null Sun 23 Dec 23:57:01 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 2p7i-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p7i-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p7i-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.6-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/2p7i-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.6-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 23:57:06 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/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.6-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 346 and 0 Target number of residues in the AU: 346 Target solvent content: 0.6574 Checking the provided sequence file Detected sequence length: 250 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 500 Adjusted target solvent content: 0.50 Input MTZ file: 2p7i-3.6-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: 97 Cell parameters: 120.769 120.769 149.904 90.000 90.000 90.000 Input sequence file: 2p7i-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4000 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: 94.045 3.600 Wilson plot Bfac: 83.07 6704 reflections ( 99.70 % complete ) and 0 restraints for refining 4403 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3299 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3227 (Rfree = 0.000) for 4403 atoms. Found 15 (28 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.58 Search for helices and strands: 0 residues in 0 chains, 4479 seeds are put forward NCS extension: 0 residues added, 4479 seeds are put forward Round 1: 205 peptides, 40 chains. Longest chain 10 peptides. Score 0.320 Round 2: 262 peptides, 42 chains. Longest chain 16 peptides. Score 0.463 Round 3: 276 peptides, 38 chains. Longest chain 21 peptides. Score 0.543 Round 4: 306 peptides, 38 chains. Longest chain 23 peptides. Score 0.612 Round 5: 308 peptides, 41 chains. Longest chain 21 peptides. Score 0.587 Taking the results from Round 4 Chains 41, Residues 268, Estimated correctness of the model 19.3 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 7912 restraints for refining 3623 atoms. 6771 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2800 (Rfree = 0.000) for 3623 atoms. Found 14 (23 requested) and removed 25 (11 requested) atoms. Cycle 2: After refmac, R = 0.2642 (Rfree = 0.000) for 3523 atoms. Found 14 (23 requested) and removed 17 (11 requested) atoms. Cycle 3: After refmac, R = 0.2496 (Rfree = 0.000) for 3485 atoms. Found 8 (22 requested) and removed 17 (11 requested) atoms. Cycle 4: After refmac, R = 0.2387 (Rfree = 0.000) for 3457 atoms. Found 5 (22 requested) and removed 17 (11 requested) atoms. Cycle 5: After refmac, R = 0.2387 (Rfree = 0.000) for 3432 atoms. Found 4 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 3.54 Search for helices and strands: 0 residues in 0 chains, 3549 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 3570 seeds are put forward Round 1: 246 peptides, 40 chains. Longest chain 20 peptides. Score 0.442 Round 2: 298 peptides, 47 chains. Longest chain 20 peptides. Score 0.500 Round 3: 310 peptides, 41 chains. Longest chain 23 peptides. Score 0.591 Round 4: 316 peptides, 40 chains. Longest chain 20 peptides. Score 0.614 Round 5: 290 peptides, 37 chains. Longest chain 26 peptides. Score 0.586 Taking the results from Round 4 Chains 40, Residues 276, Estimated correctness of the model 20.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 7975 restraints for refining 3541 atoms. 6911 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2606 (Rfree = 0.000) for 3541 atoms. Found 18 (22 requested) and removed 26 (11 requested) atoms. Cycle 7: After refmac, R = 0.2388 (Rfree = 0.000) for 3501 atoms. Found 10 (22 requested) and removed 16 (11 requested) atoms. Cycle 8: After refmac, R = 0.2302 (Rfree = 0.000) for 3477 atoms. Found 7 (22 requested) and removed 19 (11 requested) atoms. Cycle 9: After refmac, R = 0.1978 (Rfree = 0.000) for 3454 atoms. Found 2 (22 requested) and removed 13 (11 requested) atoms. Cycle 10: After refmac, R = 0.1992 (Rfree = 0.000) for 3441 atoms. Found 1 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.54 Search for helices and strands: 0 residues in 0 chains, 3568 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3590 seeds are put forward Round 1: 260 peptides, 45 chains. Longest chain 18 peptides. Score 0.421 Round 2: 277 peptides, 36 chains. Longest chain 15 peptides. Score 0.567 Round 3: 290 peptides, 38 chains. Longest chain 20 peptides. Score 0.576 Round 4: 275 peptides, 40 chains. Longest chain 18 peptides. Score 0.519 Round 5: 287 peptides, 38 chains. Longest chain 20 peptides. Score 0.569 Taking the results from Round 3 Chains 38, Residues 252, Estimated correctness of the model 5.1 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8008 restraints for refining 3626 atoms. 6997 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2310 (Rfree = 0.000) for 3626 atoms. Found 12 (23 requested) and removed 23 (11 requested) atoms. Cycle 12: After refmac, R = 0.2121 (Rfree = 0.000) for 3585 atoms. Found 11 (23 requested) and removed 16 (11 requested) atoms. Cycle 13: After refmac, R = 0.2047 (Rfree = 0.000) for 3574 atoms. Found 7 (22 requested) and removed 14 (11 requested) atoms. Cycle 14: After refmac, R = 0.2124 (Rfree = 0.000) for 3562 atoms. Found 6 (22 requested) and removed 15 (11 requested) atoms. Cycle 15: After refmac, R = 0.1993 (Rfree = 0.000) for 3548 atoms. Found 6 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.52 Search for helices and strands: 0 residues in 0 chains, 3660 seeds are put forward NCS extension: 25 residues added (6 deleted due to clashes), 3685 seeds are put forward Round 1: 240 peptides, 43 chains. Longest chain 12 peptides. Score 0.388 Round 2: 259 peptides, 46 chains. Longest chain 12 peptides. Score 0.406 Round 3: 265 peptides, 42 chains. Longest chain 16 peptides. Score 0.471 Round 4: 254 peptides, 37 chains. Longest chain 19 peptides. Score 0.499 Round 5: 265 peptides, 36 chains. Longest chain 21 peptides. Score 0.538 Taking the results from Round 5 Chains 36, Residues 229, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8412 restraints for refining 3626 atoms. 7532 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2404 (Rfree = 0.000) for 3626 atoms. Found 9 (23 requested) and removed 18 (11 requested) atoms. Cycle 17: After refmac, R = 0.2316 (Rfree = 0.000) for 3608 atoms. Found 18 (23 requested) and removed 15 (11 requested) atoms. Cycle 18: After refmac, R = 0.2083 (Rfree = 0.000) for 3600 atoms. Found 7 (23 requested) and removed 15 (11 requested) atoms. Cycle 19: After refmac, R = 0.2094 (Rfree = 0.000) for 3581 atoms. Found 9 (23 requested) and removed 13 (11 requested) atoms. Cycle 20: After refmac, R = 0.2007 (Rfree = 0.000) for 3569 atoms. Found 11 (22 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 3.55 Search for helices and strands: 0 residues in 0 chains, 3729 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3750 seeds are put forward Round 1: 211 peptides, 37 chains. Longest chain 13 peptides. Score 0.379 Round 2: 250 peptides, 36 chains. Longest chain 17 peptides. Score 0.500 Round 3: 257 peptides, 37 chains. Longest chain 16 peptides. Score 0.507 Round 4: 251 peptides, 33 chains. Longest chain 16 peptides. Score 0.537 Round 5: 256 peptides, 32 chains. Longest chain 29 peptides. Score 0.560 Taking the results from Round 5 Chains 32, Residues 224, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8392 restraints for refining 3626 atoms. 7528 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2096 (Rfree = 0.000) for 3626 atoms. Found 9 (23 requested) and removed 14 (11 requested) atoms. Cycle 22: After refmac, R = 0.1969 (Rfree = 0.000) for 3608 atoms. Found 7 (23 requested) and removed 14 (11 requested) atoms. Cycle 23: After refmac, R = 0.1779 (Rfree = 0.000) for 3590 atoms. Found 4 (23 requested) and removed 15 (11 requested) atoms. Cycle 24: After refmac, R = 0.2054 (Rfree = 0.000) for 3571 atoms. Found 10 (22 requested) and removed 16 (11 requested) atoms. Cycle 25: After refmac, R = 0.1925 (Rfree = 0.000) for 3548 atoms. Found 11 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 3.53 Search for helices and strands: 0 residues in 0 chains, 3678 seeds are put forward NCS extension: 52 residues added (1 deleted due to clashes), 3730 seeds are put forward Round 1: 229 peptides, 46 chains. Longest chain 11 peptides. Score 0.316 Round 2: 252 peptides, 43 chains. Longest chain 13 peptides. Score 0.423 Round 3: 249 peptides, 37 chains. Longest chain 15 peptides. Score 0.486 Round 4: 266 peptides, 45 chains. Longest chain 13 peptides. Score 0.438 Round 5: 257 peptides, 40 chains. Longest chain 20 peptides. Score 0.472 Taking the results from Round 3 Chains 37, Residues 212, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8236 restraints for refining 3625 atoms. 7360 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2440 (Rfree = 0.000) for 3625 atoms. Found 20 (23 requested) and removed 108 (11 requested) atoms. Cycle 27: After refmac, R = 0.2127 (Rfree = 0.000) for 3491 atoms. Found 12 (22 requested) and removed 13 (11 requested) atoms. Cycle 28: After refmac, R = 0.2137 (Rfree = 0.000) for 3476 atoms. Found 17 (22 requested) and removed 16 (11 requested) atoms. Cycle 29: After refmac, R = 0.1919 (Rfree = 0.000) for 3457 atoms. Found 10 (22 requested) and removed 14 (11 requested) atoms. Cycle 30: After refmac, R = 0.1857 (Rfree = 0.000) for 3446 atoms. Found 9 (22 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 3.52 Search for helices and strands: 0 residues in 0 chains, 3557 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3575 seeds are put forward Round 1: 211 peptides, 43 chains. Longest chain 9 peptides. Score 0.299 Round 2: 245 peptides, 42 chains. Longest chain 15 peptides. Score 0.415 Round 3: 251 peptides, 42 chains. Longest chain 15 peptides. Score 0.432 Round 4: 250 peptides, 35 chains. Longest chain 17 peptides. Score 0.512 Round 5: 252 peptides, 37 chains. Longest chain 17 peptides. Score 0.494 Taking the results from Round 4 Chains 37, Residues 215, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8044 restraints for refining 3561 atoms. 7186 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2132 (Rfree = 0.000) for 3561 atoms. Found 8 (22 requested) and removed 17 (11 requested) atoms. Cycle 32: After refmac, R = 0.1971 (Rfree = 0.000) for 3539 atoms. Found 10 (22 requested) and removed 14 (11 requested) atoms. Cycle 33: After refmac, R = 0.1911 (Rfree = 0.000) for 3530 atoms. Found 13 (22 requested) and removed 13 (11 requested) atoms. Cycle 34: After refmac, R = 0.1916 (Rfree = 0.000) for 3519 atoms. Found 13 (22 requested) and removed 13 (11 requested) atoms. Cycle 35: After refmac, R = 0.1951 (Rfree = 0.000) for 3515 atoms. Found 10 (22 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.56 Search for helices and strands: 0 residues in 0 chains, 3644 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3664 seeds are put forward Round 1: 196 peptides, 40 chains. Longest chain 8 peptides. Score 0.291 Round 2: 226 peptides, 40 chains. Longest chain 14 peptides. Score 0.385 Round 3: 238 peptides, 38 chains. Longest chain 15 peptides. Score 0.444 Round 4: 241 peptides, 38 chains. Longest chain 17 peptides. Score 0.453 Round 5: 259 peptides, 42 chains. Longest chain 16 peptides. Score 0.454 Taking the results from Round 5 Chains 43, Residues 217, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8242 restraints for refining 3626 atoms. 7377 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2346 (Rfree = 0.000) for 3626 atoms. Found 18 (23 requested) and removed 12 (11 requested) atoms. Cycle 37: After refmac, R = 0.2255 (Rfree = 0.000) for 3609 atoms. Found 14 (23 requested) and removed 13 (11 requested) atoms. Cycle 38: After refmac, R = 0.2212 (Rfree = 0.000) for 3599 atoms. Found 21 (23 requested) and removed 14 (11 requested) atoms. Cycle 39: After refmac, R = 0.2100 (Rfree = 0.000) for 3600 atoms. Found 16 (23 requested) and removed 14 (11 requested) atoms. Cycle 40: After refmac, R = 0.1689 (Rfree = 0.000) for 3594 atoms. Found 3 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.55 3.55 Search for helices and strands: 0 residues in 0 chains, 3708 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3724 seeds are put forward Round 1: 187 peptides, 37 chains. Longest chain 13 peptides. Score 0.303 Round 2: 207 peptides, 38 chains. Longest chain 9 peptides. Score 0.353 Round 3: 202 peptides, 35 chains. Longest chain 13 peptides. Score 0.377 Round 4: 209 peptides, 35 chains. Longest chain 12 peptides. Score 0.399 Round 5: 232 peptides, 38 chains. Longest chain 13 peptides. Score 0.427 Taking the results from Round 5 Chains 38, Residues 194, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6704 reflections ( 99.70 % complete ) and 8575 restraints for refining 3626 atoms. 7837 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2074 (Rfree = 0.000) for 3626 atoms. Found 8 (23 requested) and removed 17 (11 requested) atoms. Cycle 42: After refmac, R = 0.2059 (Rfree = 0.000) for 3604 atoms. Found 16 (23 requested) and removed 14 (11 requested) atoms. Cycle 43: After refmac, R = 0.2076 (Rfree = 0.000) for 3600 atoms. Found 22 (23 requested) and removed 16 (11 requested) atoms. Cycle 44: After refmac, R = 0.1727 (Rfree = 0.000) for 3599 atoms. Found 3 (23 requested) and removed 12 (11 requested) atoms. Cycle 45: After refmac, R = 0.1644 (Rfree = 0.000) for 3588 atoms. Found 2 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.58 3.58 Search for helices and strands: 0 residues in 0 chains, 3685 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3703 seeds are put forward Round 1: 169 peptides, 33 chains. Longest chain 12 peptides. Score 0.300 Round 2: 192 peptides, 30 chains. Longest chain 14 peptides. Score 0.413 Round 3: 194 peptides, 30 chains. Longest chain 14 peptides. Score 0.419 Round 4: 206 peptides, 33 chains. Longest chain 16 peptides. Score 0.415 Round 5: 209 peptides, 32 chains. Longest chain 13 peptides. Score 0.437 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 177, 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 2p7i-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6704 reflections ( 99.70 % complete ) and 8607 restraints for refining 3626 atoms. 7931 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2139 (Rfree = 0.000) for 3626 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2124 (Rfree = 0.000) for 3601 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2195 (Rfree = 0.000) for 3582 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2165 (Rfree = 0.000) for 3564 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:43:39 GMT 2018 Job finished. TimeTaking 46.64 Used memory is bytes: 18835616