Mon 24 Dec 00:14:22 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 2f4p-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2f4p-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2f4p-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.4-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/2f4p-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.4-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 00:14:27 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/2f4p-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.4-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 396 and 0 Target number of residues in the AU: 396 Target solvent content: 0.6176 Checking the provided sequence file Detected sequence length: 147 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 588 Adjusted target solvent content: 0.43 Input MTZ file: 2f4p-3.4-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: 170 Cell parameters: 71.746 71.746 188.600 90.000 90.000 120.000 Input sequence file: 2f4p-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4704 target number of atoms Had to go as low as 0.60 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: 21.543 3.400 Wilson plot Bfac: 59.95 7529 reflections ( 99.56 % complete ) and 0 restraints for refining 5176 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3260 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3547 (Rfree = 0.000) for 5176 atoms. Found 39 (39 requested) and removed 111 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.68 Search for helices and strands: 0 residues in 0 chains, 5183 seeds are put forward NCS extension: 0 residues added, 5183 seeds are put forward Round 1: 192 peptides, 40 chains. Longest chain 9 peptides. Score 0.276 Round 2: 267 peptides, 47 chains. Longest chain 14 peptides. Score 0.412 Round 3: 283 peptides, 40 chains. Longest chain 14 peptides. Score 0.532 Round 4: 304 peptides, 47 chains. Longest chain 15 peptides. Score 0.509 Round 5: 313 peptides, 45 chains. Longest chain 16 peptides. Score 0.551 Taking the results from Round 5 Chains 45, Residues 268, Estimated correctness of the model 11.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 9838 restraints for refining 4276 atoms. 8811 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3119 (Rfree = 0.000) for 4276 atoms. Found 32 (32 requested) and removed 84 (16 requested) atoms. Cycle 2: After refmac, R = 0.3211 (Rfree = 0.000) for 4170 atoms. Found 31 (31 requested) and removed 81 (15 requested) atoms. Cycle 3: After refmac, R = 0.3007 (Rfree = 0.000) for 4062 atoms. Found 31 (31 requested) and removed 52 (15 requested) atoms. Cycle 4: After refmac, R = 0.2605 (Rfree = 0.000) for 4000 atoms. Found 30 (30 requested) and removed 38 (15 requested) atoms. Cycle 5: After refmac, R = 0.2658 (Rfree = 0.000) for 3981 atoms. Found 30 (30 requested) and removed 39 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.14 3.45 Search for helices and strands: 0 residues in 0 chains, 4152 seeds are put forward NCS extension: 14 residues added (7 deleted due to clashes), 4166 seeds are put forward Round 1: 234 peptides, 44 chains. Longest chain 9 peptides. Score 0.354 Round 2: 271 peptides, 43 chains. Longest chain 13 peptides. Score 0.469 Round 3: 308 peptides, 45 chains. Longest chain 16 peptides. Score 0.539 Round 4: 307 peptides, 47 chains. Longest chain 17 peptides. Score 0.516 Round 5: 307 peptides, 42 chains. Longest chain 17 peptides. Score 0.568 Taking the results from Round 5 Chains 42, Residues 265, Estimated correctness of the model 17.9 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 8951 restraints for refining 4023 atoms. 7919 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2698 (Rfree = 0.000) for 4023 atoms. Found 29 (30 requested) and removed 50 (15 requested) atoms. Cycle 7: After refmac, R = 0.2399 (Rfree = 0.000) for 3969 atoms. Found 30 (30 requested) and removed 26 (15 requested) atoms. Cycle 8: After refmac, R = 0.2937 (Rfree = 0.000) for 3955 atoms. Found 29 (29 requested) and removed 80 (14 requested) atoms. Cycle 9: After refmac, R = 0.2294 (Rfree = 0.000) for 3877 atoms. Found 29 (29 requested) and removed 25 (14 requested) atoms. Cycle 10: After refmac, R = 0.2328 (Rfree = 0.000) for 3870 atoms. Found 29 (29 requested) and removed 28 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.51 Search for helices and strands: 0 residues in 0 chains, 4053 seeds are put forward NCS extension: 24 residues added (4 deleted due to clashes), 4077 seeds are put forward Round 1: 242 peptides, 44 chains. Longest chain 9 peptides. Score 0.378 Round 2: 293 peptides, 43 chains. Longest chain 18 peptides. Score 0.525 Round 3: 314 peptides, 47 chains. Longest chain 22 peptides. Score 0.533 Round 4: 302 peptides, 50 chains. Longest chain 14 peptides. Score 0.471 Round 5: 313 peptides, 47 chains. Longest chain 24 peptides. Score 0.531 Taking the results from Round 3 Chains 47, Residues 267, Estimated correctness of the model 5.3 % 4 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 8611 restraints for refining 3986 atoms. 7552 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2678 (Rfree = 0.000) for 3986 atoms. Found 25 (30 requested) and removed 42 (15 requested) atoms. Cycle 12: After refmac, R = 0.2358 (Rfree = 0.000) for 3921 atoms. Found 29 (29 requested) and removed 23 (14 requested) atoms. Cycle 13: After refmac, R = 0.2154 (Rfree = 0.000) for 3905 atoms. Found 29 (29 requested) and removed 21 (14 requested) atoms. Cycle 14: After refmac, R = 0.2262 (Rfree = 0.000) for 3902 atoms. Found 24 (29 requested) and removed 20 (14 requested) atoms. Cycle 15: After refmac, R = 0.2133 (Rfree = 0.000) for 3893 atoms. Found 20 (29 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 3.47 Search for helices and strands: 0 residues in 0 chains, 4060 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 4083 seeds are put forward Round 1: 236 peptides, 46 chains. Longest chain 10 peptides. Score 0.335 Round 2: 285 peptides, 47 chains. Longest chain 15 peptides. Score 0.461 Round 3: 293 peptides, 46 chains. Longest chain 15 peptides. Score 0.492 Round 4: 273 peptides, 43 chains. Longest chain 15 peptides. Score 0.475 Round 5: 291 peptides, 43 chains. Longest chain 19 peptides. Score 0.520 Taking the results from Round 5 Chains 45, Residues 248, Estimated correctness of the model 0.4 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 8683 restraints for refining 4026 atoms. 7658 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2467 (Rfree = 0.000) for 4026 atoms. Found 30 (30 requested) and removed 52 (15 requested) atoms. Cycle 17: After refmac, R = 0.2285 (Rfree = 0.000) for 3972 atoms. Found 23 (30 requested) and removed 30 (15 requested) atoms. Cycle 18: After refmac, R = 0.2147 (Rfree = 0.000) for 3947 atoms. Found 18 (29 requested) and removed 24 (14 requested) atoms. Cycle 19: After refmac, R = 0.2227 (Rfree = 0.000) for 3925 atoms. Found 26 (29 requested) and removed 24 (14 requested) atoms. Cycle 20: After refmac, R = 0.2202 (Rfree = 0.000) for 3916 atoms. Found 26 (29 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.17 3.48 Search for helices and strands: 0 residues in 0 chains, 4023 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 4043 seeds are put forward Round 1: 230 peptides, 44 chains. Longest chain 11 peptides. Score 0.342 Round 2: 286 peptides, 48 chains. Longest chain 15 peptides. Score 0.452 Round 3: 280 peptides, 44 chains. Longest chain 21 peptides. Score 0.481 Round 4: 276 peptides, 42 chains. Longest chain 16 peptides. Score 0.494 Round 5: 281 peptides, 45 chains. Longest chain 14 peptides. Score 0.473 Taking the results from Round 4 Chains 43, Residues 234, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 8993 restraints for refining 4099 atoms. 8051 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2413 (Rfree = 0.000) for 4099 atoms. Found 25 (30 requested) and removed 46 (15 requested) atoms. Cycle 22: After refmac, R = 0.2270 (Rfree = 0.000) for 4049 atoms. Found 24 (30 requested) and removed 32 (15 requested) atoms. Cycle 23: After refmac, R = 0.1807 (Rfree = 0.000) for 4019 atoms. Found 17 (30 requested) and removed 20 (15 requested) atoms. Cycle 24: After refmac, R = 0.1705 (Rfree = 0.000) for 4008 atoms. Found 10 (30 requested) and removed 19 (15 requested) atoms. Cycle 25: After refmac, R = 0.1899 (Rfree = 0.000) for 3995 atoms. Found 23 (30 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 3.48 Search for helices and strands: 0 residues in 0 chains, 4118 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4135 seeds are put forward Round 1: 218 peptides, 45 chains. Longest chain 9 peptides. Score 0.292 Round 2: 256 peptides, 44 chains. Longest chain 15 peptides. Score 0.417 Round 3: 257 peptides, 45 chains. Longest chain 14 peptides. Score 0.408 Round 4: 259 peptides, 45 chains. Longest chain 11 peptides. Score 0.414 Round 5: 262 peptides, 42 chains. Longest chain 15 peptides. Score 0.457 Taking the results from Round 5 Chains 42, Residues 220, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 9459 restraints for refining 4158 atoms. 8621 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2353 (Rfree = 0.000) for 4158 atoms. Found 31 (31 requested) and removed 46 (15 requested) atoms. Cycle 27: After refmac, R = 0.2222 (Rfree = 0.000) for 4124 atoms. Found 31 (31 requested) and removed 37 (15 requested) atoms. Cycle 28: After refmac, R = 0.2065 (Rfree = 0.000) for 4105 atoms. Found 26 (31 requested) and removed 29 (15 requested) atoms. Cycle 29: After refmac, R = 0.2301 (Rfree = 0.000) for 4094 atoms. Found 30 (30 requested) and removed 29 (15 requested) atoms. Cycle 30: After refmac, R = 0.1938 (Rfree = 0.000) for 4086 atoms. Found 24 (30 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 3.48 Search for helices and strands: 0 residues in 0 chains, 4221 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 4233 seeds are put forward Round 1: 228 peptides, 47 chains. Longest chain 11 peptides. Score 0.298 Round 2: 247 peptides, 43 chains. Longest chain 13 peptides. Score 0.404 Round 3: 255 peptides, 42 chains. Longest chain 14 peptides. Score 0.438 Round 4: 264 peptides, 46 chains. Longest chain 14 peptides. Score 0.416 Round 5: 265 peptides, 44 chains. Longest chain 15 peptides. Score 0.442 Taking the results from Round 5 Chains 44, Residues 221, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 7529 reflections ( 99.56 % complete ) and 9745 restraints for refining 4213 atoms. 8905 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2226 (Rfree = 0.000) for 4213 atoms. Found 31 (31 requested) and removed 37 (15 requested) atoms. Cycle 32: After refmac, R = 0.2093 (Rfree = 0.000) for 4184 atoms. Found 31 (31 requested) and removed 25 (15 requested) atoms. Cycle 33: After refmac, R = 0.2201 (Rfree = 0.000) for 4185 atoms. Found 31 (31 requested) and removed 24 (15 requested) atoms. Cycle 34: After refmac, R = 0.2251 (Rfree = 0.000) for 4184 atoms. Found 31 (31 requested) and removed 28 (15 requested) atoms. Cycle 35: After refmac, R = 0.2153 (Rfree = 0.000) for 4179 atoms. Found 31 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 3.49 Search for helices and strands: 0 residues in 0 chains, 4302 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 4324 seeds are put forward Round 1: 207 peptides, 43 chains. Longest chain 10 peptides. Score 0.284 Round 2: 241 peptides, 43 chains. Longest chain 17 peptides. Score 0.387 Round 3: 247 peptides, 42 chains. Longest chain 12 peptides. Score 0.416 Round 4: 239 peptides, 36 chains. Longest chain 17 peptides. Score 0.466 Round 5: 231 peptides, 39 chains. Longest chain 14 peptides. Score 0.408 Taking the results from Round 4 Chains 37, Residues 203, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 9293 restraints for refining 4189 atoms. 8465 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2468 (Rfree = 0.000) for 4189 atoms. Found 30 (31 requested) and removed 47 (15 requested) atoms. Cycle 37: After refmac, R = 0.2068 (Rfree = 0.000) for 4151 atoms. Found 25 (31 requested) and removed 21 (15 requested) atoms. Cycle 38: After refmac, R = 0.2542 (Rfree = 0.000) for 4146 atoms. Found 31 (31 requested) and removed 34 (15 requested) atoms. Cycle 39: After refmac, R = 0.2021 (Rfree = 0.000) for 4125 atoms. Found 21 (31 requested) and removed 22 (15 requested) atoms. Cycle 40: After refmac, R = 0.2151 (Rfree = 0.000) for 4116 atoms. Found 31 (31 requested) and removed 28 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.20 3.51 Search for helices and strands: 0 residues in 0 chains, 4205 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4222 seeds are put forward Round 1: 184 peptides, 38 chains. Longest chain 9 peptides. Score 0.277 Round 2: 221 peptides, 40 chains. Longest chain 11 peptides. Score 0.366 Round 3: 220 peptides, 41 chains. Longest chain 12 peptides. Score 0.350 Round 4: 229 peptides, 39 chains. Longest chain 16 peptides. Score 0.402 Round 5: 209 peptides, 40 chains. Longest chain 12 peptides. Score 0.330 Taking the results from Round 4 Chains 39, Residues 190, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7529 reflections ( 99.56 % complete ) and 9499 restraints for refining 4171 atoms. 8756 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2514 (Rfree = 0.000) for 4171 atoms. Found 31 (31 requested) and removed 45 (15 requested) atoms. Cycle 42: After refmac, R = 0.2322 (Rfree = 0.000) for 4145 atoms. Found 31 (31 requested) and removed 41 (15 requested) atoms. Cycle 43: After refmac, R = 0.2366 (Rfree = 0.000) for 4117 atoms. Found 30 (31 requested) and removed 30 (15 requested) atoms. Cycle 44: After refmac, R = 0.2312 (Rfree = 0.000) for 4103 atoms. Found 31 (31 requested) and removed 28 (15 requested) atoms. Cycle 45: After refmac, R = 0.2381 (Rfree = 0.000) for 4097 atoms. Found 31 (31 requested) and removed 35 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.53 Search for helices and strands: 0 residues in 0 chains, 4221 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 4243 seeds are put forward Round 1: 156 peptides, 32 chains. Longest chain 9 peptides. Score 0.268 Round 2: 176 peptides, 33 chains. Longest chain 11 peptides. Score 0.320 Round 3: 185 peptides, 34 chains. Longest chain 12 peptides. Score 0.335 Round 4: 179 peptides, 31 chains. Longest chain 12 peptides. Score 0.357 Round 5: 185 peptides, 33 chains. Longest chain 12 peptides. Score 0.348 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 148, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2f4p-3_warpNtrace.pdb as input Building loops using Loopy2018 31 chains (148 residues) following loop building 3 chains (14 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7529 reflections ( 99.56 % complete ) and 8758 restraints for refining 3975 atoms. 8153 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2303 (Rfree = 0.000) for 3975 atoms. Found 0 (30 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2362 (Rfree = 0.000) for 3948 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2126 (Rfree = 0.000) for 3925 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2339 (Rfree = 0.000) for 3901 atoms. TimeTaking 54.63