 0.500 Round 5: 538 peptides, 74 chains. Longest chain 18 peptides. Score 0.521 Taking the results from Round 5 Chains 75, Residues 464, Estimated correctness of the model 0.0 % 4 chains (20 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 15809 restraints for refining 7050 atoms. 13972 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3080 (Rfree = 0.000) for 7050 atoms. Found 45 (45 requested) and removed 58 (22 requested) atoms. Cycle 7: After refmac, R = 0.2731 (Rfree = 0.000) for 6941 atoms. Found 45 (45 requested) and removed 43 (22 requested) atoms. Cycle 8: After refmac, R = 0.2620 (Rfree = 0.000) for 6885 atoms. Found 44 (44 requested) and removed 39 (22 requested) atoms. Cycle 9: After refmac, R = 0.2722 (Rfree = 0.000) for 6839 atoms. Found 44 (44 requested) and removed 33 (22 requested) atoms. Cycle 10: After refmac, R = 0.2468 (Rfree = 0.000) for 6814 atoms. Found 43 (43 requested) and removed 28 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 3.43 Search for helices and strands: 0 residues in 0 chains, 7108 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 7130 seeds are put forward Round 1: 426 peptides, 81 chains. Longest chain 12 peptides. Score 0.330 Round 2: 491 peptides, 73 chains. Longest chain 17 peptides. Score 0.468 Round 3: 510 peptides, 79 chains. Longest chain 18 peptides. Score 0.459 Round 4: 499 peptides, 76 chains. Longest chain 24 peptides. Score 0.461 Round 5: 523 peptides, 79 chains. Longest chain 25 peptides. Score 0.475 Taking the results from Round 5 Chains 79, Residues 444, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 16291 restraints for refining 7242 atoms. 14584 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2781 (Rfree = 0.000) for 7242 atoms. Found 46 (46 requested) and removed 116 (23 requested) atoms. Cycle 12: After refmac, R = 0.2709 (Rfree = 0.000) for 7084 atoms. Found 46 (46 requested) and removed 38 (23 requested) atoms. Cycle 13: After refmac, R = 0.2530 (Rfree = 0.000) for 7035 atoms. Found 45 (45 requested) and removed 26 (22 requested) atoms. Cycle 14: After refmac, R = 0.2536 (Rfree = 0.000) for 7027 atoms. Found 45 (45 requested) and removed 26 (22 requested) atoms. Cycle 15: After refmac, R = 0.2423 (Rfree = 0.000) for 7023 atoms. Found 42 (45 requested) and removed 25 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 7350 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 7368 seeds are put forward Round 1: 410 peptides, 81 chains. Longest chain 13 peptides. Score 0.306 Round 2: 477 peptides, 84 chains. Longest chain 15 peptides. Score 0.385 Round 3: 508 peptides, 80 chains. Longest chain 14 peptides. Score 0.450 Round 4: 508 peptides, 79 chains. Longest chain 16 peptides. Score 0.456 Round 5: 524 peptides, 82 chains. Longest chain 15 peptides. Score 0.460 Taking the results from Round 5 Chains 82, Residues 442, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 16861 restraints for refining 7419 atoms. 15156 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2578 (Rfree = 0.000) for 7419 atoms. Found 47 (47 requested) and removed 57 (23 requested) atoms. Cycle 17: After refmac, R = 0.2583 (Rfree = 0.000) for 7321 atoms. Found 47 (47 requested) and removed 50 (23 requested) atoms. Cycle 18: After refmac, R = 0.2462 (Rfree = 0.000) for 7266 atoms. Found 46 (46 requested) and removed 41 (23 requested) atoms. Cycle 19: After refmac, R = 0.2302 (Rfree = 0.000) for 7243 atoms. Found 33 (46 requested) and removed 36 (23 requested) atoms. Cycle 20: After refmac, R = 0.1957 (Rfree = 0.000) for 7218 atoms. Found 13 (46 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 7415 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 7432 seeds are put forward Round 1: 411 peptides, 77 chains. Longest chain 11 peptides. Score 0.333 Round 2: 456 peptides, 77 chains. Longest chain 15 peptides. Score 0.398 Round 3: 444 peptides, 70 chains. Longest chain 12 peptides. Score 0.424 Round 4: 467 peptides, 77 chains. Longest chain 17 peptides. Score 0.413 Round 5: 479 peptides, 73 chains. Longest chain 15 peptides. Score 0.453 Taking the results from Round 5 Chains 73, Residues 406, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 17335 restraints for refining 7474 atoms. 15765 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2683 (Rfree = 0.000) for 7474 atoms. Found 47 (47 requested) and removed 51 (23 requested) atoms. Cycle 22: After refmac, R = 0.2519 (Rfree = 0.000) for 7407 atoms. Found 47 (47 requested) and removed 42 (23 requested) atoms. Cycle 23: After refmac, R = 0.2514 (Rfree = 0.000) for 7374 atoms. Found 47 (47 requested) and removed 41 (23 requested) atoms. Cycle 24: After refmac, R = 0.2014 (Rfree = 0.000) for 7357 atoms. Found 19 (47 requested) and removed 29 (23 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1921 (Rfree = 0.000) for 7335 atoms. Found 9 (47 requested) and removed 26 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 3.48 Search for helices and strands: 0 residues in 0 chains, 7525 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 7539 seeds are put forward Round 1: 395 peptides, 76 chains. Longest chain 11 peptides. Score 0.316 Round 2: 430 peptides, 74 chains. Longest chain 12 peptides. Score 0.380 Round 3: 466 peptides, 70 chains. Longest chain 18 peptides. Score 0.453 Round 4: 461 peptides, 67 chains. Longest chain 18 peptides. Score 0.464 Round 5: 456 peptides, 68 chains. Longest chain 17 peptides. Score 0.452 Taking the results from Round 4 Chains 67, Residues 394, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 17394 restraints for refining 7505 atoms. 15885 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2451 (Rfree = 0.000) for 7505 atoms. Found 48 (48 requested) and removed 41 (24 requested) atoms. Cycle 27: After refmac, R = 0.2490 (Rfree = 0.000) for 7451 atoms. Found 48 (48 requested) and removed 42 (24 requested) atoms. Cycle 28: After refmac, R = 0.2411 (Rfree = 0.000) for 7419 atoms. Found 47 (47 requested) and removed 38 (23 requested) atoms. Cycle 29: After refmac, R = 0.2535 (Rfree = 0.000) for 7394 atoms. Found 47 (47 requested) and removed 34 (23 requested) atoms. Cycle 30: After refmac, R = 0.2344 (Rfree = 0.000) for 7377 atoms. Found 47 (47 requested) and removed 29 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.46 Search for helices and strands: 0 residues in 0 chains, 7648 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 7668 seeds are put forward Round 1: 345 peptides, 74 chains. Longest chain 9 peptides. Score 0.250 Round 2: 439 peptides, 79 chains. Longest chain 11 peptides. Score 0.362 Round 3: 435 peptides, 77 chains. Longest chain 14 peptides. Score 0.368 Round 4: 440 peptides, 72 chains. Longest chain 14 peptides. Score 0.406 Round 5: 450 peptides, 72 chains. Longest chain 14 peptides. Score 0.420 Taking the results from Round 5 Chains 72, Residues 378, Estimated correctness of the model 0.0 % 4 chains (17 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 17070 restraints for refining 7506 atoms. 15589 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2554 (Rfree = 0.000) for 7506 atoms. Found 48 (48 requested) and removed 53 (24 requested) atoms. Cycle 32: After refmac, R = 0.2483 (Rfree = 0.000) for 7430 atoms. Found 48 (48 requested) and removed 39 (24 requested) atoms. Cycle 33: After refmac, R = 0.2456 (Rfree = 0.000) for 7396 atoms. Found 47 (47 requested) and removed 39 (23 requested) atoms. Cycle 34: After refmac, R = 0.2400 (Rfree = 0.000) for 7364 atoms. Found 47 (47 requested) and removed 35 (23 requested) atoms. Cycle 35: After refmac, R = 0.2324 (Rfree = 0.000) for 7336 atoms. Found 47 (47 requested) and removed 33 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 3.45 Search for helices and strands: 0 residues in 0 chains, 7546 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 7559 seeds are put forward Round 1: 317 peptides, 70 chains. Longest chain 12 peptides. Score 0.231 Round 2: 371 peptides, 74 chains. Longest chain 13 peptides. Score 0.292 Round 3: 372 peptides, 68 chains. Longest chain 12 peptides. Score 0.333 Round 4: 397 peptides, 75 chains. Longest chain 13 peptides. Score 0.325 Round 5: 385 peptides, 70 chains. Longest chain 11 peptides. Score 0.339 Taking the results from Round 5 Chains 70, Residues 315, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 17317 restraints for refining 7411 atoms. 16090 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2485 (Rfree = 0.000) for 7411 atoms. Found 47 (47 requested) and removed 38 (23 requested) atoms. Cycle 37: After refmac, R = 0.2345 (Rfree = 0.000) for 7356 atoms. Found 47 (47 requested) and removed 33 (23 requested) atoms. Cycle 38: After refmac, R = 0.2495 (Rfree = 0.000) for 7334 atoms. Found 47 (47 requested) and removed 32 (23 requested) atoms. Cycle 39: After refmac, R = 0.2236 (Rfree = 0.000) for 7320 atoms. Found 47 (47 requested) and removed 29 (23 requested) atoms. Cycle 40: After refmac, R = 0.2363 (Rfree = 0.000) for 7328 atoms. Found 47 (47 requested) and removed 30 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 3.50 Search for helices and strands: 0 residues in 0 chains, 7534 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 7548 seeds are put forward Round 1: 342 peptides, 76 chains. Longest chain 8 peptides. Score 0.232 Round 2: 420 peptides, 82 chains. Longest chain 15 peptides. Score 0.315 Round 3: 410 peptides, 75 chains. Longest chain 15 peptides. Score 0.345 Round 4: 423 peptides, 76 chains. Longest chain 11 peptides. Score 0.357 Round 5: 429 peptides, 77 chains. Longest chain 12 peptides. Score 0.360 Taking the results from Round 5 Chains 77, Residues 352, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 14118 reflections ( 99.56 % complete ) and 16877 restraints for refining 7369 atoms. 15529 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2648 (Rfree = 0.000) for 7369 atoms. Found 47 (47 requested) and removed 62 (23 requested) atoms. Cycle 42: After refmac, R = 0.2449 (Rfree = 0.000) for 7297 atoms. Found 47 (47 requested) and removed 43 (23 requested) atoms. Cycle 43: After refmac, R = 0.2423 (Rfree = 0.000) for 7258 atoms. Found 46 (46 requested) and removed 34 (23 requested) atoms. Cycle 44: After refmac, R = 0.2277 (Rfree = 0.000) for 7238 atoms. Found 46 (46 requested) and removed 31 (23 requested) atoms. Cycle 45: After refmac, R = 0.2272 (Rfree = 0.000) for 7232 atoms. Found 46 (46 requested) and removed 29 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.42 Search for helices and strands: 0 residues in 0 chains, 7436 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 7449 seeds are put forward Round 1: 277 peptides, 60 chains. Longest chain 9 peptides. Score 0.234 Round 2: 344 peptides, 69 chains. Longest chain 9 peptides. Score 0.283 Round 3: 342 peptides, 67 chains. Longest chain 10 peptides. Score 0.293 Round 4: 340 peptides, 66 chains. Longest chain 9 peptides. Score 0.297 Round 5: 339 peptides, 64 chains. Longest chain 11 peptides. Score 0.309 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 64, Residues 275, 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 2pgc-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14118 reflections ( 99.56 % complete ) and 16690 restraints for refining 7287 atoms. 15654 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2501 (Rfree = 0.000) for 7287 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2287 (Rfree = 0.000) for 7220 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2214 (Rfree = 0.000) for 7170 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.2215 (Rfree = 0.000) for 7127 atoms. TimeTaking 72.6