Mon 24 Dec 08:01:11 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-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pgc-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pgc-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pgc-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/2pgc-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pgc-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 08:01:15 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-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pgc-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 708 and 0 Target number of residues in the AU: 708 Target solvent content: 0.6719 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-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: 18 Cell parameters: 137.477 139.862 60.737 90.000 90.000 90.000 Input sequence file: 2pgc-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 8280 target number of atoms Had to go as low as 0.80 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 4.000 Wilson plot Bfac: 93.78 10366 reflections ( 99.41 % complete ) and 0 restraints for refining 9194 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3522 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3403 (Rfree = 0.000) for 9194 atoms. Found 43 (43 requested) and removed 67 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.93 3.83 Search for helices and strands: 0 residues in 0 chains, 9325 seeds are put forward NCS extension: 0 residues added, 9325 seeds are put forward Round 1: 289 peptides, 61 chains. Longest chain 15 peptides. Score 0.248 Round 2: 384 peptides, 69 chains. Longest chain 11 peptides. Score 0.344 Round 3: 426 peptides, 66 chains. Longest chain 19 peptides. Score 0.423 Round 4: 440 peptides, 64 chains. Longest chain 19 peptides. Score 0.454 Round 5: 439 peptides, 64 chains. Longest chain 16 peptides. Score 0.453 Taking the results from Round 4 Chains 64, Residues 376, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17861 restraints for refining 7474 atoms. 16357 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3010 (Rfree = 0.000) for 7474 atoms. Found 19 (35 requested) and removed 63 (17 requested) atoms. Cycle 2: After refmac, R = 0.2654 (Rfree = 0.000) for 7289 atoms. Found 27 (35 requested) and removed 63 (17 requested) atoms. Cycle 3: After refmac, R = 0.2263 (Rfree = 0.000) for 7159 atoms. Found 19 (34 requested) and removed 28 (17 requested) atoms. Cycle 4: After refmac, R = 0.2205 (Rfree = 0.000) for 7110 atoms. Found 12 (33 requested) and removed 22 (16 requested) atoms. Cycle 5: After refmac, R = 0.2173 (Rfree = 0.000) for 7087 atoms. Found 8 (33 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.83 3.73 Search for helices and strands: 0 residues in 0 chains, 7300 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 7327 seeds are put forward Round 1: 396 peptides, 78 chains. Longest chain 10 peptides. Score 0.304 Round 2: 452 peptides, 75 chains. Longest chain 12 peptides. Score 0.405 Round 3: 481 peptides, 77 chains. Longest chain 22 peptides. Score 0.432 Round 4: 472 peptides, 70 chains. Longest chain 21 peptides. Score 0.461 Round 5: 483 peptides, 71 chains. Longest chain 15 peptides. Score 0.469 Taking the results from Round 5 Chains 71, Residues 412, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 16776 restraints for refining 7128 atoms. 15199 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2378 (Rfree = 0.000) for 7128 atoms. Found 22 (33 requested) and removed 95 (16 requested) atoms. Cycle 7: After refmac, R = 0.2274 (Rfree = 0.000) for 6999 atoms. Found 9 (33 requested) and removed 20 (16 requested) atoms. Cycle 8: After refmac, R = 0.2258 (Rfree = 0.000) for 6972 atoms. Found 10 (33 requested) and removed 16 (16 requested) atoms. Cycle 9: After refmac, R = 0.2259 (Rfree = 0.000) for 6964 atoms. Found 1 (33 requested) and removed 18 (16 requested) atoms. Cycle 10: After refmac, R = 0.2256 (Rfree = 0.000) for 6947 atoms. Found 1 (33 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.85 3.75 Search for helices and strands: 0 residues in 0 chains, 7156 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 7177 seeds are put forward Round 1: 430 peptides, 82 chains. Longest chain 13 peptides. Score 0.330 Round 2: 470 peptides, 75 chains. Longest chain 17 peptides. Score 0.429 Round 3: 484 peptides, 69 chains. Longest chain 21 peptides. Score 0.482 Round 4: 497 peptides, 72 chains. Longest chain 17 peptides. Score 0.481 Round 5: 511 peptides, 69 chains. Longest chain 20 peptides. Score 0.515 Taking the results from Round 5 Chains 69, Residues 442, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 10366 reflections ( 99.41 % complete ) and 17499 restraints for refining 7477 atoms. 15761 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2468 (Rfree = 0.000) for 7477 atoms. Found 23 (35 requested) and removed 30 (17 requested) atoms. Cycle 12: After refmac, R = 0.2385 (Rfree = 0.000) for 7420 atoms. Found 11 (35 requested) and removed 21 (17 requested) atoms. Cycle 13: After refmac, R = 0.2366 (Rfree = 0.000) for 7399 atoms. Found 5 (35 requested) and removed 25 (17 requested) atoms. Cycle 14: After refmac, R = 0.2368 (Rfree = 0.000) for 7378 atoms. Found 10 (35 requested) and removed 67 (17 requested) atoms. Cycle 15: After refmac, R = 0.2351 (Rfree = 0.000) for 7315 atoms. Found 8 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.86 3.76 Search for helices and strands: 0 residues in 0 chains, 7491 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 7516 seeds are put forward Round 1: 428 peptides, 77 chains. Longest chain 13 peptides. Score 0.358 Round 2: 484 peptides, 72 chains. Longest chain 17 peptides. Score 0.465 Round 3: 485 peptides, 68 chains. Longest chain 20 peptides. Score 0.489 Round 4: 481 peptides, 67 chains. Longest chain 16 peptides. Score 0.489 Round 5: 486 peptides, 73 chains. Longest chain 17 peptides. Score 0.462 Taking the results from Round 4 Chains 68, Residues 414, Estimated correctness of the model 0.0 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17526 restraints for refining 7476 atoms. 15853 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2292 (Rfree = 0.000) for 7476 atoms. Found 20 (35 requested) and removed 106 (17 requested) atoms. Cycle 17: After refmac, R = 0.2257 (Rfree = 0.000) for 7344 atoms. Found 22 (35 requested) and removed 24 (17 requested) atoms. Cycle 18: After refmac, R = 0.2215 (Rfree = 0.000) for 7326 atoms. Found 6 (34 requested) and removed 19 (17 requested) atoms. Cycle 19: After refmac, R = 0.2179 (Rfree = 0.000) for 7306 atoms. Found 5 (34 requested) and removed 42 (17 requested) atoms. Cycle 20: After refmac, R = 0.2158 (Rfree = 0.000) for 7260 atoms. Found 6 (34 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 7420 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 7446 seeds are put forward Round 1: 416 peptides, 78 chains. Longest chain 15 peptides. Score 0.334 Round 2: 464 peptides, 77 chains. Longest chain 15 peptides. Score 0.409 Round 3: 470 peptides, 76 chains. Longest chain 15 peptides. Score 0.423 Round 4: 481 peptides, 71 chains. Longest chain 16 peptides. Score 0.467 Round 5: 476 peptides, 67 chains. Longest chain 28 peptides. Score 0.483 Taking the results from Round 5 Chains 67, Residues 409, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17836 restraints for refining 7478 atoms. 16267 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2385 (Rfree = 0.000) for 7478 atoms. Found 31 (35 requested) and removed 46 (17 requested) atoms. Cycle 22: After refmac, R = 0.1979 (Rfree = 0.000) for 7397 atoms. Found 19 (35 requested) and removed 26 (17 requested) atoms. Cycle 23: After refmac, R = 0.1813 (Rfree = 0.000) for 7348 atoms. Found 15 (35 requested) and removed 26 (17 requested) atoms. Cycle 24: After refmac, R = 0.1777 (Rfree = 0.000) for 7325 atoms. Found 6 (34 requested) and removed 20 (17 requested) atoms. Cycle 25: After refmac, R = 0.1772 (Rfree = 0.000) for 7301 atoms. Found 7 (34 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.78 3.68 Search for helices and strands: 0 residues in 0 chains, 7483 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 7497 seeds are put forward Round 1: 392 peptides, 79 chains. Longest chain 12 peptides. Score 0.292 Round 2: 432 peptides, 74 chains. Longest chain 18 peptides. Score 0.383 Round 3: 444 peptides, 74 chains. Longest chain 17 peptides. Score 0.400 Round 4: 442 peptides, 72 chains. Longest chain 15 peptides. Score 0.409 Round 5: 445 peptides, 69 chains. Longest chain 13 peptides. Score 0.431 Taking the results from Round 5 Chains 69, Residues 376, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17615 restraints for refining 7478 atoms. 16153 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2185 (Rfree = 0.000) for 7478 atoms. Found 26 (35 requested) and removed 34 (17 requested) atoms. Cycle 27: After refmac, R = 0.2052 (Rfree = 0.000) for 7396 atoms. Found 24 (35 requested) and removed 31 (17 requested) atoms. Cycle 28: After refmac, R = 0.2089 (Rfree = 0.000) for 7356 atoms. Found 30 (35 requested) and removed 32 (17 requested) atoms. Cycle 29: After refmac, R = 0.1686 (Rfree = 0.000) for 7325 atoms. Found 12 (34 requested) and removed 21 (17 requested) atoms. Cycle 30: After refmac, R = 0.1609 (Rfree = 0.000) for 7296 atoms. Found 6 (34 requested) and removed 23 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.77 3.67 Search for helices and strands: 0 residues in 0 chains, 7587 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 7599 seeds are put forward Round 1: 336 peptides, 74 chains. Longest chain 8 peptides. Score 0.236 Round 2: 402 peptides, 77 chains. Longest chain 14 peptides. Score 0.320 Round 3: 418 peptides, 77 chains. Longest chain 13 peptides. Score 0.344 Round 4: 428 peptides, 73 chains. Longest chain 14 peptides. Score 0.383 Round 5: 422 peptides, 74 chains. Longest chain 15 peptides. Score 0.368 Taking the results from Round 4 Chains 73, Residues 355, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17454 restraints for refining 7437 atoms. 16107 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2228 (Rfree = 0.000) for 7437 atoms. Found 34 (35 requested) and removed 45 (17 requested) atoms. Cycle 32: After refmac, R = 0.2292 (Rfree = 0.000) for 7381 atoms. Found 35 (35 requested) and removed 41 (17 requested) atoms. Cycle 33: After refmac, R = 0.2029 (Rfree = 0.000) for 7329 atoms. Found 35 (35 requested) and removed 37 (17 requested) atoms. Cycle 34: After refmac, R = 0.2036 (Rfree = 0.000) for 7293 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. Cycle 35: After refmac, R = 0.1981 (Rfree = 0.000) for 7261 atoms. Found 34 (34 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.82 3.72 Search for helices and strands: 0 residues in 0 chains, 7464 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 7489 seeds are put forward Round 1: 298 peptides, 65 chains. Longest chain 8 peptides. Score 0.235 Round 2: 365 peptides, 74 chains. Longest chain 11 peptides. Score 0.282 Round 3: 399 peptides, 74 chains. Longest chain 13 peptides. Score 0.335 Round 4: 399 peptides, 76 chains. Longest chain 11 peptides. Score 0.322 Round 5: 409 peptides, 76 chains. Longest chain 15 peptides. Score 0.337 Taking the results from Round 5 Chains 76, Residues 333, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 16991 restraints for refining 7318 atoms. 15735 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1953 (Rfree = 0.000) for 7318 atoms. Found 26 (34 requested) and removed 50 (17 requested) atoms. Cycle 37: After refmac, R = 0.1977 (Rfree = 0.000) for 7248 atoms. Found 34 (34 requested) and removed 37 (17 requested) atoms. Cycle 38: After refmac, R = 0.2002 (Rfree = 0.000) for 7224 atoms. Found 34 (34 requested) and removed 25 (17 requested) atoms. Cycle 39: After refmac, R = 0.1857 (Rfree = 0.000) for 7200 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. Cycle 40: After refmac, R = 0.1844 (Rfree = 0.000) for 7183 atoms. Found 34 (34 requested) and removed 28 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.84 3.74 Search for helices and strands: 0 residues in 0 chains, 7397 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 7423 seeds are put forward Round 1: 334 peptides, 69 chains. Longest chain 10 peptides. Score 0.267 Round 2: 367 peptides, 71 chains. Longest chain 11 peptides. Score 0.305 Round 3: 352 peptides, 65 chains. Longest chain 14 peptides. Score 0.322 Round 4: 359 peptides, 65 chains. Longest chain 12 peptides. Score 0.333 Round 5: 354 peptides, 64 chains. Longest chain 16 peptides. Score 0.332 Taking the results from Round 4 Chains 65, Residues 294, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10366 reflections ( 99.41 % complete ) and 17152 restraints for refining 7343 atoms. 16041 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2153 (Rfree = 0.000) for 7343 atoms. Found 34 (34 requested) and removed 57 (17 requested) atoms. Cycle 42: After refmac, R = 0.1877 (Rfree = 0.000) for 7289 atoms. Found 27 (34 requested) and removed 35 (17 requested) atoms. Cycle 43: After refmac, R = 0.1472 (Rfree = 0.000) for 7261 atoms. Found 9 (34 requested) and removed 21 (17 requested) atoms. Cycle 44: After refmac, R = 0.1363 (Rfree = 0.000) for 7236 atoms. Found 11 (34 requested) and removed 19 (17 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1342 (Rfree = 0.000) for 7222 atoms. Found 8 (34 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.78 3.68 Search for helices and strands: 0 residues in 0 chains, 7357 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 7372 seeds are put forward Round 1: 290 peptides, 64 chains. Longest chain 10 peptides. Score 0.228 Round 2: 333 peptides, 65 chains. Longest chain 11 peptides. Score 0.292 Round 3: 350 peptides, 66 chains. Longest chain 11 peptides. Score 0.312 Round 4: 357 peptides, 66 chains. Longest chain 18 peptides. Score 0.323 Round 5: 323 peptides, 59 chains. Longest chain 10 peptides. Score 0.318 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 66, Residues 291, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2pgc-4_warpNtrace.pdb as input Building loops using Loopy2018 66 chains (291 residues) following loop building 2 chains (7 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10366 reflections ( 99.41 % complete ) and 17320 restraints for refining 7411 atoms. 16208 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1714 (Rfree = 0.000) for 7411 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.1649 (Rfree = 0.000) for 7368 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.1804 (Rfree = 0.000) for 7338 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.1470 (Rfree = 0.000) for 7309 atoms. TimeTaking 78.55