Sun 23 Dec 22:22:56 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p8j-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p8j-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p8j-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-3.6-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-3.6-parrot-hancs ############### 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 22:23:06 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/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p8j-3.6-parrot-hancs/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 420 and 0 Target number of residues in the AU: 420 Target solvent content: 0.6483 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.65 Input MTZ file: 2p8j-3.6-parrot-hancs.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: 152 Cell parameters: 83.860 83.860 159.200 90.000 90.000 120.000 Input sequence file: 2p8j-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3344 target number of atoms Had to go as low as 1.05 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: 72.625 3.600 Wilson plot Bfac: 77.09 7821 reflections ( 98.53 % complete ) and 0 restraints for refining 3715 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3403 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2912 (Rfree = 0.000) for 3715 atoms. Found 23 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 2.86 Search for helices and strands: 0 residues in 0 chains, 3780 seeds are put forward NCS extension: 0 residues added, 3780 seeds are put forward Round 1: 257 peptides, 40 chains. Longest chain 15 peptides. Score 0.438 Round 2: 282 peptides, 36 chains. Longest chain 22 peptides. Score 0.535 Round 3: 306 peptides, 33 chains. Longest chain 26 peptides. Score 0.609 Round 4: 302 peptides, 32 chains. Longest chain 20 peptides. Score 0.611 Round 5: 309 peptides, 27 chains. Longest chain 28 peptides. Score 0.665 Taking the results from Round 5 Chains 27, Residues 282, Estimated correctness of the model 38.3 % 2 chains (45 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 5882 restraints for refining 3036 atoms. 4605 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2595 (Rfree = 0.000) for 3036 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 2: After refmac, R = 0.2380 (Rfree = 0.000) for 3001 atoms. Found 13 (19 requested) and removed 14 (9 requested) atoms. Cycle 3: After refmac, R = 0.2281 (Rfree = 0.000) for 2980 atoms. Found 10 (19 requested) and removed 10 (9 requested) atoms. Cycle 4: After refmac, R = 0.2292 (Rfree = 0.000) for 2971 atoms. Found 15 (19 requested) and removed 16 (9 requested) atoms. Cycle 5: After refmac, R = 0.2194 (Rfree = 0.000) for 2965 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 2.86 Search for helices and strands: 0 residues in 0 chains, 3090 seeds are put forward NCS extension: 36 residues added (6 deleted due to clashes), 3126 seeds are put forward Round 1: 277 peptides, 34 chains. Longest chain 15 peptides. Score 0.543 Round 2: 292 peptides, 28 chains. Longest chain 51 peptides. Score 0.627 Round 3: 299 peptides, 28 chains. Longest chain 37 peptides. Score 0.639 Round 4: 298 peptides, 26 chains. Longest chain 27 peptides. Score 0.654 Round 5: 311 peptides, 31 chains. Longest chain 44 peptides. Score 0.635 Taking the results from Round 4 Chains 28, Residues 272, Estimated correctness of the model 34.5 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 6411 restraints for refining 3032 atoms. 5319 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2466 (Rfree = 0.000) for 3032 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 7: After refmac, R = 0.2206 (Rfree = 0.000) for 3020 atoms. Found 7 (19 requested) and removed 11 (9 requested) atoms. Cycle 8: After refmac, R = 0.2137 (Rfree = 0.000) for 3009 atoms. Found 8 (19 requested) and removed 13 (9 requested) atoms. Cycle 9: After refmac, R = 0.2153 (Rfree = 0.000) for 3002 atoms. Found 6 (19 requested) and removed 10 (9 requested) atoms. Cycle 10: After refmac, R = 0.2102 (Rfree = 0.000) for 2997 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.52 2.86 Search for helices and strands: 0 residues in 0 chains, 3116 seeds are put forward NCS extension: 36 residues added (3 deleted due to clashes), 3152 seeds are put forward Round 1: 273 peptides, 32 chains. Longest chain 29 peptides. Score 0.554 Round 2: 296 peptides, 30 chains. Longest chain 34 peptides. Score 0.617 Round 3: 298 peptides, 28 chains. Longest chain 51 peptides. Score 0.638 Round 4: 306 peptides, 25 chains. Longest chain 42 peptides. Score 0.676 Round 5: 305 peptides, 27 chains. Longest chain 38 peptides. Score 0.658 Taking the results from Round 4 Chains 26, Residues 281, Estimated correctness of the model 42.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 6264 restraints for refining 3032 atoms. 5143 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2568 (Rfree = 0.000) for 3032 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 12: After refmac, R = 0.2289 (Rfree = 0.000) for 3022 atoms. Found 9 (19 requested) and removed 12 (9 requested) atoms. Cycle 13: After refmac, R = 0.2183 (Rfree = 0.000) for 3012 atoms. Found 5 (19 requested) and removed 10 (9 requested) atoms. Cycle 14: After refmac, R = 0.2137 (Rfree = 0.000) for 3005 atoms. Found 3 (19 requested) and removed 9 (9 requested) atoms. Cycle 15: After refmac, R = 0.2110 (Rfree = 0.000) for 2994 atoms. Found 4 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 2.87 Search for helices and strands: 0 residues in 0 chains, 3091 seeds are put forward NCS extension: 58 residues added (4 deleted due to clashes), 3149 seeds are put forward Round 1: 287 peptides, 38 chains. Longest chain 19 peptides. Score 0.526 Round 2: 301 peptides, 29 chains. Longest chain 31 peptides. Score 0.635 Round 3: 307 peptides, 32 chains. Longest chain 26 peptides. Score 0.620 Round 4: 298 peptides, 27 chains. Longest chain 51 peptides. Score 0.646 Round 5: 294 peptides, 29 chains. Longest chain 40 peptides. Score 0.622 Taking the results from Round 4 Chains 29, Residues 271, Estimated correctness of the model 31.8 % 2 chains (73 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 5606 restraints for refining 3030 atoms. 4239 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2645 (Rfree = 0.000) for 3030 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Cycle 17: After refmac, R = 0.2440 (Rfree = 0.000) for 3004 atoms. Found 9 (19 requested) and removed 14 (9 requested) atoms. Cycle 18: After refmac, R = 0.2351 (Rfree = 0.000) for 2991 atoms. Found 9 (19 requested) and removed 16 (9 requested) atoms. Cycle 19: After refmac, R = 0.2239 (Rfree = 0.000) for 2981 atoms. Found 8 (19 requested) and removed 12 (9 requested) atoms. Cycle 20: After refmac, R = 0.2198 (Rfree = 0.000) for 2972 atoms. Found 4 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.49 2.84 Search for helices and strands: 0 residues in 0 chains, 3063 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 3097 seeds are put forward Round 1: 277 peptides, 35 chains. Longest chain 33 peptides. Score 0.534 Round 2: 285 peptides, 35 chains. Longest chain 21 peptides. Score 0.550 Round 3: 293 peptides, 28 chains. Longest chain 41 peptides. Score 0.629 Round 4: 299 peptides, 34 chains. Longest chain 41 peptides. Score 0.587 Round 5: 287 peptides, 30 chains. Longest chain 40 peptides. Score 0.600 Taking the results from Round 3 Chains 30, Residues 265, Estimated correctness of the model 25.6 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 6289 restraints for refining 3032 atoms. 5159 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2571 (Rfree = 0.000) for 3032 atoms. Found 18 (19 requested) and removed 15 (9 requested) atoms. Cycle 22: After refmac, R = 0.2383 (Rfree = 0.000) for 3023 atoms. Found 5 (19 requested) and removed 14 (9 requested) atoms. Cycle 23: After refmac, R = 0.2344 (Rfree = 0.000) for 3003 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. Cycle 24: After refmac, R = 0.2276 (Rfree = 0.000) for 2994 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. Cycle 25: After refmac, R = 0.2230 (Rfree = 0.000) for 2986 atoms. Found 4 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 2.86 Search for helices and strands: 0 residues in 0 chains, 3083 seeds are put forward NCS extension: 21 residues added (6 deleted due to clashes), 3104 seeds are put forward Round 1: 277 peptides, 30 chains. Longest chain 40 peptides. Score 0.581 Round 2: 291 peptides, 28 chains. Longest chain 40 peptides. Score 0.625 Round 3: 297 peptides, 32 chains. Longest chain 21 peptides. Score 0.601 Round 4: 291 peptides, 30 chains. Longest chain 40 peptides. Score 0.608 Round 5: 297 peptides, 30 chains. Longest chain 22 peptides. Score 0.619 Taking the results from Round 2 Chains 28, Residues 263, Estimated correctness of the model 24.2 % 2 chains (64 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 5675 restraints for refining 3030 atoms. 4360 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2473 (Rfree = 0.000) for 3030 atoms. Found 16 (19 requested) and removed 33 (9 requested) atoms. Cycle 27: After refmac, R = 0.2290 (Rfree = 0.000) for 2997 atoms. Found 6 (19 requested) and removed 13 (9 requested) atoms. Cycle 28: After refmac, R = 0.2302 (Rfree = 0.000) for 2977 atoms. Found 10 (19 requested) and removed 12 (9 requested) atoms. Cycle 29: After refmac, R = 0.2239 (Rfree = 0.000) for 2968 atoms. Found 10 (19 requested) and removed 11 (9 requested) atoms. Cycle 30: After refmac, R = 0.2166 (Rfree = 0.000) for 2961 atoms. Found 8 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 2.85 Search for helices and strands: 0 residues in 0 chains, 3064 seeds are put forward NCS extension: 61 residues added (1 deleted due to clashes), 3125 seeds are put forward Round 1: 251 peptides, 29 chains. Longest chain 24 peptides. Score 0.537 Round 2: 292 peptides, 28 chains. Longest chain 26 peptides. Score 0.627 Round 3: 295 peptides, 30 chains. Longest chain 25 peptides. Score 0.615 Round 4: 284 peptides, 31 chains. Longest chain 22 peptides. Score 0.585 Round 5: 269 peptides, 31 chains. Longest chain 32 peptides. Score 0.555 Taking the results from Round 2 Chains 29, Residues 264, Estimated correctness of the model 24.9 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 6078 restraints for refining 3031 atoms. 4906 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2356 (Rfree = 0.000) for 3031 atoms. Found 14 (19 requested) and removed 14 (9 requested) atoms. Cycle 32: After refmac, R = 0.2224 (Rfree = 0.000) for 3018 atoms. Found 5 (19 requested) and removed 12 (9 requested) atoms. Cycle 33: After refmac, R = 0.2187 (Rfree = 0.000) for 3005 atoms. Found 11 (19 requested) and removed 9 (9 requested) atoms. Cycle 34: After refmac, R = 0.2132 (Rfree = 0.000) for 3006 atoms. Found 7 (19 requested) and removed 10 (9 requested) atoms. Cycle 35: After refmac, R = 0.2083 (Rfree = 0.000) for 3000 atoms. Found 11 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 2.83 Search for helices and strands: 0 residues in 0 chains, 3100 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 3122 seeds are put forward Round 1: 258 peptides, 37 chains. Longest chain 30 peptides. Score 0.471 Round 2: 289 peptides, 30 chains. Longest chain 35 peptides. Score 0.604 Round 3: 289 peptides, 28 chains. Longest chain 33 peptides. Score 0.622 Round 4: 289 peptides, 26 chains. Longest chain 23 peptides. Score 0.639 Round 5: 274 peptides, 28 chains. Longest chain 44 peptides. Score 0.593 Taking the results from Round 4 Chains 26, Residues 263, Estimated correctness of the model 29.3 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 6295 restraints for refining 3032 atoms. 5223 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2309 (Rfree = 0.000) for 3032 atoms. Found 15 (19 requested) and removed 11 (9 requested) atoms. Cycle 37: After refmac, R = 0.2140 (Rfree = 0.000) for 3025 atoms. Found 10 (19 requested) and removed 13 (9 requested) atoms. Cycle 38: After refmac, R = 0.2136 (Rfree = 0.000) for 3016 atoms. Found 4 (19 requested) and removed 17 (9 requested) atoms. Cycle 39: After refmac, R = 0.2144 (Rfree = 0.000) for 3001 atoms. Found 9 (19 requested) and removed 9 (9 requested) atoms. Cycle 40: After refmac, R = 0.2109 (Rfree = 0.000) for 2994 atoms. Found 6 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 2.83 Search for helices and strands: 0 residues in 0 chains, 3083 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 3104 seeds are put forward Round 1: 251 peptides, 37 chains. Longest chain 23 peptides. Score 0.455 Round 2: 268 peptides, 27 chains. Longest chain 20 peptides. Score 0.591 Round 3: 267 peptides, 29 chains. Longest chain 29 peptides. Score 0.570 Round 4: 271 peptides, 32 chains. Longest chain 34 peptides. Score 0.550 Round 5: 284 peptides, 30 chains. Longest chain 29 peptides. Score 0.594 Taking the results from Round 5 Chains 30, Residues 254, Estimated correctness of the model 12.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 6563 restraints for refining 3032 atoms. 5577 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2411 (Rfree = 0.000) for 3032 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 42: After refmac, R = 0.2195 (Rfree = 0.000) for 3029 atoms. Found 9 (19 requested) and removed 9 (9 requested) atoms. Cycle 43: After refmac, R = 0.2148 (Rfree = 0.000) for 3024 atoms. Found 12 (19 requested) and removed 11 (9 requested) atoms. Cycle 44: After refmac, R = 0.2079 (Rfree = 0.000) for 3018 atoms. Found 4 (19 requested) and removed 11 (9 requested) atoms. Cycle 45: After refmac, R = 0.2008 (Rfree = 0.000) for 3006 atoms. Found 4 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 2.83 Search for helices and strands: 0 residues in 0 chains, 3128 seeds are put forward NCS extension: 33 residues added (2 deleted due to clashes), 3161 seeds are put forward Round 1: 228 peptides, 33 chains. Longest chain 22 peptides. Score 0.443 Round 2: 258 peptides, 30 chains. Longest chain 27 peptides. Score 0.542 Round 3: 261 peptides, 27 chains. Longest chain 22 peptides. Score 0.577 Round 4: 259 peptides, 24 chains. Longest chain 31 peptides. Score 0.601 Round 5: 247 peptides, 26 chains. Longest chain 27 peptides. Score 0.558 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 235, Estimated correctness of the model 15.0 % 3 chains (64 residues) have been docked in sequence Sequence coverage is 27 % Consider running further cycles of model building using 2p8j-3_warpNtrace.pdb as input Building loops using Loopy2018 25 chains (235 residues) following loop building 3 chains (64 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7821 reflections ( 98.53 % complete ) and 5887 restraints for refining 3032 atoms. 4701 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2355 (Rfree = 0.000) for 3032 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2297 (Rfree = 0.000) for 3008 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2321 (Rfree = 0.000) for 2987 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2249 (Rfree = 0.000) for 2970 atoms. TimeTaking 57.8