Mon 24 Dec 00:30:13 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 2p8j-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p8j-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p8j-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.6-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/2p8j-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.6-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 00:30:18 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/2p8j-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.6-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 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-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: 152 Cell parameters: 83.860 83.860 159.200 90.000 90.000 120.000 Input sequence file: 2p8j-3.6-parrot-mrncs.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 3731 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3387 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2538 (Rfree = 0.000) for 3731 atoms. Found 23 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 2.86 Search for helices and strands: 0 residues in 0 chains, 3828 seeds are put forward NCS extension: 0 residues added, 3828 seeds are put forward Round 1: 267 peptides, 40 chains. Longest chain 16 peptides. Score 0.461 Round 2: 279 peptides, 32 chains. Longest chain 20 peptides. Score 0.566 Round 3: 279 peptides, 32 chains. Longest chain 20 peptides. Score 0.566 Round 4: 303 peptides, 34 chains. Longest chain 21 peptides. Score 0.595 Round 5: 306 peptides, 29 chains. Longest chain 25 peptides. Score 0.643 Taking the results from Round 5 Chains 30, Residues 277, Estimated correctness of the model 30.7 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 6336 restraints for refining 3132 atoms. 5173 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2583 (Rfree = 0.000) for 3132 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 2: After refmac, R = 0.2411 (Rfree = 0.000) for 3090 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 3: After refmac, R = 0.2369 (Rfree = 0.000) for 3070 atoms. Found 14 (19 requested) and removed 14 (9 requested) atoms. Cycle 4: After refmac, R = 0.2377 (Rfree = 0.000) for 3065 atoms. Found 12 (19 requested) and removed 12 (9 requested) atoms. Cycle 5: After refmac, R = 0.2397 (Rfree = 0.000) for 3059 atoms. Found 8 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 2.89 Search for helices and strands: 0 residues in 0 chains, 3177 seeds are put forward NCS extension: 26 residues added (7 deleted due to clashes), 3203 seeds are put forward Round 1: 272 peptides, 32 chains. Longest chain 19 peptides. Score 0.552 Round 2: 288 peptides, 28 chains. Longest chain 26 peptides. Score 0.620 Round 3: 298 peptides, 29 chains. Longest chain 40 peptides. Score 0.629 Round 4: 285 peptides, 29 chains. Longest chain 29 peptides. Score 0.605 Round 5: 290 peptides, 29 chains. Longest chain 41 peptides. Score 0.615 Taking the results from Round 3 Chains 32, Residues 269, Estimated correctness of the model 25.6 % 3 chains (58 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 5819 restraints for refining 3032 atoms. 4551 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2605 (Rfree = 0.000) for 3032 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 7: After refmac, R = 0.2371 (Rfree = 0.000) for 3010 atoms. Found 16 (19 requested) and removed 20 (9 requested) atoms. Cycle 8: After refmac, R = 0.2298 (Rfree = 0.000) for 2998 atoms. Found 9 (19 requested) and removed 14 (9 requested) atoms. Cycle 9: After refmac, R = 0.2288 (Rfree = 0.000) for 2984 atoms. Found 12 (19 requested) and removed 15 (9 requested) atoms. Cycle 10: After refmac, R = 0.2268 (Rfree = 0.000) for 2979 atoms. Found 11 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 2.86 Search for helices and strands: 0 residues in 0 chains, 3079 seeds are put forward NCS extension: 29 residues added (4 deleted due to clashes), 3108 seeds are put forward Round 1: 271 peptides, 33 chains. Longest chain 22 peptides. Score 0.540 Round 2: 294 peptides, 36 chains. Longest chain 33 peptides. Score 0.559 Round 3: 301 peptides, 28 chains. Longest chain 33 peptides. Score 0.643 Round 4: 303 peptides, 27 chains. Longest chain 40 peptides. Score 0.655 Round 5: 307 peptides, 28 chains. Longest chain 23 peptides. Score 0.653 Taking the results from Round 4 Chains 28, Residues 276, Estimated correctness of the model 34.9 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 6090 restraints for refining 3032 atoms. 4899 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2902 (Rfree = 0.000) for 3032 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 12: After refmac, R = 0.2714 (Rfree = 0.000) for 3030 atoms. Found 11 (19 requested) and removed 10 (9 requested) atoms. Cycle 13: After refmac, R = 0.2567 (Rfree = 0.000) for 3027 atoms. Found 7 (19 requested) and removed 9 (9 requested) atoms. Cycle 14: After refmac, R = 0.2507 (Rfree = 0.000) for 3019 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. Cycle 15: After refmac, R = 0.2470 (Rfree = 0.000) for 3014 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 2.91 Search for helices and strands: 0 residues in 0 chains, 3129 seeds are put forward NCS extension: 36 residues added (3 deleted due to clashes), 3165 seeds are put forward Round 1: 289 peptides, 35 chains. Longest chain 25 peptides. Score 0.558 Round 2: 302 peptides, 28 chains. Longest chain 34 peptides. Score 0.645 Round 3: 303 peptides, 28 chains. Longest chain 33 peptides. Score 0.646 Round 4: 304 peptides, 30 chains. Longest chain 31 peptides. Score 0.631 Round 5: 301 peptides, 29 chains. Longest chain 32 peptides. Score 0.635 Taking the results from Round 3 Chains 28, Residues 275, Estimated correctness of the model 31.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 6354 restraints for refining 3032 atoms. 5282 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2656 (Rfree = 0.000) for 3032 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. Cycle 17: After refmac, R = 0.2492 (Rfree = 0.000) for 3023 atoms. Found 10 (19 requested) and removed 10 (9 requested) atoms. Cycle 18: After refmac, R = 0.2382 (Rfree = 0.000) for 3020 atoms. Found 5 (19 requested) and removed 10 (9 requested) atoms. Cycle 19: After refmac, R = 0.2338 (Rfree = 0.000) for 3010 atoms. Found 4 (19 requested) and removed 9 (9 requested) atoms. Cycle 20: After refmac, R = 0.2335 (Rfree = 0.000) for 3003 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 2.90 Search for helices and strands: 0 residues in 0 chains, 3096 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 3126 seeds are put forward Round 1: 288 peptides, 38 chains. Longest chain 16 peptides. Score 0.528 Round 2: 287 peptides, 27 chains. Longest chain 24 peptides. Score 0.627 Round 3: 277 peptides, 32 chains. Longest chain 20 peptides. Score 0.562 Round 4: 291 peptides, 28 chains. Longest chain 24 peptides. Score 0.625 Round 5: 296 peptides, 33 chains. Longest chain 24 peptides. Score 0.591 Taking the results from Round 2 Chains 27, Residues 260, Estimated correctness of the model 24.9 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 6284 restraints for refining 3032 atoms. 5166 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2770 (Rfree = 0.000) for 3032 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 22: After refmac, R = 0.2501 (Rfree = 0.000) for 3026 atoms. Found 18 (19 requested) and removed 16 (9 requested) atoms. Cycle 23: After refmac, R = 0.2437 (Rfree = 0.000) for 3020 atoms. Found 11 (19 requested) and removed 19 (9 requested) atoms. Cycle 24: After refmac, R = 0.2367 (Rfree = 0.000) for 3007 atoms. Found 15 (19 requested) and removed 19 (9 requested) atoms. Cycle 25: After refmac, R = 0.2295 (Rfree = 0.000) for 2998 atoms. Found 8 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 2.91 Search for helices and strands: 0 residues in 0 chains, 3094 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 3125 seeds are put forward Round 1: 273 peptides, 37 chains. Longest chain 18 peptides. Score 0.505 Round 2: 294 peptides, 33 chains. Longest chain 22 peptides. Score 0.587 Round 3: 281 peptides, 30 chains. Longest chain 26 peptides. Score 0.589 Round 4: 296 peptides, 33 chains. Longest chain 25 peptides. Score 0.591 Round 5: 275 peptides, 28 chains. Longest chain 39 peptides. Score 0.595 Taking the results from Round 5 Chains 30, Residues 247, Estimated correctness of the model 12.7 % 4 chains (51 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 6008 restraints for refining 3032 atoms. 4840 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3287 (Rfree = 0.000) for 3032 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.3026 (Rfree = 0.000) for 3028 atoms. Found 19 (19 requested) and removed 9 (9 requested) atoms. Cycle 28: After refmac, R = 0.2931 (Rfree = 0.000) for 3035 atoms. Found 7 (19 requested) and removed 9 (9 requested) atoms. Cycle 29: After refmac, R = 0.2797 (Rfree = 0.000) for 3032 atoms. Found 4 (19 requested) and removed 9 (9 requested) atoms. Cycle 30: After refmac, R = 0.2657 (Rfree = 0.000) for 3026 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 2.90 Search for helices and strands: 0 residues in 0 chains, 3113 seeds are put forward NCS extension: 49 residues added (4 deleted due to clashes), 3162 seeds are put forward Round 1: 259 peptides, 35 chains. Longest chain 14 peptides. Score 0.494 Round 2: 286 peptides, 32 chains. Longest chain 27 peptides. Score 0.580 Round 3: 286 peptides, 35 chains. Longest chain 21 peptides. Score 0.552 Round 4: 281 peptides, 35 chains. Longest chain 19 peptides. Score 0.542 Round 5: 283 peptides, 31 chains. Longest chain 21 peptides. Score 0.583 Taking the results from Round 5 Chains 31, Residues 252, Estimated correctness of the model 7.9 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 6349 restraints for refining 3031 atoms. 5326 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3004 (Rfree = 0.000) for 3031 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. Cycle 32: After refmac, R = 0.2713 (Rfree = 0.000) for 3039 atoms. Found 16 (19 requested) and removed 11 (9 requested) atoms. Cycle 33: After refmac, R = 0.2505 (Rfree = 0.000) for 3039 atoms. Found 7 (19 requested) and removed 9 (9 requested) atoms. Cycle 34: After refmac, R = 0.2425 (Rfree = 0.000) for 3033 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. Cycle 35: After refmac, R = 0.2354 (Rfree = 0.000) for 3028 atoms. Found 2 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 2.90 Search for helices and strands: 0 residues in 0 chains, 3104 seeds are put forward NCS extension: 29 residues added (4 deleted due to clashes), 3133 seeds are put forward Round 1: 255 peptides, 41 chains. Longest chain 18 peptides. Score 0.422 Round 2: 280 peptides, 35 chains. Longest chain 23 peptides. Score 0.540 Round 3: 271 peptides, 33 chains. Longest chain 35 peptides. Score 0.540 Round 4: 272 peptides, 34 chains. Longest chain 15 peptides. Score 0.533 Round 5: 275 peptides, 36 chains. Longest chain 22 peptides. Score 0.520 Taking the results from Round 3 Chains 35, Residues 238, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 6511 restraints for refining 3032 atoms. 5529 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2538 (Rfree = 0.000) for 3032 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. Cycle 37: After refmac, R = 0.2327 (Rfree = 0.000) for 3028 atoms. Found 9 (19 requested) and removed 10 (9 requested) atoms. Cycle 38: After refmac, R = 0.2220 (Rfree = 0.000) for 3019 atoms. Found 9 (19 requested) and removed 11 (9 requested) atoms. Cycle 39: After refmac, R = 0.2207 (Rfree = 0.000) for 3012 atoms. Found 7 (19 requested) and removed 9 (9 requested) atoms. Cycle 40: After refmac, R = 0.2205 (Rfree = 0.000) for 3007 atoms. Found 8 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.49 2.84 Search for helices and strands: 0 residues in 0 chains, 3120 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3138 seeds are put forward Round 1: 246 peptides, 37 chains. Longest chain 21 peptides. Score 0.443 Round 2: 283 peptides, 34 chains. Longest chain 27 peptides. Score 0.556 Round 3: 286 peptides, 33 chains. Longest chain 31 peptides. Score 0.571 Round 4: 289 peptides, 33 chains. Longest chain 29 peptides. Score 0.577 Round 5: 277 peptides, 35 chains. Longest chain 32 peptides. Score 0.534 Taking the results from Round 4 Chains 34, Residues 256, Estimated correctness of the model 5.5 % 4 chains (73 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 5754 restraints for refining 3032 atoms. 4460 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2555 (Rfree = 0.000) for 3032 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 42: After refmac, R = 0.2377 (Rfree = 0.000) for 3018 atoms. Found 5 (19 requested) and removed 14 (9 requested) atoms. Cycle 43: After refmac, R = 0.2362 (Rfree = 0.000) for 3000 atoms. Found 3 (19 requested) and removed 11 (9 requested) atoms. Cycle 44: After refmac, R = 0.2382 (Rfree = 0.000) for 2988 atoms. Found 10 (19 requested) and removed 10 (9 requested) atoms. Cycle 45: After refmac, R = 0.2339 (Rfree = 0.000) for 2983 atoms. Found 7 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 2.86 Search for helices and strands: 0 residues in 0 chains, 3077 seeds are put forward NCS extension: 25 residues added (5 deleted due to clashes), 3102 seeds are put forward Round 1: 268 peptides, 40 chains. Longest chain 21 peptides. Score 0.464 Round 2: 275 peptides, 37 chains. Longest chain 22 peptides. Score 0.510 Round 3: 252 peptides, 32 chains. Longest chain 23 peptides. Score 0.509 Round 4: 251 peptides, 34 chains. Longest chain 20 peptides. Score 0.486 Round 5: 271 peptides, 31 chains. Longest chain 36 peptides. Score 0.559 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 240, Estimated correctness of the model 0.0 % 1 chains (35 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2p8j-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7821 reflections ( 98.53 % complete ) and 6233 restraints for refining 3031 atoms. 5142 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2618 (Rfree = 0.000) for 3031 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2509 (Rfree = 0.000) for 3014 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2566 (Rfree = 0.000) for 3000 atoms. Found 0 (19 requested) and removed 8 (9 requested) atoms. Cycle 49: After refmac, R = 0.2556 (Rfree = 0.000) for 2987 atoms. TimeTaking 46.4