Tue 25 Dec 19:27:55 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 1vmi-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vmi-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vmi-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-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/1vmi-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-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 ============================================================ Tue 25 Dec 19:28:05 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/1vmi-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vmi-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 289 and 0 Target number of residues in the AU: 289 Target solvent content: 0.6533 Checking the provided sequence file Detected sequence length: 355 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 355 Adjusted target solvent content: 0.57 Input MTZ file: 1vmi-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: 182 Cell parameters: 94.674 94.674 174.359 90.000 90.000 120.000 Input sequence file: 1vmi-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2840 target number of atoms Had to go as low as 0.70 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 Loops will be built when appropriate and at the last cycle Resolution range: 87.180 3.601 Wilson plot Bfac: 79.92 5807 reflections ( 99.64 % complete ) and 0 restraints for refining 3156 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3404 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3696 (Rfree = 0.000) for 3156 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.26 Search for helices and strands: 0 residues in 0 chains, 3227 seeds are put forward Round 1: 137 peptides, 27 chains. Longest chain 10 peptides. Score 0.293 Round 2: 178 peptides, 25 chains. Longest chain 18 peptides. Score 0.476 Round 3: 208 peptides, 26 chains. Longest chain 15 peptides. Score 0.556 Round 4: 215 peptides, 21 chains. Longest chain 21 peptides. Score 0.637 Round 5: 217 peptides, 22 chains. Longest chain 23 peptides. Score 0.630 Taking the results from Round 4 Chains 27, Residues 194, Estimated correctness of the model 28.5 % 8 chains (75 residues) have been docked in sequence ------------------------------------------------------ 5807 reflections ( 99.64 % complete ) and 4712 restraints for refining 2445 atoms. 3735 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3237 (Rfree = 0.000) for 2445 atoms. Found 15 (15 requested) and removed 46 (7 requested) atoms. Cycle 2: After refmac, R = 0.3417 (Rfree = 0.000) for 2335 atoms. Found 15 (15 requested) and removed 46 (7 requested) atoms. Cycle 3: After refmac, R = 0.3180 (Rfree = 0.000) for 2246 atoms. Found 14 (14 requested) and removed 26 (7 requested) atoms. Cycle 4: After refmac, R = 0.3326 (Rfree = 0.000) for 2184 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.3283 (Rfree = 0.000) for 2128 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 3.39 Search for helices and strands: 0 residues in 0 chains, 2234 seeds are put forward Round 1: 193 peptides, 24 chains. Longest chain 22 peptides. Score 0.538 Round 2: 195 peptides, 22 chains. Longest chain 35 peptides. Score 0.571 Round 3: 195 peptides, 18 chains. Longest chain 29 peptides. Score 0.623 Round 4: 200 peptides, 23 chains. Longest chain 20 peptides. Score 0.572 Round 5: 211 peptides, 20 chains. Longest chain 30 peptides. Score 0.639 Taking the results from Round 5 Chains 24, Residues 191, Estimated correctness of the model 29.2 % 7 chains (75 residues) have been docked in sequence ------------------------------------------------------ 5807 reflections ( 99.64 % complete ) and 4520 restraints for refining 2405 atoms. 3519 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3414 (Rfree = 0.000) for 2405 atoms. Found 15 (15 requested) and removed 67 (7 requested) atoms. Cycle 7: After refmac, R = 0.3224 (Rfree = 0.000) for 2297 atoms. Found 15 (15 requested) and removed 39 (7 requested) atoms. Cycle 8: After refmac, R = 0.3144 (Rfree = 0.000) for 2233 atoms. Found 13 (14 requested) and removed 26 (7 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.3148 (Rfree = 0.000) for 2189 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.3285 (Rfree = 0.000) for 2160 atoms. Found 9 (14 requested) and removed 35 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.02 3.66 Search for helices and strands: 0 residues in 0 chains, 2231 seeds are put forward Round 1: 168 peptides, 25 chains. Longest chain 12 peptides. Score 0.443 Round 2: 206 peptides, 27 chains. Longest chain 19 peptides. Score 0.536 Round 3: 197 peptides, 19 chains. Longest chain 25 peptides. Score 0.616 Round 4: 199 peptides, 25 chains. Longest chain 18 peptides. Score 0.542 Round 5: 202 peptides, 24 chains. Longest chain 19 peptides. Score 0.565 Taking the results from Round 3 Chains 21, Residues 178, Estimated correctness of the model 20.7 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5807 reflections ( 99.64 % complete ) and 4650 restraints for refining 2273 atoms. 3856 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3338 (Rfree = 0.000) for 2273 atoms. Found 14 (14 requested) and removed 41 (7 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.3129 (Rfree = 0.000) for 2201 atoms. Found 11 (14 requested) and removed 33 (7 requested) atoms. Cycle 13: After refmac, R = 0.3035 (Rfree = 0.000) for 2153 atoms. Found 13 (13 requested) and removed 20 (6 requested) atoms. Cycle 14: After refmac, R = 0.3089 (Rfree = 0.000) for 2122 atoms. Found 13 (13 requested) and removed 27 (6 requested) atoms. Cycle 15: After refmac, R = 0.3031 (Rfree = 0.000) for 2091 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.38 Search for helices and strands: 0 residues in 0 chains, 2273 seeds are put forward Round 1: 186 peptides, 29 chains. Longest chain 17 peptides. Score 0.444 Round 2: 197 peptides, 22 chains. Longest chain 21 peptides. Score 0.577 Round 3: 207 peptides, 23 chains. Longest chain 22 peptides. Score 0.592 Round 4: 207 peptides, 21 chains. Longest chain 23 peptides. Score 0.617 Round 5: 214 peptides, 22 chains. Longest chain 24 peptides. Score 0.623 Taking the results from Round 5 Chains 25, Residues 192, Estimated correctness of the model 23.4 % 7 chains (69 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5807 reflections ( 99.64 % complete ) and 4461 restraints for refining 2418 atoms. 3488 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3320 (Rfree = 0.000) for 2418 atoms. Found 15 (15 requested) and removed 92 (7 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.3160 (Rfree = 0.000) for 2298 atoms. Found 14 (15 requested) and removed 24 (7 requested) atoms. Cycle 18: After refmac, R = 0.3083 (Rfree = 0.000) for 2251 atoms. Found 14 (14 requested) and removed 19 (7 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2996 (Rfree = 0.000) for 2226 atoms. Found 12 (14 requested) and removed 31 (7 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2833 (Rfree = 0.000) for 2190 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.59 3.27 Search for helices and strands: 0 residues in 0 chains, 2280 seeds are put forward Round 1: 185 peptides, 25 chains. Longest chain 19 peptides. Score 0.499 Round 2: 198 peptides, 24 chains. Longest chain 26 peptides. Score 0.553 Round 3: 199 peptides, 20 chains. Longest chain 38 peptides. Score 0.608 Round 4: 199 peptides, 22 chains. Longest chain 24 peptides. Score 0.583 Round 5: 195 peptides, 23 chains. Longest chain 27 peptides. Score 0.558 Taking the results from Round 3 Chains 24, Residues 179, Estimated correctness of the model 17.7 % 4 chains (41 residues) have been docked in sequence ------------------------------------------------------ 5807 reflections ( 99.64 % complete ) and 4614 restraints for refining 2321 atoms. 3808 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3229 (Rfree = 0.000) for 2321 atoms. Found 14 (14 requested) and removed 37 (7 requested) atoms. Cycle 22: After refmac, R = 0.2954 (Rfree = 0.000) for 2252 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2823 (Rfree = 0.000) for 2228 atoms. Found 12 (14 requested) and removed 15 (7 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2766 (Rfree = 0.000) for 2207 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 25: After refmac, R = 0.2941 (Rfree = 0.000) for 2192 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 3.21 Search for helices and strands: 0 residues in 0 chains, 2294 seeds are put forward Round 1: 180 peptides, 30 chains. Longest chain 13 peptides. Score 0.408 Round 2: 188 peptides, 23 chains. Longest chain 16 peptides. Score 0.537 Round 3: 200 peptides, 24 chains. Longest chain 26 peptides. Score 0.559 Round 4: 195 peptides, 22 chains. Longest chain 27 peptides. Score 0.571 Round 5: 190 peptides, 24 chains. Longest chain 18 peptides. Score 0.529 Taking the results from Round 4 Chains 27, Residues 173, Estimated correctness of the model 2.9 % 4 chains (50 residues) have been docked in sequence ------------------------------------------------------ 5807 reflections ( 99.64 % complete ) and 4771 restraints for refining 2385 atoms. 3951 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3328 (Rfree = 0.000) for 2385 atoms. Found 15 (15 requested) and removed 44 (7 requested) atoms. Cycle 27: After refmac, R = 0.2982 (Rfree = 0.000) for 2308 atoms. Found 13 (15 requested) and removed 28 (7 requested) atoms. Cycle 28: After refmac, R = 0.2883 (Rfree = 0.000) for 2272 atoms. Found 9 (14 requested) and removed 20 (7 requested) atoms. Cycle 29: After refmac, R = 0.2814 (Rfree = 0.000) for 2237 atoms. Found 10 (14 requested) and removed 18 (7 requested) atoms. Cycle 30: After refmac, R = 0.2886 (Rfree = 0.000) for 2212 atoms. Found 10 (14 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.24 Search for helices and strands: 0 residues in 0 chains, 2313 seeds are put forward Round 1: 169 peptides, 28 chains. Longest chain 21 peptides. Score 0.400 Round 2: 193 peptides, 25 chains. Longest chain 17 peptides. Score 0.524 Round 3: 199 peptides, 27 chains. Longest chain 40 peptides. Score 0.515 Round 4: 196 peptides, 26 chains. Longest chain 33 peptides. Score 0.520 Round 5: 195 peptides, 26 chains. Longest chain 24 peptides. Score 0.517 Taking the results from Round 2 Chains 25, Residues 168, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5807 reflections ( 99.64 % complete ) and 4673 restraints for refining 2248 atoms. 3999 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3189 (Rfree = 0.000) for 2248 atoms. Found 14 (14 requested) and removed 47 (7 requested) atoms. Cycle 32: After refmac, R = 0.3016 (Rfree = 0.000) for 2202 atoms. Found 13 (14 requested) and removed 26 (7 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2877 (Rfree = 0.000) for 2176 atoms. Found 12 (14 requested) and removed 20 (7 requested) atoms. Cycle 34: After refmac, R = 0.2867 (Rfree = 0.000) for 2158 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 35: After refmac, R = 0.2788 (Rfree = 0.000) for 2140 atoms. Found 6 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.29 Search for helices and strands: 0 residues in 0 chains, 2228 seeds are put forward Round 1: 167 peptides, 29 chains. Longest chain 10 peptides. Score 0.376 Round 2: 183 peptides, 25 chains. Longest chain 15 peptides. Score 0.493 Round 3: 201 peptides, 23 chains. Longest chain 28 peptides. Score 0.575 Round 4: 193 peptides, 25 chains. Longest chain 23 peptides. Score 0.524 Round 5: 195 peptides, 24 chains. Longest chain 21 peptides. Score 0.544 Taking the results from Round 3 Chains 24, Residues 178, Estimated correctness of the model 4.6 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 5807 reflections ( 99.64 % complete ) and 4416 restraints for refining 2256 atoms. 3610 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3072 (Rfree = 0.000) for 2256 atoms. Found 12 (14 requested) and removed 17 (7 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.3176 (Rfree = 0.000) for 2233 atoms. Found 12 (14 requested) and removed 21 (7 requested) atoms. Cycle 38: After refmac, R = 0.3134 (Rfree = 0.000) for 2205 atoms. Found 13 (14 requested) and removed 18 (7 requested) atoms. Cycle 39: After refmac, R = 0.2940 (Rfree = 0.000) for 2180 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2865 (Rfree = 0.000) for 2169 atoms. Found 5 (13 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.26 Search for helices and strands: 0 residues in 0 chains, 2252 seeds are put forward Round 1: 144 peptides, 23 chains. Longest chain 21 peptides. Score 0.389 Round 2: 158 peptides, 24 chains. Longest chain 14 peptides. Score 0.423 Round 3: 165 peptides, 23 chains. Longest chain 16 peptides. Score 0.463 Round 4: 169 peptides, 22 chains. Longest chain 15 peptides. Score 0.492 Round 5: 162 peptides, 21 chains. Longest chain 17 peptides. Score 0.484 Taking the results from Round 4 Chains 22, Residues 147, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5807 reflections ( 99.64 % complete ) and 5078 restraints for refining 2302 atoms. 4512 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3360 (Rfree = 0.000) for 2302 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 42: After refmac, R = 0.3033 (Rfree = 0.000) for 2274 atoms. Found 14 (14 requested) and removed 27 (7 requested) atoms. Cycle 43: After refmac, R = 0.3126 (Rfree = 0.000) for 2237 atoms. Found 14 (14 requested) and removed 31 (7 requested) atoms. Cycle 44: After refmac, R = 0.3099 (Rfree = 0.000) for 2200 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. Cycle 45: After refmac, R = 0.3368 (Rfree = 0.000) for 2180 atoms. Found 13 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.87 3.52 Search for helices and strands: 0 residues in 0 chains, 2317 seeds are put forward Round 1: 131 peptides, 24 chains. Longest chain 13 peptides. Score 0.321 Round 2: 140 peptides, 22 chains. Longest chain 14 peptides. Score 0.390 Round 3: 156 peptides, 21 chains. Longest chain 17 peptides. Score 0.464 Round 4: 163 peptides, 23 chains. Longest chain 17 peptides. Score 0.456 Round 5: 177 peptides, 20 chains. Longest chain 26 peptides. Score 0.546 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 157, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 1vmi-3_warpNtrace.pdb as input Building loops using Loopy2018 22 chains (157 residues) following loop building 2 chains (23 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5807 reflections ( 99.64 % complete ) and 4555 restraints for refining 2246 atoms. 3864 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3469 (Rfree = 0.000) for 2246 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.3238 (Rfree = 0.000) for 2207 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.3027 (Rfree = 0.000) for 2170 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2874 (Rfree = 0.000) for 2153 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... TimeTaking 58.52