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 2od6-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2od6-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2od6-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od6-3.8-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/2od6-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od6-3.8-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/2od6-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od6-3.8-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 304 and 0 Target number of residues in the AU: 304 Target solvent content: 0.6639 Checking the provided sequence file Detected sequence length: 110 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 440 Adjusted target solvent content: 0.51 Input MTZ file: 2od6-3.8-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: 19 Cell parameters: 36.403 92.834 144.837 90.000 90.000 90.000 Input sequence file: 2od6-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3520 target number of atoms Had to go as low as 0.75 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: 29.066 3.800 Wilson plot Bfac: 87.53 5189 reflections ( 98.56 % complete ) and 0 restraints for refining 3879 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3481 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3349 (Rfree = 0.000) for 3879 atoms. Found 13 (21 requested) and removed 23 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 3.62 Search for helices and strands: 0 residues in 0 chains, 3974 seeds are put forward NCS extension: 0 residues added, 3974 seeds are put forward Round 1: 139 peptides, 29 chains. Longest chain 10 peptides. Score 0.261 Round 2: 200 peptides, 35 chains. Longest chain 14 peptides. Score 0.389 Round 3: 225 peptides, 37 chains. Longest chain 12 peptides. Score 0.441 Round 4: 235 peptides, 34 chains. Longest chain 17 peptides. Score 0.510 Round 5: 246 peptides, 34 chains. Longest chain 17 peptides. Score 0.541 Taking the results from Round 5 Chains 34, Residues 212, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 7310 restraints for refining 3183 atoms. 6496 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2999 (Rfree = 0.000) for 3183 atoms. Found 10 (17 requested) and removed 25 (8 requested) atoms. Cycle 2: After refmac, R = 0.2936 (Rfree = 0.000) for 3105 atoms. Found 12 (17 requested) and removed 14 (8 requested) atoms. Cycle 3: After refmac, R = 0.2871 (Rfree = 0.000) for 3062 atoms. Found 14 (17 requested) and removed 17 (8 requested) atoms. Cycle 4: After refmac, R = 0.2786 (Rfree = 0.000) for 3033 atoms. Found 11 (16 requested) and removed 12 (8 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2793 (Rfree = 0.000) for 3011 atoms. Found 9 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 3.66 Search for helices and strands: 0 residues in 0 chains, 3163 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 3190 seeds are put forward Round 1: 191 peptides, 38 chains. Longest chain 10 peptides. Score 0.314 Round 2: 238 peptides, 36 chains. Longest chain 15 peptides. Score 0.493 Round 3: 234 peptides, 35 chains. Longest chain 17 peptides. Score 0.494 Round 4: 223 peptides, 31 chains. Longest chain 17 peptides. Score 0.514 Round 5: 239 peptides, 30 chains. Longest chain 21 peptides. Score 0.570 Taking the results from Round 5 Chains 30, Residues 209, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 7055 restraints for refining 3084 atoms. 6249 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2772 (Rfree = 0.000) for 3084 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2601 (Rfree = 0.000) for 3046 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2628 (Rfree = 0.000) for 3022 atoms. Found 11 (16 requested) and removed 20 (8 requested) atoms. Cycle 9: After refmac, R = 0.2381 (Rfree = 0.000) for 3000 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 10: After refmac, R = 0.2361 (Rfree = 0.000) for 2989 atoms. Found 8 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.76 3.71 Search for helices and strands: 0 residues in 0 chains, 3126 seeds are put forward NCS extension: 32 residues added (3 deleted due to clashes), 3158 seeds are put forward Round 1: 198 peptides, 39 chains. Longest chain 9 peptides. Score 0.324 Round 2: 238 peptides, 36 chains. Longest chain 17 peptides. Score 0.493 Round 3: 245 peptides, 37 chains. Longest chain 13 peptides. Score 0.501 Round 4: 226 peptides, 32 chains. Longest chain 19 peptides. Score 0.510 Round 5: 233 peptides, 32 chains. Longest chain 29 peptides. Score 0.529 Taking the results from Round 5 Chains 32, Residues 201, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 7191 restraints for refining 3183 atoms. 6419 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2769 (Rfree = 0.000) for 3183 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2566 (Rfree = 0.000) for 3140 atoms. Found 11 (17 requested) and removed 20 (8 requested) atoms. Cycle 13: After refmac, R = 0.2520 (Rfree = 0.000) for 3104 atoms. Found 11 (17 requested) and removed 17 (8 requested) atoms. Cycle 14: After refmac, R = 0.2420 (Rfree = 0.000) for 3086 atoms. Found 11 (17 requested) and removed 14 (8 requested) atoms. Cycle 15: After refmac, R = 0.2392 (Rfree = 0.000) for 3071 atoms. Found 12 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 3.66 Search for helices and strands: 0 residues in 0 chains, 3214 seeds are put forward NCS extension: 39 residues added (2 deleted due to clashes), 3253 seeds are put forward Round 1: 177 peptides, 37 chains. Longest chain 8 peptides. Score 0.278 Round 2: 203 peptides, 35 chains. Longest chain 14 peptides. Score 0.398 Round 3: 215 peptides, 35 chains. Longest chain 12 peptides. Score 0.437 Round 4: 225 peptides, 35 chains. Longest chain 13 peptides. Score 0.468 Round 5: 206 peptides, 32 chains. Longest chain 17 peptides. Score 0.450 Taking the results from Round 4 Chains 35, Residues 190, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5189 reflections ( 98.56 % complete ) and 7096 restraints for refining 3123 atoms. 6371 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2551 (Rfree = 0.000) for 3123 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 17: After refmac, R = 0.2506 (Rfree = 0.000) for 3095 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 18: After refmac, R = 0.2407 (Rfree = 0.000) for 3075 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 19: After refmac, R = 0.2456 (Rfree = 0.000) for 3060 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2392 (Rfree = 0.000) for 3044 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.72 3.67 Search for helices and strands: 0 residues in 0 chains, 3174 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 3191 seeds are put forward Round 1: 183 peptides, 38 chains. Longest chain 8 peptides. Score 0.285 Round 2: 200 peptides, 32 chains. Longest chain 14 peptides. Score 0.431 Round 3: 202 peptides, 32 chains. Longest chain 13 peptides. Score 0.437 Round 4: 211 peptides, 31 chains. Longest chain 17 peptides. Score 0.479 Round 5: 213 peptides, 32 chains. Longest chain 18 peptides. Score 0.471 Taking the results from Round 4 Chains 31, Residues 180, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5189 reflections ( 98.56 % complete ) and 7159 restraints for refining 3133 atoms. 6470 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2702 (Rfree = 0.000) for 3133 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 22: After refmac, R = 0.2545 (Rfree = 0.000) for 3093 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2312 (Rfree = 0.000) for 3074 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2500 (Rfree = 0.000) for 3060 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 25: After refmac, R = 0.2403 (Rfree = 0.000) for 3046 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.72 3.67 Search for helices and strands: 0 residues in 0 chains, 3175 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 3188 seeds are put forward Round 1: 136 peptides, 27 chains. Longest chain 9 peptides. Score 0.283 Round 2: 178 peptides, 32 chains. Longest chain 10 peptides. Score 0.358 Round 3: 191 peptides, 34 chains. Longest chain 14 peptides. Score 0.373 Round 4: 186 peptides, 32 chains. Longest chain 15 peptides. Score 0.385 Round 5: 203 peptides, 31 chains. Longest chain 14 peptides. Score 0.454 Taking the results from Round 5 Chains 31, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 7103 restraints for refining 3147 atoms. 6446 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2561 (Rfree = 0.000) for 3147 atoms. Found 17 (17 requested) and removed 24 (8 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2531 (Rfree = 0.000) for 3116 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 28: After refmac, R = 0.2505 (Rfree = 0.000) for 3101 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2310 (Rfree = 0.000) for 3097 atoms. Found 15 (17 requested) and removed 12 (8 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2370 (Rfree = 0.000) for 3085 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.70 3.65 Search for helices and strands: 0 residues in 0 chains, 3228 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3244 seeds are put forward Round 1: 168 peptides, 34 chains. Longest chain 9 peptides. Score 0.292 Round 2: 190 peptides, 32 chains. Longest chain 11 peptides. Score 0.398 Round 3: 183 peptides, 29 chains. Longest chain 11 peptides. Score 0.419 Round 4: 180 peptides, 30 chains. Longest chain 12 peptides. Score 0.394 Round 5: 197 peptides, 31 chains. Longest chain 13 peptides. Score 0.435 Taking the results from Round 5 Chains 31, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5189 reflections ( 98.56 % complete ) and 7200 restraints for refining 3178 atoms. 6567 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2467 (Rfree = 0.000) for 3178 atoms. Found 17 (17 requested) and removed 28 (8 requested) atoms. Cycle 32: After refmac, R = 0.2505 (Rfree = 0.000) for 3144 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2417 (Rfree = 0.000) for 3132 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 34: After refmac, R = 0.2345 (Rfree = 0.000) for 3118 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 35: After refmac, R = 0.2499 (Rfree = 0.000) for 3113 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.67 3.62 Search for helices and strands: 0 residues in 0 chains, 3244 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3261 seeds are put forward Round 1: 124 peptides, 26 chains. Longest chain 7 peptides. Score 0.252 Round 2: 158 peptides, 32 chains. Longest chain 8 peptides. Score 0.286 Round 3: 155 peptides, 28 chains. Longest chain 13 peptides. Score 0.337 Round 4: 156 peptides, 26 chains. Longest chain 14 peptides. Score 0.372 Round 5: 167 peptides, 27 chains. Longest chain 10 peptides. Score 0.395 Taking the results from Round 5 Chains 27, Residues 140, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 7440 restraints for refining 3172 atoms. 6907 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2578 (Rfree = 0.000) for 3172 atoms. Found 17 (17 requested) and removed 30 (8 requested) atoms. Cycle 37: After refmac, R = 0.2423 (Rfree = 0.000) for 3134 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 38: After refmac, R = 0.2750 (Rfree = 0.000) for 3117 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2334 (Rfree = 0.000) for 3099 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 40: After refmac, R = 0.2399 (Rfree = 0.000) for 3098 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.70 3.65 Search for helices and strands: 0 residues in 0 chains, 3195 seeds are put forward NCS extension: 0 residues added, 3195 seeds are put forward Round 1: 120 peptides, 27 chains. Longest chain 6 peptides. Score 0.218 Round 2: 137 peptides, 28 chains. Longest chain 7 peptides. Score 0.270 Round 3: 137 peptides, 26 chains. Longest chain 8 peptides. Score 0.303 Round 4: 130 peptides, 22 chains. Longest chain 12 peptides. Score 0.342 Round 5: 133 peptides, 23 chains. Longest chain 10 peptides. Score 0.337 Taking the results from Round 4 Chains 22, Residues 108, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5189 reflections ( 98.56 % complete ) and 7306 restraints for refining 3108 atoms. 6896 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2617 (Rfree = 0.000) for 3108 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 42: After refmac, R = 0.2544 (Rfree = 0.000) for 3088 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 43: After refmac, R = 0.2551 (Rfree = 0.000) for 3083 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 44: After refmac, R = 0.2714 (Rfree = 0.000) for 3066 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 45: After refmac, R = 0.2391 (Rfree = 0.000) for 3055 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.65 3.60 Search for helices and strands: 0 residues in 0 chains, 3150 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 3165 seeds are put forward Round 1: 102 peptides, 24 chains. Longest chain 6 peptides. Score 0.194 Round 2: 124 peptides, 26 chains. Longest chain 8 peptides. Score 0.252 Round 3: 131 peptides, 28 chains. Longest chain 7 peptides. Score 0.246 Round 4: 146 peptides, 29 chains. Longest chain 8 peptides. Score 0.288 Round 5: 136 peptides, 26 chains. Longest chain 7 peptides. Score 0.299 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 110, 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 2od6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5189 reflections ( 98.56 % complete ) and 6893 restraints for refining 2981 atoms. 6479 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2561 (Rfree = 0.000) for 2981 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2411 (Rfree = 0.000) for 2952 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2570 (Rfree = 0.000) for 2935 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2581 (Rfree = 0.000) for 2917 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... TimeTaking 55.14