Sun 23 Dec 22:22:49 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 1vra-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vra-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vra-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vra-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/1vra-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vra-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 ============================================================ Sun 23 Dec 22:22:58 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/1vra-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vra-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 386 and 0 Target number of residues in the AU: 386 Target solvent content: 0.6235 Checking the provided sequence file Detected sequence length: 423 Maximum limit of NCS related copies: 30 Number of NCS-related molecules: 1 Adjusted target number of residues: 423 Adjusted target solvent content: 0.59 Input MTZ file: 1vra-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: 92 Cell parameters: 70.658 70.658 222.292 90.000 90.000 90.000 Input sequence file: 1vra-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3384 target number of atoms Had to go as low as 0.85 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: 29.814 3.800 Wilson plot Bfac: 62.98 6048 reflections ( 99.60 % complete ) and 0 restraints for refining 3759 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3737 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3650 (Rfree = 0.000) for 3759 atoms. Found 20 (20 requested) and removed 27 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.37 2.99 Search for helices and strands: 0 residues in 0 chains, 3828 seeds are put forward Round 1: 199 peptides, 35 chains. Longest chain 10 peptides. Score 0.366 Round 2: 225 peptides, 35 chains. Longest chain 14 peptides. Score 0.442 Round 3: 249 peptides, 34 chains. Longest chain 23 peptides. Score 0.517 Round 4: 259 peptides, 35 chains. Longest chain 21 peptides. Score 0.531 Round 5: 253 peptides, 34 chains. Longest chain 25 peptides. Score 0.527 Taking the results from Round 4 Chains 35, Residues 224, Estimated correctness of the model 0.0 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 6048 reflections ( 99.60 % complete ) and 6582 restraints for refining 3060 atoms. 5653 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3164 (Rfree = 0.000) for 3060 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 2: After refmac, R = 0.2886 (Rfree = 0.000) for 2986 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 3: After refmac, R = 0.2670 (Rfree = 0.000) for 2945 atoms. Found 10 (16 requested) and removed 21 (8 requested) atoms. Cycle 4: After refmac, R = 0.2641 (Rfree = 0.000) for 2913 atoms. Found 9 (16 requested) and removed 25 (8 requested) atoms. Cycle 5: After refmac, R = 0.2463 (Rfree = 0.000) for 2884 atoms. Found 9 (15 requested) and removed 22 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.35 2.97 Search for helices and strands: 0 residues in 0 chains, 3014 seeds are put forward Round 1: 220 peptides, 35 chains. Longest chain 20 peptides. Score 0.428 Round 2: 240 peptides, 35 chains. Longest chain 16 peptides. Score 0.482 Round 3: 248 peptides, 31 chains. Longest chain 17 peptides. Score 0.548 Round 4: 239 peptides, 31 chains. Longest chain 23 peptides. Score 0.526 Round 5: 239 peptides, 29 chains. Longest chain 25 peptides. Score 0.548 Taking the results from Round 5 Chains 33, Residues 210, Estimated correctness of the model 0.0 % 6 chains (47 residues) have been docked in sequence ------------------------------------------------------ 6048 reflections ( 99.60 % complete ) and 6457 restraints for refining 3060 atoms. 5510 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2799 (Rfree = 0.000) for 3060 atoms. Found 12 (16 requested) and removed 30 (8 requested) atoms. Cycle 7: After refmac, R = 0.2664 (Rfree = 0.000) for 2998 atoms. Found 14 (16 requested) and removed 26 (8 requested) atoms. Cycle 8: After refmac, R = 0.2634 (Rfree = 0.000) for 2972 atoms. Found 12 (16 requested) and removed 28 (8 requested) atoms. Cycle 9: After refmac, R = 0.2537 (Rfree = 0.000) for 2941 atoms. Found 16 (16 requested) and removed 31 (8 requested) atoms. Cycle 10: After refmac, R = 0.2523 (Rfree = 0.000) for 2914 atoms. Found 14 (16 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 2.96 Search for helices and strands: 0 residues in 0 chains, 3039 seeds are put forward Round 1: 226 peptides, 39 chains. Longest chain 13 peptides. Score 0.395 Round 2: 228 peptides, 37 chains. Longest chain 24 peptides. Score 0.425 Round 3: 243 peptides, 30 chains. Longest chain 21 peptides. Score 0.547 Round 4: 259 peptides, 37 chains. Longest chain 21 peptides. Score 0.508 Round 5: 258 peptides, 31 chains. Longest chain 24 peptides. Score 0.571 Taking the results from Round 5 Chains 35, Residues 227, Estimated correctness of the model 0.0 % 3 chains (36 residues) have been docked in sequence ------------------------------------------------------ 6048 reflections ( 99.60 % complete ) and 6394 restraints for refining 3060 atoms. 5393 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2733 (Rfree = 0.000) for 3060 atoms. Found 16 (16 requested) and removed 31 (8 requested) atoms. Cycle 12: After refmac, R = 0.2532 (Rfree = 0.000) for 3004 atoms. Found 8 (16 requested) and removed 26 (8 requested) atoms. Cycle 13: After refmac, R = 0.2559 (Rfree = 0.000) for 2960 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. Cycle 14: After refmac, R = 0.2475 (Rfree = 0.000) for 2941 atoms. Found 11 (16 requested) and removed 21 (8 requested) atoms. Cycle 15: After refmac, R = 0.2444 (Rfree = 0.000) for 2920 atoms. Found 15 (16 requested) and removed 16 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.34 2.96 Search for helices and strands: 0 residues in 0 chains, 3029 seeds are put forward Round 1: 246 peptides, 42 chains. Longest chain 18 peptides. Score 0.415 Round 2: 254 peptides, 35 chains. Longest chain 21 peptides. Score 0.518 Round 3: 268 peptides, 36 chains. Longest chain 28 peptides. Score 0.542 Round 4: 250 peptides, 33 chains. Longest chain 16 peptides. Score 0.531 Round 5: 265 peptides, 34 chains. Longest chain 25 peptides. Score 0.556 Taking the results from Round 5 Chains 39, Residues 231, Estimated correctness of the model 0.0 % 5 chains (46 residues) have been docked in sequence ------------------------------------------------------ 6048 reflections ( 99.60 % complete ) and 6343 restraints for refining 3059 atoms. 5300 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2770 (Rfree = 0.000) for 3059 atoms. Found 14 (16 requested) and removed 35 (8 requested) atoms. Cycle 17: After refmac, R = 0.2710 (Rfree = 0.000) for 3000 atoms. Found 13 (16 requested) and removed 35 (8 requested) atoms. Cycle 18: After refmac, R = 0.2623 (Rfree = 0.000) for 2964 atoms. Found 16 (16 requested) and removed 33 (8 requested) atoms. Cycle 19: After refmac, R = 0.2646 (Rfree = 0.000) for 2941 atoms. Found 16 (16 requested) and removed 24 (8 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2520 (Rfree = 0.000) for 2929 atoms. Found 12 (16 requested) and removed 23 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 2.94 Search for helices and strands: 0 residues in 0 chains, 3036 seeds are put forward Round 1: 227 peptides, 39 chains. Longest chain 16 peptides. Score 0.398 Round 2: 259 peptides, 35 chains. Longest chain 20 peptides. Score 0.531 Round 3: 255 peptides, 36 chains. Longest chain 21 peptides. Score 0.510 Round 4: 244 peptides, 33 chains. Longest chain 19 peptides. Score 0.516 Round 5: 245 peptides, 32 chains. Longest chain 18 peptides. Score 0.529 Taking the results from Round 2 Chains 35, Residues 224, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6048 reflections ( 99.60 % complete ) and 6726 restraints for refining 3060 atoms. 5824 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2594 (Rfree = 0.000) for 3060 atoms. Found 8 (16 requested) and removed 32 (8 requested) atoms. Cycle 22: After refmac, R = 0.2577 (Rfree = 0.000) for 3025 atoms. Found 16 (16 requested) and removed 29 (8 requested) atoms. Cycle 23: After refmac, R = 0.2547 (Rfree = 0.000) for 3003 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 24: After refmac, R = 0.2593 (Rfree = 0.000) for 2999 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 25: After refmac, R = 0.2512 (Rfree = 0.000) for 2989 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.02 Search for helices and strands: 0 residues in 0 chains, 3135 seeds are put forward Round 1: 217 peptides, 41 chains. Longest chain 15 peptides. Score 0.342 Round 2: 233 peptides, 34 chains. Longest chain 18 peptides. Score 0.476 Round 3: 241 peptides, 36 chains. Longest chain 19 peptides. Score 0.473 Round 4: 244 peptides, 31 chains. Longest chain 20 peptides. Score 0.538 Round 5: 250 peptides, 32 chains. Longest chain 21 peptides. Score 0.542 Taking the results from Round 5 Chains 34, Residues 218, Estimated correctness of the model 0.0 % 5 chains (31 residues) have been docked in sequence ------------------------------------------------------ 6048 reflections ( 99.60 % complete ) and 6581 restraints for refining 3060 atoms. 5638 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2830 (Rfree = 0.000) for 3060 atoms. Found 16 (16 requested) and removed 29 (8 requested) atoms. Cycle 27: After refmac, R = 0.2728 (Rfree = 0.000) for 3012 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 28: After refmac, R = 0.2583 (Rfree = 0.000) for 2993 atoms. Found 11 (16 requested) and removed 17 (8 requested) atoms. Cycle 29: After refmac, R = 0.2587 (Rfree = 0.000) for 2969 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 30: After refmac, R = 0.2270 (Rfree = 0.000) for 2958 atoms. Found 6 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.33 2.95 Search for helices and strands: 0 residues in 0 chains, 3045 seeds are put forward Round 1: 211 peptides, 40 chains. Longest chain 12 peptides. Score 0.337 Round 2: 225 peptides, 34 chains. Longest chain 16 peptides. Score 0.454 Round 3: 230 peptides, 35 chains. Longest chain 14 peptides. Score 0.455 Round 4: 237 peptides, 32 chains. Longest chain 20 peptides. Score 0.509 Round 5: 229 peptides, 30 chains. Longest chain 20 peptides. Score 0.512 Taking the results from Round 5 Chains 34, Residues 199, Estimated correctness of the model 0.0 % 3 chains (39 residues) have been docked in sequence ------------------------------------------------------ 6048 reflections ( 99.60 % complete ) and 6442 restraints for refining 3060 atoms. 5542 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2658 (Rfree = 0.000) for 3060 atoms. Found 15 (16 requested) and removed 26 (8 requested) atoms. Cycle 32: After refmac, R = 0.2528 (Rfree = 0.000) for 3033 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 33: After refmac, R = 0.2586 (Rfree = 0.000) for 3017 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 34: After refmac, R = 0.2460 (Rfree = 0.000) for 3002 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 35: After refmac, R = 0.2484 (Rfree = 0.000) for 2992 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 2.98 Search for helices and strands: 0 residues in 0 chains, 3138 seeds are put forward Round 1: 184 peptides, 34 chains. Longest chain 16 peptides. Score 0.333 Round 2: 215 peptides, 35 chains. Longest chain 15 peptides. Score 0.413 Round 3: 203 peptides, 33 chains. Longest chain 12 peptides. Score 0.404 Round 4: 206 peptides, 29 chains. Longest chain 14 peptides. Score 0.463 Round 5: 209 peptides, 31 chains. Longest chain 22 peptides. Score 0.446 Taking the results from Round 4 Chains 29, Residues 177, Estimated correctness of the model 0.0 % 6 chains (39 residues) have been docked in sequence ------------------------------------------------------ 6048 reflections ( 99.60 % complete ) and 6548 restraints for refining 3060 atoms. 5760 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2568 (Rfree = 0.000) for 3060 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 37: After refmac, R = 0.2567 (Rfree = 0.000) for 3045 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 38: After refmac, R = 0.2478 (Rfree = 0.000) for 3035 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 39: After refmac, R = 0.2509 (Rfree = 0.000) for 3023 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. Cycle 40: After refmac, R = 0.2440 (Rfree = 0.000) for 3007 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 2.95 Search for helices and strands: 0 residues in 0 chains, 3126 seeds are put forward Round 1: 168 peptides, 32 chains. Longest chain 12 peptides. Score 0.309 Round 2: 196 peptides, 29 chains. Longest chain 24 peptides. Score 0.435 Round 3: 193 peptides, 30 chains. Longest chain 16 peptides. Score 0.413 Round 4: 190 peptides, 28 chains. Longest chain 19 peptides. Score 0.431 Round 5: 209 peptides, 32 chains. Longest chain 21 peptides. Score 0.434 Taking the results from Round 2 Chains 31, Residues 167, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6048 reflections ( 99.60 % complete ) and 6637 restraints for refining 3060 atoms. 5944 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2496 (Rfree = 0.000) for 3060 atoms. Found 16 (16 requested) and removed 36 (8 requested) atoms. Cycle 42: After refmac, R = 0.2436 (Rfree = 0.000) for 3022 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. Cycle 43: After refmac, R = 0.2380 (Rfree = 0.000) for 3004 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 44: After refmac, R = 0.2288 (Rfree = 0.000) for 2999 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 45: After refmac, R = 0.2338 (Rfree = 0.000) for 3000 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 2.94 Search for helices and strands: 0 residues in 0 chains, 3099 seeds are put forward Round 1: 160 peptides, 32 chains. Longest chain 14 peptides. Score 0.282 Round 2: 172 peptides, 31 chains. Longest chain 13 peptides. Score 0.336 Round 3: 167 peptides, 27 chains. Longest chain 20 peptides. Score 0.375 Round 4: 190 peptides, 28 chains. Longest chain 31 peptides. Score 0.431 Round 5: 186 peptides, 30 chains. Longest chain 24 peptides. Score 0.393 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 162, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 1vra-3_warpNtrace.pdb as input Building loops using Loopy2018 30 chains (162 residues) following loop building 2 chains (25 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6048 reflections ( 99.60 % complete ) and 6748 restraints for refining 3060 atoms. 6051 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2606 (Rfree = 0.000) for 3060 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2530 (Rfree = 0.000) for 3033 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2397 (Rfree = 0.000) for 3015 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2339 (Rfree = 0.000) for 3001 atoms. TimeTaking 55.02