Sun 23 Dec 23:47:54 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 2fea-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fea-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fea-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-3.2-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/2fea-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-3.2-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 ============================================================ Sun 23 Dec 23:47:58 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/2fea-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fea-3.2-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 390 and 0 Target number of residues in the AU: 390 Target solvent content: 0.6168 Checking the provided sequence file Detected sequence length: 236 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 472 Adjusted target solvent content: 0.54 Input MTZ file: 2fea-3.2-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: 59.005 43.112 109.575 90.000 98.912 90.000 Input sequence file: 2fea-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3776 target number of atoms Had to go as low as 0.65 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: 22.949 3.200 Wilson plot Bfac: 59.58 9144 reflections ( 98.33 % complete ) and 0 restraints for refining 4173 atoms. Observations/parameters ratio is 0.55 ------------------------------------------------------ Starting model: R = 0.3126 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2492 (Rfree = 0.000) for 4173 atoms. Found 37 (37 requested) and removed 45 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.08 2.92 Search for helices and strands: 0 residues in 0 chains, 4277 seeds are put forward NCS extension: 0 residues added, 4277 seeds are put forward Round 1: 229 peptides, 40 chains. Longest chain 11 peptides. Score 0.392 Round 2: 299 peptides, 41 chains. Longest chain 26 peptides. Score 0.564 Round 3: 296 peptides, 34 chains. Longest chain 43 peptides. Score 0.626 Round 4: 309 peptides, 31 chains. Longest chain 31 peptides. Score 0.679 Round 5: 301 peptides, 30 chains. Longest chain 32 peptides. Score 0.673 Taking the results from Round 4 Chains 31, Residues 278, Estimated correctness of the model 60.6 % 1 chains (30 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 7036 restraints for refining 3447 atoms. 5798 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2557 (Rfree = 0.000) for 3447 atoms. Found 30 (30 requested) and removed 36 (15 requested) atoms. Cycle 2: After refmac, R = 0.2345 (Rfree = 0.000) for 3420 atoms. Found 10 (30 requested) and removed 24 (15 requested) atoms. Cycle 3: After refmac, R = 0.2257 (Rfree = 0.000) for 3397 atoms. Found 8 (30 requested) and removed 18 (15 requested) atoms. Cycle 4: After refmac, R = 0.2213 (Rfree = 0.000) for 3378 atoms. Found 15 (30 requested) and removed 17 (15 requested) atoms. Cycle 5: After refmac, R = 0.2168 (Rfree = 0.000) for 3369 atoms. Found 9 (30 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 2.97 Search for helices and strands: 0 residues in 0 chains, 3499 seeds are put forward NCS extension: 20 residues added (16 deleted due to clashes), 3519 seeds are put forward Round 1: 294 peptides, 33 chains. Longest chain 25 peptides. Score 0.632 Round 2: 311 peptides, 31 chains. Longest chain 32 peptides. Score 0.682 Round 3: 308 peptides, 32 chains. Longest chain 31 peptides. Score 0.668 Round 4: 312 peptides, 31 chains. Longest chain 33 peptides. Score 0.684 Round 5: 317 peptides, 29 chains. Longest chain 24 peptides. Score 0.709 Taking the results from Round 5 Chains 29, Residues 288, Estimated correctness of the model 67.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 7339 restraints for refining 3447 atoms. 6216 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2405 (Rfree = 0.000) for 3447 atoms. Found 30 (30 requested) and removed 20 (15 requested) atoms. Cycle 7: After refmac, R = 0.2215 (Rfree = 0.000) for 3452 atoms. Found 14 (30 requested) and removed 18 (15 requested) atoms. Cycle 8: After refmac, R = 0.2155 (Rfree = 0.000) for 3440 atoms. Found 8 (29 requested) and removed 15 (15 requested) atoms. Cycle 9: After refmac, R = 0.2096 (Rfree = 0.000) for 3429 atoms. Found 3 (28 requested) and removed 15 (15 requested) atoms. Cycle 10: After refmac, R = 0.2084 (Rfree = 0.000) for 3417 atoms. Found 2 (28 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 2.96 Search for helices and strands: 0 residues in 0 chains, 3525 seeds are put forward NCS extension: 18 residues added (7 deleted due to clashes), 3543 seeds are put forward Round 1: 291 peptides, 38 chains. Longest chain 21 peptides. Score 0.576 Round 2: 313 peptides, 33 chains. Longest chain 29 peptides. Score 0.669 Round 3: 298 peptides, 29 chains. Longest chain 26 peptides. Score 0.676 Round 4: 306 peptides, 33 chains. Longest chain 31 peptides. Score 0.656 Round 5: 319 peptides, 32 chains. Longest chain 32 peptides. Score 0.688 Taking the results from Round 5 Chains 34, Residues 287, Estimated correctness of the model 62.6 % 4 chains (69 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 6599 restraints for refining 3447 atoms. 5167 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2587 (Rfree = 0.000) for 3447 atoms. Found 27 (27 requested) and removed 28 (15 requested) atoms. Cycle 12: After refmac, R = 0.2277 (Rfree = 0.000) for 3438 atoms. Found 16 (27 requested) and removed 20 (15 requested) atoms. Cycle 13: After refmac, R = 0.2118 (Rfree = 0.000) for 3417 atoms. Found 11 (27 requested) and removed 15 (15 requested) atoms. Cycle 14: After refmac, R = 0.2049 (Rfree = 0.000) for 3405 atoms. Found 11 (27 requested) and removed 15 (15 requested) atoms. Cycle 15: After refmac, R = 0.2010 (Rfree = 0.000) for 3400 atoms. Found 8 (27 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.09 2.93 Search for helices and strands: 0 residues in 0 chains, 3501 seeds are put forward NCS extension: 21 residues added (16 deleted due to clashes), 3522 seeds are put forward Round 1: 272 peptides, 35 chains. Longest chain 18 peptides. Score 0.564 Round 2: 292 peptides, 30 chains. Longest chain 26 peptides. Score 0.656 Round 3: 286 peptides, 33 chains. Longest chain 29 peptides. Score 0.615 Round 4: 300 peptides, 32 chains. Longest chain 32 peptides. Score 0.653 Round 5: 307 peptides, 33 chains. Longest chain 34 peptides. Score 0.658 Taking the results from Round 5 Chains 34, Residues 274, Estimated correctness of the model 55.7 % 2 chains (46 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 6960 restraints for refining 3445 atoms. 5705 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2432 (Rfree = 0.000) for 3445 atoms. Found 27 (27 requested) and removed 26 (15 requested) atoms. Cycle 17: After refmac, R = 0.2223 (Rfree = 0.000) for 3440 atoms. Found 12 (27 requested) and removed 16 (15 requested) atoms. Cycle 18: After refmac, R = 0.2117 (Rfree = 0.000) for 3432 atoms. Found 7 (27 requested) and removed 15 (15 requested) atoms. Cycle 19: After refmac, R = 0.2036 (Rfree = 0.000) for 3417 atoms. Found 5 (27 requested) and removed 15 (15 requested) atoms. Cycle 20: After refmac, R = 0.1932 (Rfree = 0.000) for 3406 atoms. Found 6 (27 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 2.92 Search for helices and strands: 0 residues in 0 chains, 3514 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 3530 seeds are put forward Round 1: 272 peptides, 38 chains. Longest chain 16 peptides. Score 0.532 Round 2: 306 peptides, 37 chains. Longest chain 24 peptides. Score 0.619 Round 3: 297 peptides, 34 chains. Longest chain 27 peptides. Score 0.629 Round 4: 298 peptides, 33 chains. Longest chain 34 peptides. Score 0.640 Round 5: 289 peptides, 33 chains. Longest chain 39 peptides. Score 0.621 Taking the results from Round 4 Chains 35, Residues 265, Estimated correctness of the model 51.4 % 3 chains (49 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 6814 restraints for refining 3447 atoms. 5565 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2312 (Rfree = 0.000) for 3447 atoms. Found 25 (27 requested) and removed 27 (15 requested) atoms. Cycle 22: After refmac, R = 0.2147 (Rfree = 0.000) for 3438 atoms. Found 10 (27 requested) and removed 19 (15 requested) atoms. Cycle 23: After refmac, R = 0.2100 (Rfree = 0.000) for 3424 atoms. Found 8 (27 requested) and removed 15 (15 requested) atoms. Cycle 24: After refmac, R = 0.2078 (Rfree = 0.000) for 3416 atoms. Found 4 (27 requested) and removed 16 (15 requested) atoms. Cycle 25: After refmac, R = 0.2053 (Rfree = 0.000) for 3403 atoms. Found 3 (27 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.12 2.96 Search for helices and strands: 0 residues in 0 chains, 3501 seeds are put forward NCS extension: 32 residues added (10 deleted due to clashes), 3533 seeds are put forward Round 1: 271 peptides, 33 chains. Longest chain 21 peptides. Score 0.582 Round 2: 295 peptides, 28 chains. Longest chain 28 peptides. Score 0.679 Round 3: 290 peptides, 28 chains. Longest chain 26 peptides. Score 0.670 Round 4: 294 peptides, 31 chains. Longest chain 29 peptides. Score 0.650 Round 5: 297 peptides, 35 chains. Longest chain 20 peptides. Score 0.619 Taking the results from Round 2 Chains 31, Residues 267, Estimated correctness of the model 60.6 % 2 chains (41 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 6976 restraints for refining 3447 atoms. 5780 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2295 (Rfree = 0.000) for 3447 atoms. Found 25 (27 requested) and removed 25 (15 requested) atoms. Cycle 27: After refmac, R = 0.2149 (Rfree = 0.000) for 3440 atoms. Found 9 (27 requested) and removed 15 (15 requested) atoms. Cycle 28: After refmac, R = 0.2063 (Rfree = 0.000) for 3428 atoms. Found 5 (27 requested) and removed 15 (15 requested) atoms. Cycle 29: After refmac, R = 0.2048 (Rfree = 0.000) for 3417 atoms. Found 1 (27 requested) and removed 16 (15 requested) atoms. Cycle 30: After refmac, R = 0.2042 (Rfree = 0.000) for 3400 atoms. Found 7 (27 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.11 2.95 Search for helices and strands: 0 residues in 0 chains, 3508 seeds are put forward NCS extension: 11 residues added (12 deleted due to clashes), 3519 seeds are put forward Round 1: 266 peptides, 35 chains. Longest chain 19 peptides. Score 0.550 Round 2: 296 peptides, 34 chains. Longest chain 28 peptides. Score 0.626 Round 3: 299 peptides, 32 chains. Longest chain 25 peptides. Score 0.651 Round 4: 296 peptides, 31 chains. Longest chain 36 peptides. Score 0.654 Round 5: 305 peptides, 35 chains. Longest chain 23 peptides. Score 0.635 Taking the results from Round 4 Chains 34, Residues 265, Estimated correctness of the model 54.8 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 7249 restraints for refining 3447 atoms. 6091 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2303 (Rfree = 0.000) for 3447 atoms. Found 27 (27 requested) and removed 21 (15 requested) atoms. Cycle 32: After refmac, R = 0.2090 (Rfree = 0.000) for 3442 atoms. Found 16 (27 requested) and removed 15 (15 requested) atoms. Cycle 33: After refmac, R = 0.2051 (Rfree = 0.000) for 3436 atoms. Found 9 (27 requested) and removed 15 (15 requested) atoms. Cycle 34: After refmac, R = 0.1968 (Rfree = 0.000) for 3427 atoms. Found 6 (27 requested) and removed 15 (15 requested) atoms. Cycle 35: After refmac, R = 0.2021 (Rfree = 0.000) for 3416 atoms. Found 2 (27 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.09 2.93 Search for helices and strands: 0 residues in 0 chains, 3524 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3543 seeds are put forward Round 1: 245 peptides, 35 chains. Longest chain 15 peptides. Score 0.497 Round 2: 271 peptides, 36 chains. Longest chain 17 peptides. Score 0.551 Round 3: 265 peptides, 31 chains. Longest chain 19 peptides. Score 0.589 Round 4: 260 peptides, 33 chains. Longest chain 19 peptides. Score 0.557 Round 5: 265 peptides, 31 chains. Longest chain 20 peptides. Score 0.589 Taking the results from Round 5 Chains 31, Residues 234, Estimated correctness of the model 38.1 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 7470 restraints for refining 3446 atoms. 6501 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2229 (Rfree = 0.000) for 3446 atoms. Found 24 (27 requested) and removed 18 (15 requested) atoms. Cycle 37: After refmac, R = 0.2073 (Rfree = 0.000) for 3444 atoms. Found 12 (27 requested) and removed 18 (15 requested) atoms. Cycle 38: After refmac, R = 0.2035 (Rfree = 0.000) for 3434 atoms. Found 8 (27 requested) and removed 16 (15 requested) atoms. Cycle 39: After refmac, R = 0.1966 (Rfree = 0.000) for 3418 atoms. Found 4 (27 requested) and removed 16 (15 requested) atoms. Cycle 40: After refmac, R = 0.1974 (Rfree = 0.000) for 3405 atoms. Found 7 (27 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.13 2.97 Search for helices and strands: 0 residues in 0 chains, 3486 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 3503 seeds are put forward Round 1: 242 peptides, 36 chains. Longest chain 17 peptides. Score 0.478 Round 2: 275 peptides, 35 chains. Longest chain 18 peptides. Score 0.571 Round 3: 267 peptides, 35 chains. Longest chain 19 peptides. Score 0.552 Round 4: 253 peptides, 35 chains. Longest chain 13 peptides. Score 0.518 Round 5: 276 peptides, 39 chains. Longest chain 15 peptides. Score 0.531 Taking the results from Round 2 Chains 35, Residues 240, Estimated correctness of the model 33.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9144 reflections ( 98.33 % complete ) and 7602 restraints for refining 3447 atoms. 6677 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2077 (Rfree = 0.000) for 3447 atoms. Found 18 (27 requested) and removed 16 (15 requested) atoms. Cycle 42: After refmac, R = 0.1953 (Rfree = 0.000) for 3446 atoms. Found 11 (27 requested) and removed 15 (15 requested) atoms. Cycle 43: After refmac, R = 0.1884 (Rfree = 0.000) for 3439 atoms. Found 4 (27 requested) and removed 16 (15 requested) atoms. Cycle 44: After refmac, R = 0.1876 (Rfree = 0.000) for 3427 atoms. Found 3 (27 requested) and removed 15 (15 requested) atoms. Cycle 45: After refmac, R = 0.1838 (Rfree = 0.000) for 3412 atoms. Found 4 (27 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 2.94 Search for helices and strands: 0 residues in 0 chains, 3503 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3521 seeds are put forward Round 1: 234 peptides, 38 chains. Longest chain 13 peptides. Score 0.432 Round 2: 271 peptides, 37 chains. Longest chain 17 peptides. Score 0.540 Round 3: 263 peptides, 38 chains. Longest chain 14 peptides. Score 0.509 Round 4: 266 peptides, 34 chains. Longest chain 20 peptides. Score 0.560 Round 5: 249 peptides, 35 chains. Longest chain 14 peptides. Score 0.507 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 232, Estimated correctness of the model 29.8 % 1 chains (19 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2fea-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9144 reflections ( 98.33 % complete ) and 7377 restraints for refining 3447 atoms. 6392 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2193 (Rfree = 0.000) for 3447 atoms. Found 0 (27 requested) and removed 5 (15 requested) atoms. Cycle 47: After refmac, R = 0.2059 (Rfree = 0.000) for 3439 atoms. Found 0 (27 requested) and removed 2 (15 requested) atoms. Cycle 48: After refmac, R = 0.2099 (Rfree = 0.000) for 3434 atoms. Found 0 (27 requested) and removed 7 (15 requested) atoms. Cycle 49: After refmac, R = 0.2045 (Rfree = 0.000) for 3426 atoms. Found 0 (27 requested) and removed 2 (15 requested) atoms. Writing output files ... TimeTaking 40.5