Mon 24 Dec 00:11:24 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 2opk-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2opk-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2opk-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opk-3.8-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/2opk-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opk-3.8-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 00:11:28 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/2opk-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opk-3.8-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 400 and 0 Target number of residues in the AU: 400 Target solvent content: 0.6190 Checking the provided sequence file Detected sequence length: 112 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 448 Adjusted target solvent content: 0.57 Input MTZ file: 2opk-3.8-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: 96 Cell parameters: 75.570 75.570 198.970 90.000 90.000 90.000 Input sequence file: 2opk-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3584 target number of atoms Had to go as low as 0.85 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: 28.177 3.801 Wilson plot Bfac: 60.71 6142 reflections ( 99.53 % complete ) and 0 restraints for refining 3965 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3033 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2244 (Rfree = 0.000) for 3965 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 3.07 Search for helices and strands: 0 residues in 0 chains, 3999 seeds are put forward NCS extension: 0 residues added, 3999 seeds are put forward Round 1: 228 peptides, 38 chains. Longest chain 14 peptides. Score 0.409 Round 2: 305 peptides, 36 chains. Longest chain 25 peptides. Score 0.617 Round 3: 309 peptides, 35 chains. Longest chain 42 peptides. Score 0.634 Round 4: 343 peptides, 38 chains. Longest chain 23 peptides. Score 0.672 Round 5: 359 peptides, 38 chains. Longest chain 34 peptides. Score 0.699 Taking the results from Round 5 Chains 41, Residues 321, Estimated correctness of the model 39.9 % 3 chains (43 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 6114 restraints for refining 3240 atoms. 4694 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2791 (Rfree = 0.000) for 3240 atoms. Found 17 (17 requested) and removed 30 (8 requested) atoms. Cycle 2: After refmac, R = 0.2654 (Rfree = 0.000) for 3157 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 3: After refmac, R = 0.2635 (Rfree = 0.000) for 3122 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 4: After refmac, R = 0.2390 (Rfree = 0.000) for 3094 atoms. Found 10 (17 requested) and removed 21 (8 requested) atoms. Cycle 5: After refmac, R = 0.2428 (Rfree = 0.000) for 3071 atoms. Found 15 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.06 Search for helices and strands: 0 residues in 0 chains, 3124 seeds are put forward NCS extension: 10 residues added (5 deleted due to clashes), 3134 seeds are put forward Round 1: 289 peptides, 42 chains. Longest chain 19 peptides. Score 0.522 Round 2: 321 peptides, 40 chains. Longest chain 20 peptides. Score 0.613 Round 3: 315 peptides, 37 chains. Longest chain 20 peptides. Score 0.628 Round 4: 320 peptides, 34 chains. Longest chain 22 peptides. Score 0.664 Round 5: 327 peptides, 40 chains. Longest chain 23 peptides. Score 0.625 Taking the results from Round 4 Chains 38, Residues 286, Estimated correctness of the model 26.5 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 6600 restraints for refining 3241 atoms. 5365 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2476 (Rfree = 0.000) for 3241 atoms. Found 17 (17 requested) and removed 28 (8 requested) atoms. Cycle 7: After refmac, R = 0.2390 (Rfree = 0.000) for 3203 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 8: After refmac, R = 0.2287 (Rfree = 0.000) for 3188 atoms. Found 14 (17 requested) and removed 24 (8 requested) atoms. Cycle 9: After refmac, R = 0.2202 (Rfree = 0.000) for 3170 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 10: After refmac, R = 0.2134 (Rfree = 0.000) for 3156 atoms. Found 10 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.10 Search for helices and strands: 0 residues in 0 chains, 3231 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 3252 seeds are put forward Round 1: 266 peptides, 38 chains. Longest chain 17 peptides. Score 0.509 Round 2: 303 peptides, 39 chains. Longest chain 25 peptides. Score 0.585 Round 3: 289 peptides, 35 chains. Longest chain 17 peptides. Score 0.593 Round 4: 305 peptides, 36 chains. Longest chain 29 peptides. Score 0.617 Round 5: 310 peptides, 35 chains. Longest chain 25 peptides. Score 0.636 Taking the results from Round 5 Chains 36, Residues 275, Estimated correctness of the model 14.8 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6142 reflections ( 99.53 % complete ) and 6893 restraints for refining 3241 atoms. 5788 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2559 (Rfree = 0.000) for 3241 atoms. Found 15 (17 requested) and removed 18 (8 requested) atoms. Cycle 12: After refmac, R = 0.2286 (Rfree = 0.000) for 3224 atoms. Found 10 (17 requested) and removed 14 (8 requested) atoms. Cycle 13: After refmac, R = 0.2289 (Rfree = 0.000) for 3213 atoms. Found 6 (17 requested) and removed 13 (8 requested) atoms. Cycle 14: After refmac, R = 0.2285 (Rfree = 0.000) for 3201 atoms. Found 6 (17 requested) and removed 9 (8 requested) atoms. Cycle 15: After refmac, R = 0.2268 (Rfree = 0.000) for 3194 atoms. Found 4 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.09 Search for helices and strands: 0 residues in 0 chains, 3243 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 3269 seeds are put forward Round 1: 284 peptides, 43 chains. Longest chain 20 peptides. Score 0.499 Round 2: 289 peptides, 40 chains. Longest chain 19 peptides. Score 0.543 Round 3: 296 peptides, 36 chains. Longest chain 24 peptides. Score 0.599 Round 4: 302 peptides, 37 chains. Longest chain 42 peptides. Score 0.602 Round 5: 296 peptides, 34 chains. Longest chain 21 peptides. Score 0.618 Taking the results from Round 5 Chains 34, Residues 262, Estimated correctness of the model 7.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6142 reflections ( 99.53 % complete ) and 7077 restraints for refining 3239 atoms. 6063 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2759 (Rfree = 0.000) for 3239 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 17: After refmac, R = 0.2418 (Rfree = 0.000) for 3216 atoms. Found 17 (17 requested) and removed 24 (8 requested) atoms. Cycle 18: After refmac, R = 0.2085 (Rfree = 0.000) for 3197 atoms. Found 9 (17 requested) and removed 11 (8 requested) atoms. Cycle 19: After refmac, R = 0.2094 (Rfree = 0.000) for 3187 atoms. Found 12 (17 requested) and removed 13 (8 requested) atoms. Cycle 20: After refmac, R = 0.2001 (Rfree = 0.000) for 3180 atoms. Found 5 (17 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.07 Search for helices and strands: 0 residues in 0 chains, 3229 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 3252 seeds are put forward Round 1: 255 peptides, 38 chains. Longest chain 17 peptides. Score 0.482 Round 2: 262 peptides, 37 chains. Longest chain 14 peptides. Score 0.510 Round 3: 265 peptides, 32 chains. Longest chain 16 peptides. Score 0.571 Round 4: 291 peptides, 34 chains. Longest chain 23 peptides. Score 0.607 Round 5: 287 peptides, 35 chains. Longest chain 22 peptides. Score 0.589 Taking the results from Round 4 Chains 35, Residues 257, Estimated correctness of the model 2.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 7045 restraints for refining 3241 atoms. 6028 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2381 (Rfree = 0.000) for 3241 atoms. Found 12 (17 requested) and removed 19 (8 requested) atoms. Cycle 22: After refmac, R = 0.2280 (Rfree = 0.000) for 3229 atoms. Found 13 (17 requested) and removed 19 (8 requested) atoms. Cycle 23: After refmac, R = 0.2349 (Rfree = 0.000) for 3221 atoms. Found 16 (17 requested) and removed 16 (8 requested) atoms. Cycle 24: After refmac, R = 0.2281 (Rfree = 0.000) for 3216 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 25: After refmac, R = 0.2053 (Rfree = 0.000) for 3219 atoms. Found 2 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.36 3.06 Search for helices and strands: 0 residues in 0 chains, 3254 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 3276 seeds are put forward Round 1: 223 peptides, 38 chains. Longest chain 16 peptides. Score 0.395 Round 2: 260 peptides, 38 chains. Longest chain 17 peptides. Score 0.494 Round 3: 261 peptides, 37 chains. Longest chain 18 peptides. Score 0.508 Round 4: 268 peptides, 37 chains. Longest chain 25 peptides. Score 0.525 Round 5: 248 peptides, 35 chains. Longest chain 14 peptides. Score 0.498 Taking the results from Round 4 Chains 38, Residues 231, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 7129 restraints for refining 3240 atoms. 6214 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2350 (Rfree = 0.000) for 3240 atoms. Found 14 (17 requested) and removed 13 (8 requested) atoms. Cycle 27: After refmac, R = 0.2155 (Rfree = 0.000) for 3224 atoms. Found 8 (17 requested) and removed 15 (8 requested) atoms. Cycle 28: After refmac, R = 0.2238 (Rfree = 0.000) for 3209 atoms. Found 16 (17 requested) and removed 13 (8 requested) atoms. Cycle 29: After refmac, R = 0.2142 (Rfree = 0.000) for 3200 atoms. Found 16 (17 requested) and removed 16 (8 requested) atoms. Cycle 30: After refmac, R = 0.2147 (Rfree = 0.000) for 3194 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 3.05 Search for helices and strands: 0 residues in 0 chains, 3249 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 3278 seeds are put forward Round 1: 228 peptides, 44 chains. Longest chain 9 peptides. Score 0.334 Round 2: 249 peptides, 38 chains. Longest chain 19 peptides. Score 0.466 Round 3: 272 peptides, 43 chains. Longest chain 17 peptides. Score 0.469 Round 4: 250 peptides, 34 chains. Longest chain 18 peptides. Score 0.514 Round 5: 284 peptides, 36 chains. Longest chain 20 peptides. Score 0.573 Taking the results from Round 5 Chains 39, Residues 248, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 6870 restraints for refining 3241 atoms. 5827 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2393 (Rfree = 0.000) for 3241 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 32: After refmac, R = 0.2316 (Rfree = 0.000) for 3224 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 33: After refmac, R = 0.2292 (Rfree = 0.000) for 3214 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 34: After refmac, R = 0.2016 (Rfree = 0.000) for 3204 atoms. Found 9 (17 requested) and removed 14 (8 requested) atoms. Cycle 35: After refmac, R = 0.2034 (Rfree = 0.000) for 3194 atoms. Found 11 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.10 Search for helices and strands: 0 residues in 0 chains, 3274 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3296 seeds are put forward Round 1: 202 peptides, 37 chains. Longest chain 10 peptides. Score 0.346 Round 2: 258 peptides, 39 chains. Longest chain 16 peptides. Score 0.478 Round 3: 268 peptides, 42 chains. Longest chain 17 peptides. Score 0.470 Round 4: 255 peptides, 39 chains. Longest chain 15 peptides. Score 0.470 Round 5: 268 peptides, 34 chains. Longest chain 26 peptides. Score 0.557 Taking the results from Round 5 Chains 34, Residues 234, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 7266 restraints for refining 3239 atoms. 6364 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2388 (Rfree = 0.000) for 3239 atoms. Found 10 (17 requested) and removed 17 (8 requested) atoms. Cycle 37: After refmac, R = 0.2495 (Rfree = 0.000) for 3219 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 38: After refmac, R = 0.2412 (Rfree = 0.000) for 3207 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 39: After refmac, R = 0.2361 (Rfree = 0.000) for 3195 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 40: After refmac, R = 0.2152 (Rfree = 0.000) for 3193 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 3.02 Search for helices and strands: 0 residues in 0 chains, 3277 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 3307 seeds are put forward Round 1: 205 peptides, 40 chains. Longest chain 10 peptides. Score 0.316 Round 2: 255 peptides, 44 chains. Longest chain 19 peptides. Score 0.412 Round 3: 263 peptides, 40 chains. Longest chain 16 peptides. Score 0.480 Round 4: 254 peptides, 39 chains. Longest chain 18 peptides. Score 0.468 Round 5: 272 peptides, 39 chains. Longest chain 18 peptides. Score 0.513 Taking the results from Round 5 Chains 40, Residues 233, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6142 reflections ( 99.53 % complete ) and 6999 restraints for refining 3241 atoms. 6065 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2626 (Rfree = 0.000) for 3241 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 42: After refmac, R = 0.2483 (Rfree = 0.000) for 3209 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 43: After refmac, R = 0.2072 (Rfree = 0.000) for 3187 atoms. Found 9 (17 requested) and removed 15 (8 requested) atoms. Cycle 44: After refmac, R = 0.2217 (Rfree = 0.000) for 3178 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 45: After refmac, R = 0.2377 (Rfree = 0.000) for 3172 atoms. Found 17 (17 requested) and removed 30 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 3.01 Search for helices and strands: 0 residues in 0 chains, 3206 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3221 seeds are put forward Round 1: 208 peptides, 42 chains. Longest chain 11 peptides. Score 0.299 Round 2: 233 peptides, 39 chains. Longest chain 17 peptides. Score 0.411 Round 3: 239 peptides, 39 chains. Longest chain 17 peptides. Score 0.427 Round 4: 232 peptides, 40 chains. Longest chain 17 peptides. Score 0.396 Round 5: 246 peptides, 39 chains. Longest chain 17 peptides. Score 0.446 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 207, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2opk-3_warpNtrace.pdb as input Building loops using Loopy2018 40 chains (207 residues) following loop building 2 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6142 reflections ( 99.53 % complete ) and 7274 restraints for refining 3241 atoms. 6439 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2687 (Rfree = 0.000) for 3241 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2530 (Rfree = 0.000) for 3211 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2505 (Rfree = 0.000) for 3197 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2538 (Rfree = 0.000) for 3184 atoms. TimeTaking 45.73