Mon 24 Dec 00:55:13 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 2it9-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2it9-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2it9-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2it9-4.0-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/2it9-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2it9-4.0-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 ============================================================ Mon 24 Dec 00:55:18 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/2it9-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2it9-4.0-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 378 and 0 Target number of residues in the AU: 378 Target solvent content: 0.6600 Checking the provided sequence file Detected sequence length: 127 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 508 Adjusted target solvent content: 0.54 Input MTZ file: 2it9-4.0-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: 19 Cell parameters: 59.723 81.014 124.347 90.000 90.000 90.000 Input sequence file: 2it9-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4064 target number of atoms Had to go as low as 0.90 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: 67.879 4.000 Wilson plot Bfac: 84.33 5337 reflections ( 98.03 % complete ) and 0 restraints for refining 4496 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3706 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3228 (Rfree = 0.000) for 4496 atoms. Found 21 (21 requested) and removed 183 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 4360 seeds are put forward NCS extension: 0 residues added, 4360 seeds are put forward Round 1: 183 peptides, 33 chains. Longest chain 14 peptides. Score 0.333 Round 2: 239 peptides, 40 chains. Longest chain 11 peptides. Score 0.405 Round 3: 257 peptides, 39 chains. Longest chain 14 peptides. Score 0.463 Round 4: 268 peptides, 38 chains. Longest chain 17 peptides. Score 0.500 Round 5: 266 peptides, 35 chains. Longest chain 19 peptides. Score 0.527 Taking the results from Round 5 Chains 35, Residues 231, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 5337 reflections ( 98.03 % complete ) and 8350 restraints for refining 3669 atoms. 7436 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2833 (Rfree = 0.000) for 3669 atoms. Found 14 (17 requested) and removed 48 (8 requested) atoms. Cycle 2: After refmac, R = 0.2636 (Rfree = 0.000) for 3592 atoms. Found 10 (17 requested) and removed 31 (8 requested) atoms. Cycle 3: After refmac, R = 0.2357 (Rfree = 0.000) for 3554 atoms. Found 6 (16 requested) and removed 26 (8 requested) atoms. Cycle 4: After refmac, R = 0.2405 (Rfree = 0.000) for 3513 atoms. Found 8 (16 requested) and removed 22 (8 requested) atoms. Cycle 5: After refmac, R = 0.2328 (Rfree = 0.000) for 3487 atoms. Found 6 (16 requested) and removed 28 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.66 3.47 Search for helices and strands: 0 residues in 0 chains, 3601 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 3619 seeds are put forward Round 1: 214 peptides, 39 chains. Longest chain 13 peptides. Score 0.348 Round 2: 250 peptides, 42 chains. Longest chain 14 peptides. Score 0.411 Round 3: 246 peptides, 39 chains. Longest chain 14 peptides. Score 0.435 Round 4: 248 peptides, 36 chains. Longest chain 17 peptides. Score 0.473 Round 5: 241 peptides, 37 chains. Longest chain 18 peptides. Score 0.445 Taking the results from Round 4 Chains 36, Residues 212, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5337 reflections ( 98.03 % complete ) and 8670 restraints for refining 3667 atoms. 7858 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2518 (Rfree = 0.000) for 3667 atoms. Found 15 (17 requested) and removed 39 (8 requested) atoms. Cycle 7: After refmac, R = 0.2286 (Rfree = 0.000) for 3628 atoms. Found 4 (17 requested) and removed 21 (8 requested) atoms. Cycle 8: After refmac, R = 0.2187 (Rfree = 0.000) for 3603 atoms. Found 14 (17 requested) and removed 22 (8 requested) atoms. Cycle 9: After refmac, R = 0.2307 (Rfree = 0.000) for 3578 atoms. Found 13 (17 requested) and removed 20 (8 requested) atoms. Cycle 10: After refmac, R = 0.2085 (Rfree = 0.000) for 3559 atoms. Found 9 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 3707 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 3733 seeds are put forward Round 1: 217 peptides, 40 chains. Longest chain 10 peptides. Score 0.344 Round 2: 251 peptides, 38 chains. Longest chain 18 peptides. Score 0.459 Round 3: 267 peptides, 42 chains. Longest chain 18 peptides. Score 0.455 Round 4: 266 peptides, 37 chains. Longest chain 18 peptides. Score 0.506 Round 5: 252 peptides, 35 chains. Longest chain 16 peptides. Score 0.494 Taking the results from Round 4 Chains 37, Residues 229, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5337 reflections ( 98.03 % complete ) and 8543 restraints for refining 3668 atoms. 7664 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2340 (Rfree = 0.000) for 3668 atoms. Found 13 (17 requested) and removed 27 (8 requested) atoms. Cycle 12: After refmac, R = 0.2196 (Rfree = 0.000) for 3640 atoms. Found 15 (17 requested) and removed 21 (8 requested) atoms. Cycle 13: After refmac, R = 0.2092 (Rfree = 0.000) for 3625 atoms. Found 16 (17 requested) and removed 18 (8 requested) atoms. Cycle 14: After refmac, R = 0.2102 (Rfree = 0.000) for 3615 atoms. Found 15 (17 requested) and removed 19 (8 requested) atoms. Cycle 15: After refmac, R = 0.2020 (Rfree = 0.000) for 3605 atoms. Found 13 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 3746 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3767 seeds are put forward Round 1: 217 peptides, 42 chains. Longest chain 11 peptides. Score 0.320 Round 2: 255 peptides, 41 chains. Longest chain 16 peptides. Score 0.435 Round 3: 249 peptides, 41 chains. Longest chain 15 peptides. Score 0.420 Round 4: 247 peptides, 40 chains. Longest chain 18 peptides. Score 0.426 Round 5: 235 peptides, 38 chains. Longest chain 18 peptides. Score 0.418 Taking the results from Round 2 Chains 41, Residues 214, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5337 reflections ( 98.03 % complete ) and 8357 restraints for refining 3670 atoms. 7542 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2141 (Rfree = 0.000) for 3670 atoms. Found 7 (17 requested) and removed 19 (8 requested) atoms. Cycle 17: After refmac, R = 0.2097 (Rfree = 0.000) for 3630 atoms. Found 13 (17 requested) and removed 17 (8 requested) atoms. Cycle 18: After refmac, R = 0.2116 (Rfree = 0.000) for 3612 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 19: After refmac, R = 0.1971 (Rfree = 0.000) for 3602 atoms. Found 15 (17 requested) and removed 17 (8 requested) atoms. Cycle 20: After refmac, R = 0.1958 (Rfree = 0.000) for 3591 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.70 3.51 Search for helices and strands: 0 residues in 0 chains, 3700 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3719 seeds are put forward Round 1: 234 peptides, 48 chains. Longest chain 8 peptides. Score 0.296 Round 2: 238 peptides, 40 chains. Longest chain 14 peptides. Score 0.402 Round 3: 246 peptides, 40 chains. Longest chain 11 peptides. Score 0.423 Round 4: 237 peptides, 36 chains. Longest chain 15 peptides. Score 0.446 Round 5: 232 peptides, 37 chains. Longest chain 19 peptides. Score 0.421 Taking the results from Round 4 Chains 36, Residues 201, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5337 reflections ( 98.03 % complete ) and 8561 restraints for refining 3669 atoms. 7793 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2265 (Rfree = 0.000) for 3669 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 22: After refmac, R = 0.2183 (Rfree = 0.000) for 3651 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 23: After refmac, R = 0.2058 (Rfree = 0.000) for 3633 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 24: After refmac, R = 0.2019 (Rfree = 0.000) for 3619 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 25: After refmac, R = 0.1977 (Rfree = 0.000) for 3619 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.76 3.56 Search for helices and strands: 0 residues in 0 chains, 3736 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3754 seeds are put forward Round 1: 180 peptides, 38 chains. Longest chain 9 peptides. Score 0.259 Round 2: 217 peptides, 40 chains. Longest chain 17 peptides. Score 0.344 Round 3: 195 peptides, 37 chains. Longest chain 14 peptides. Score 0.318 Round 4: 216 peptides, 35 chains. Longest chain 15 peptides. Score 0.402 Round 5: 223 peptides, 36 chains. Longest chain 14 peptides. Score 0.409 Taking the results from Round 5 Chains 36, Residues 187, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5337 reflections ( 98.03 % complete ) and 8684 restraints for refining 3670 atoms. 7947 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2232 (Rfree = 0.000) for 3670 atoms. Found 14 (17 requested) and removed 16 (8 requested) atoms. Cycle 27: After refmac, R = 0.2203 (Rfree = 0.000) for 3641 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 28: After refmac, R = 0.1998 (Rfree = 0.000) for 3631 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 29: After refmac, R = 0.2005 (Rfree = 0.000) for 3613 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 30: After refmac, R = 0.1569 (Rfree = 0.000) for 3602 atoms. Found 3 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 3704 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3724 seeds are put forward Round 1: 191 peptides, 39 chains. Longest chain 10 peptides. Score 0.280 Round 2: 211 peptides, 36 chains. Longest chain 11 peptides. Score 0.376 Round 3: 214 peptides, 38 chains. Longest chain 11 peptides. Score 0.360 Round 4: 209 peptides, 39 chains. Longest chain 12 peptides. Score 0.334 Round 5: 213 peptides, 38 chains. Longest chain 11 peptides. Score 0.357 Taking the results from Round 2 Chains 36, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5337 reflections ( 98.03 % complete ) and 8466 restraints for refining 3667 atoms. 7802 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2216 (Rfree = 0.000) for 3667 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 32: After refmac, R = 0.2068 (Rfree = 0.000) for 3648 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.2063 (Rfree = 0.000) for 3652 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 34: After refmac, R = 0.1954 (Rfree = 0.000) for 3642 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 35: After refmac, R = 0.1858 (Rfree = 0.000) for 3640 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.67 3.48 Search for helices and strands: 0 residues in 0 chains, 3767 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3783 seeds are put forward Round 1: 184 peptides, 39 chains. Longest chain 8 peptides. Score 0.259 Round 2: 217 peptides, 40 chains. Longest chain 9 peptides. Score 0.344 Round 3: 218 peptides, 39 chains. Longest chain 11 peptides. Score 0.359 Round 4: 213 peptides, 38 chains. Longest chain 13 peptides. Score 0.357 Round 5: 211 peptides, 38 chains. Longest chain 11 peptides. Score 0.352 Taking the results from Round 3 Chains 39, Residues 179, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5337 reflections ( 98.03 % complete ) and 8480 restraints for refining 3670 atoms. 7803 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2224 (Rfree = 0.000) for 3670 atoms. Found 14 (17 requested) and removed 20 (8 requested) atoms. Cycle 37: After refmac, R = 0.2188 (Rfree = 0.000) for 3636 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 38: After refmac, R = 0.2144 (Rfree = 0.000) for 3624 atoms. Found 15 (17 requested) and removed 19 (8 requested) atoms. Cycle 39: After refmac, R = 0.2047 (Rfree = 0.000) for 3604 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 40: After refmac, R = 0.1748 (Rfree = 0.000) for 3594 atoms. Found 3 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 3691 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3705 seeds are put forward Round 1: 149 peptides, 33 chains. Longest chain 6 peptides. Score 0.226 Round 2: 180 peptides, 34 chains. Longest chain 10 peptides. Score 0.311 Round 3: 204 peptides, 39 chains. Longest chain 9 peptides. Score 0.319 Round 4: 212 peptides, 37 chains. Longest chain 12 peptides. Score 0.367 Round 5: 200 peptides, 36 chains. Longest chain 11 peptides. Score 0.345 Taking the results from Round 4 Chains 37, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5337 reflections ( 98.03 % complete ) and 8664 restraints for refining 3670 atoms. 8001 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2398 (Rfree = 0.000) for 3670 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 42: After refmac, R = 0.2289 (Rfree = 0.000) for 3656 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 43: After refmac, R = 0.2182 (Rfree = 0.000) for 3641 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 44: After refmac, R = 0.2111 (Rfree = 0.000) for 3630 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 45: After refmac, R = 0.2008 (Rfree = 0.000) for 3625 atoms. Found 12 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.73 3.54 Search for helices and strands: 0 residues in 0 chains, 3727 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3742 seeds are put forward Round 1: 155 peptides, 35 chains. Longest chain 7 peptides. Score 0.218 Round 2: 180 peptides, 35 chains. Longest chain 10 peptides. Score 0.298 Round 3: 174 peptides, 32 chains. Longest chain 10 peptides. Score 0.319 Round 4: 193 peptides, 36 chains. Longest chain 8 peptides. Score 0.324 Round 5: 177 peptides, 31 chains. Longest chain 12 peptides. Score 0.341 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 146, 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 2it9-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5337 reflections ( 98.03 % complete ) and 8797 restraints for refining 3669 atoms. 8244 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2394 (Rfree = 0.000) for 3669 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2235 (Rfree = 0.000) for 3642 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2112 (Rfree = 0.000) for 3625 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2148 (Rfree = 0.000) for 3605 atoms. TimeTaking 38.68