Mon 24 Dec 08:08:39 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p8j-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p8j-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p8j-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.6-parrot-noncs ############### 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 08:08:43 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/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p8j-3.6-parrot-noncs/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-noncs.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-noncs.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 3712 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3400 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2923 (Rfree = 0.000) for 3712 atoms. Found 23 (23 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 2.85 Search for helices and strands: 0 residues in 0 chains, 3801 seeds are put forward NCS extension: 0 residues added, 3801 seeds are put forward Round 1: 270 peptides, 41 chains. Longest chain 19 peptides. Score 0.458 Round 2: 303 peptides, 32 chains. Longest chain 27 peptides. Score 0.613 Round 3: 309 peptides, 33 chains. Longest chain 27 peptides. Score 0.615 Round 4: 316 peptides, 32 chains. Longest chain 34 peptides. Score 0.636 Round 5: 304 peptides, 28 chains. Longest chain 44 peptides. Score 0.648 Taking the results from Round 5 Chains 30, Residues 276, Estimated correctness of the model 32.5 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 6300 restraints for refining 3029 atoms. 5197 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2751 (Rfree = 0.000) for 3029 atoms. Found 16 (19 requested) and removed 14 (9 requested) atoms. Cycle 2: After refmac, R = 0.2512 (Rfree = 0.000) for 3004 atoms. Found 7 (19 requested) and removed 12 (9 requested) atoms. Cycle 3: After refmac, R = 0.2429 (Rfree = 0.000) for 2982 atoms. Found 5 (19 requested) and removed 13 (9 requested) atoms. Cycle 4: After refmac, R = 0.2311 (Rfree = 0.000) for 2972 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. Cycle 5: After refmac, R = 0.2276 (Rfree = 0.000) for 2963 atoms. Found 4 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.52 2.86 Search for helices and strands: 0 residues in 0 chains, 3086 seeds are put forward NCS extension: 24 residues added (13 deleted due to clashes), 3110 seeds are put forward Round 1: 285 peptides, 32 chains. Longest chain 24 peptides. Score 0.578 Round 2: 291 peptides, 35 chains. Longest chain 24 peptides. Score 0.563 Round 3: 302 peptides, 30 chains. Longest chain 32 peptides. Score 0.628 Round 4: 324 peptides, 26 chains. Longest chain 51 peptides. Score 0.696 Round 5: 321 peptides, 31 chains. Longest chain 31 peptides. Score 0.653 Taking the results from Round 4 Chains 27, Residues 298, Estimated correctness of the model 48.4 % 2 chains (42 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 5832 restraints for refining 3031 atoms. 4487 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2745 (Rfree = 0.000) for 3031 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 7: After refmac, R = 0.2394 (Rfree = 0.000) for 3019 atoms. Found 9 (19 requested) and removed 19 (9 requested) atoms. Cycle 8: After refmac, R = 0.2255 (Rfree = 0.000) for 2998 atoms. Found 7 (19 requested) and removed 17 (9 requested) atoms. Cycle 9: After refmac, R = 0.2182 (Rfree = 0.000) for 2985 atoms. Found 5 (19 requested) and removed 9 (9 requested) atoms. Cycle 10: After refmac, R = 0.2148 (Rfree = 0.000) for 2974 atoms. Found 2 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 2.86 Search for helices and strands: 0 residues in 0 chains, 3061 seeds are put forward NCS extension: 20 residues added (7 deleted due to clashes), 3081 seeds are put forward Round 1: 278 peptides, 34 chains. Longest chain 21 peptides. Score 0.545 Round 2: 308 peptides, 29 chains. Longest chain 40 peptides. Score 0.647 Round 3: 308 peptides, 33 chains. Longest chain 28 peptides. Score 0.613 Round 4: 303 peptides, 32 chains. Longest chain 23 peptides. Score 0.613 Round 5: 311 peptides, 28 chains. Longest chain 40 peptides. Score 0.660 Taking the results from Round 5 Chains 29, Residues 283, Estimated correctness of the model 36.6 % 1 chains (36 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 6038 restraints for refining 3031 atoms. 4792 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2581 (Rfree = 0.000) for 3031 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 12: After refmac, R = 0.2389 (Rfree = 0.000) for 3010 atoms. Found 7 (19 requested) and removed 21 (9 requested) atoms. Cycle 13: After refmac, R = 0.2278 (Rfree = 0.000) for 2989 atoms. Found 2 (19 requested) and removed 15 (9 requested) atoms. Cycle 14: After refmac, R = 0.2230 (Rfree = 0.000) for 2970 atoms. Found 4 (19 requested) and removed 11 (9 requested) atoms. Cycle 15: After refmac, R = 0.2176 (Rfree = 0.000) for 2960 atoms. Found 3 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 2.85 Search for helices and strands: 0 residues in 0 chains, 3045 seeds are put forward NCS extension: 27 residues added (11 deleted due to clashes), 3072 seeds are put forward Round 1: 280 peptides, 34 chains. Longest chain 25 peptides. Score 0.549 Round 2: 303 peptides, 32 chains. Longest chain 22 peptides. Score 0.613 Round 3: 288 peptides, 30 chains. Longest chain 25 peptides. Score 0.602 Round 4: 282 peptides, 29 chains. Longest chain 24 peptides. Score 0.600 Round 5: 292 peptides, 30 chains. Longest chain 25 peptides. Score 0.610 Taking the results from Round 2 Chains 32, Residues 271, Estimated correctness of the model 19.7 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 6141 restraints for refining 3032 atoms. 5000 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2491 (Rfree = 0.000) for 3032 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 17: After refmac, R = 0.2315 (Rfree = 0.000) for 3036 atoms. Found 9 (19 requested) and removed 11 (9 requested) atoms. Cycle 18: After refmac, R = 0.2248 (Rfree = 0.000) for 3029 atoms. Found 2 (19 requested) and removed 9 (9 requested) atoms. Cycle 19: After refmac, R = 0.2234 (Rfree = 0.000) for 3018 atoms. Found 4 (19 requested) and removed 9 (9 requested) atoms. Cycle 20: After refmac, R = 0.2239 (Rfree = 0.000) for 3009 atoms. Found 3 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 2.86 Search for helices and strands: 0 residues in 0 chains, 3101 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 3128 seeds are put forward Round 1: 292 peptides, 29 chains. Longest chain 41 peptides. Score 0.618 Round 2: 298 peptides, 35 chains. Longest chain 35 peptides. Score 0.577 Round 3: 298 peptides, 33 chains. Longest chain 23 peptides. Score 0.594 Round 4: 291 peptides, 31 chains. Longest chain 23 peptides. Score 0.599 Round 5: 307 peptides, 32 chains. Longest chain 24 peptides. Score 0.620 Taking the results from Round 5 Chains 34, Residues 275, Estimated correctness of the model 22.3 % 3 chains (57 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 5921 restraints for refining 3032 atoms. 4613 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2747 (Rfree = 0.000) for 3032 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 22: After refmac, R = 0.2542 (Rfree = 0.000) for 3014 atoms. Found 8 (19 requested) and removed 14 (9 requested) atoms. Cycle 23: After refmac, R = 0.2496 (Rfree = 0.000) for 2999 atoms. Found 6 (19 requested) and removed 10 (9 requested) atoms. Cycle 24: After refmac, R = 0.2474 (Rfree = 0.000) for 2993 atoms. Found 6 (19 requested) and removed 11 (9 requested) atoms. Cycle 25: After refmac, R = 0.2464 (Rfree = 0.000) for 2987 atoms. Found 8 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 2.87 Search for helices and strands: 0 residues in 0 chains, 3087 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 3113 seeds are put forward Round 1: 269 peptides, 36 chains. Longest chain 16 peptides. Score 0.506 Round 2: 315 peptides, 35 chains. Longest chain 33 peptides. Score 0.609 Round 3: 311 peptides, 36 chains. Longest chain 42 peptides. Score 0.593 Round 4: 319 peptides, 34 chains. Longest chain 36 peptides. Score 0.625 Round 5: 292 peptides, 27 chains. Longest chain 37 peptides. Score 0.636 Taking the results from Round 5 Chains 29, Residues 265, Estimated correctness of the model 28.2 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 6258 restraints for refining 3031 atoms. 5155 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2706 (Rfree = 0.000) for 3031 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 27: After refmac, R = 0.2574 (Rfree = 0.000) for 3023 atoms. Found 7 (19 requested) and removed 13 (9 requested) atoms. Cycle 28: After refmac, R = 0.2591 (Rfree = 0.000) for 3010 atoms. Found 11 (19 requested) and removed 14 (9 requested) atoms. Cycle 29: After refmac, R = 0.2542 (Rfree = 0.000) for 3005 atoms. Found 7 (19 requested) and removed 11 (9 requested) atoms. Cycle 30: After refmac, R = 0.2493 (Rfree = 0.000) for 2999 atoms. Found 8 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 2.85 Search for helices and strands: 0 residues in 0 chains, 3114 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 3142 seeds are put forward Round 1: 257 peptides, 32 chains. Longest chain 22 peptides. Score 0.520 Round 2: 270 peptides, 30 chains. Longest chain 27 peptides. Score 0.567 Round 3: 290 peptides, 33 chains. Longest chain 29 peptides. Score 0.579 Round 4: 284 peptides, 30 chains. Longest chain 28 peptides. Score 0.594 Round 5: 290 peptides, 31 chains. Longest chain 29 peptides. Score 0.597 Taking the results from Round 5 Chains 31, Residues 259, Estimated correctness of the model 13.5 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 6346 restraints for refining 3032 atoms. 5232 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2638 (Rfree = 0.000) for 3032 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 32: After refmac, R = 0.2488 (Rfree = 0.000) for 3025 atoms. Found 7 (19 requested) and removed 10 (9 requested) atoms. Cycle 33: After refmac, R = 0.2452 (Rfree = 0.000) for 3018 atoms. Found 13 (19 requested) and removed 15 (9 requested) atoms. Cycle 34: After refmac, R = 0.2498 (Rfree = 0.000) for 3010 atoms. Found 12 (19 requested) and removed 11 (9 requested) atoms. Cycle 35: After refmac, R = 0.2434 (Rfree = 0.000) for 3010 atoms. Found 15 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 2.86 Search for helices and strands: 0 residues in 0 chains, 3113 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 3138 seeds are put forward Round 1: 256 peptides, 37 chains. Longest chain 13 peptides. Score 0.467 Round 2: 280 peptides, 32 chains. Longest chain 27 peptides. Score 0.568 Round 3: 293 peptides, 31 chains. Longest chain 28 peptides. Score 0.603 Round 4: 293 peptides, 25 chains. Longest chain 51 peptides. Score 0.654 Round 5: 277 peptides, 25 chains. Longest chain 35 peptides. Score 0.626 Taking the results from Round 4 Chains 29, Residues 268, Estimated correctness of the model 34.5 % 3 chains (42 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 6012 restraints for refining 3032 atoms. 4784 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2709 (Rfree = 0.000) for 3032 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 37: After refmac, R = 0.2571 (Rfree = 0.000) for 3011 atoms. Found 4 (19 requested) and removed 15 (9 requested) atoms. Cycle 38: After refmac, R = 0.2497 (Rfree = 0.000) for 2993 atoms. Found 5 (19 requested) and removed 16 (9 requested) atoms. Cycle 39: After refmac, R = 0.2475 (Rfree = 0.000) for 2979 atoms. Found 6 (19 requested) and removed 14 (9 requested) atoms. Cycle 40: After refmac, R = 0.2494 (Rfree = 0.000) for 2970 atoms. Found 7 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.44 2.80 Search for helices and strands: 0 residues in 0 chains, 3083 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3098 seeds are put forward Round 1: 252 peptides, 33 chains. Longest chain 23 peptides. Score 0.499 Round 2: 270 peptides, 25 chains. Longest chain 39 peptides. Score 0.613 Round 3: 251 peptides, 28 chains. Longest chain 26 peptides. Score 0.547 Round 4: 265 peptides, 27 chains. Longest chain 42 peptides. Score 0.585 Round 5: 268 peptides, 28 chains. Longest chain 29 peptides. Score 0.582 Taking the results from Round 2 Chains 25, Residues 245, Estimated correctness of the model 19.7 % 2 chains (51 residues) have been docked in sequence ------------------------------------------------------ 7821 reflections ( 98.53 % complete ) and 5921 restraints for refining 3032 atoms. 4744 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2502 (Rfree = 0.000) for 3032 atoms. Found 16 (19 requested) and removed 17 (9 requested) atoms. Cycle 42: After refmac, R = 0.2352 (Rfree = 0.000) for 3023 atoms. Found 15 (19 requested) and removed 12 (9 requested) atoms. Cycle 43: After refmac, R = 0.2296 (Rfree = 0.000) for 3024 atoms. Found 3 (19 requested) and removed 9 (9 requested) atoms. Cycle 44: After refmac, R = 0.2286 (Rfree = 0.000) for 3015 atoms. Found 7 (19 requested) and removed 10 (9 requested) atoms. Cycle 45: After refmac, R = 0.2242 (Rfree = 0.000) for 3011 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 2.86 Search for helices and strands: 0 residues in 0 chains, 3113 seeds are put forward NCS extension: 33 residues added (12 deleted due to clashes), 3146 seeds are put forward Round 1: 237 peptides, 35 chains. Longest chain 24 peptides. Score 0.443 Round 2: 263 peptides, 33 chains. Longest chain 39 peptides. Score 0.523 Round 3: 257 peptides, 31 chains. Longest chain 21 peptides. Score 0.530 Round 4: 263 peptides, 30 chains. Longest chain 37 peptides. Score 0.553 Round 5: 252 peptides, 28 chains. Longest chain 24 peptides. Score 0.549 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 233, Estimated correctness of the model 0.0 % 1 chains (21 residues) have been docked in sequence Sequence coverage is 8 % 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 6407 restraints for refining 3032 atoms. 5423 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2516 (Rfree = 0.000) for 3032 atoms. Found 0 (19 requested) and removed 8 (9 requested) atoms. Cycle 47: After refmac, R = 0.2347 (Rfree = 0.000) for 3012 atoms. Found 0 (19 requested) and removed 1 (9 requested) atoms. Cycle 48: After refmac, R = 0.2301 (Rfree = 0.000) for 3011 atoms. Found 0 (19 requested) and removed 0 (9 requested) atoms. Cycle 49: After refmac, R = 0.2334 (Rfree = 0.000) for 3010 atoms. TimeTaking 41.95