null 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 2p97-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p97-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p97-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p97-3.4-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/2p97-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p97-3.4-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/2p97-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p97-3.4-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 354 and 0 Target number of residues in the AU: 354 Target solvent content: 0.6250 Checking the provided sequence file Detected sequence length: 201 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 402 Adjusted target solvent content: 0.57 Input MTZ file: 2p97-3.4-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: 94 Cell parameters: 103.080 103.080 96.168 90.000 90.000 90.000 Input sequence file: 2p97-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3216 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 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: 72.889 3.400 Wilson plot Bfac: 63.69 7539 reflections ( 99.76 % complete ) and 0 restraints for refining 3539 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3286 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2912 (Rfree = 0.000) for 3539 atoms. Found 26 (26 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 2.99 Search for helices and strands: 0 residues in 0 chains, 3605 seeds are put forward NCS extension: 0 residues added, 3605 seeds are put forward Round 1: 227 peptides, 37 chains. Longest chain 12 peptides. Score 0.439 Round 2: 277 peptides, 35 chains. Longest chain 19 peptides. Score 0.596 Round 3: 298 peptides, 31 chains. Longest chain 20 peptides. Score 0.680 Round 4: 312 peptides, 30 chains. Longest chain 32 peptides. Score 0.715 Round 5: 313 peptides, 30 chains. Longest chain 27 peptides. Score 0.717 Taking the results from Round 5 Chains 32, Residues 283, Estimated correctness of the model 62.1 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 5824 restraints for refining 2925 atoms. 4645 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2840 (Rfree = 0.000) for 2925 atoms. Found 19 (22 requested) and removed 21 (11 requested) atoms. Cycle 2: After refmac, R = 0.2670 (Rfree = 0.000) for 2872 atoms. Found 10 (22 requested) and removed 15 (11 requested) atoms. Cycle 3: After refmac, R = 0.2585 (Rfree = 0.000) for 2852 atoms. Found 9 (20 requested) and removed 16 (10 requested) atoms. Cycle 4: After refmac, R = 0.2484 (Rfree = 0.000) for 2839 atoms. Found 7 (20 requested) and removed 13 (10 requested) atoms. Cycle 5: After refmac, R = 0.2398 (Rfree = 0.000) for 2830 atoms. Found 5 (19 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.24 2.95 Search for helices and strands: 0 residues in 0 chains, 2925 seeds are put forward NCS extension: 25 residues added (5 deleted due to clashes), 2950 seeds are put forward Round 1: 273 peptides, 36 chains. Longest chain 19 peptides. Score 0.576 Round 2: 293 peptides, 33 chains. Longest chain 25 peptides. Score 0.652 Round 3: 306 peptides, 28 chains. Longest chain 25 peptides. Score 0.721 Round 4: 310 peptides, 26 chains. Longest chain 35 peptides. Score 0.744 Round 5: 320 peptides, 28 chains. Longest chain 26 peptides. Score 0.745 Taking the results from Round 5 Chains 30, Residues 292, Estimated correctness of the model 68.7 % 2 chains (30 residues) have been docked in sequence Building loops using Loopy2018 30 chains (292 residues) following loop building 2 chains (30 residues) in sequence following loop building ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 5631 restraints for refining 2924 atoms. 4353 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2692 (Rfree = 0.000) for 2924 atoms. Found 20 (20 requested) and removed 15 (11 requested) atoms. Cycle 7: After refmac, R = 0.2495 (Rfree = 0.000) for 2911 atoms. Found 12 (19 requested) and removed 15 (11 requested) atoms. Cycle 8: After refmac, R = 0.2441 (Rfree = 0.000) for 2899 atoms. Found 7 (18 requested) and removed 11 (10 requested) atoms. Cycle 9: After refmac, R = 0.2429 (Rfree = 0.000) for 2889 atoms. Found 7 (18 requested) and removed 10 (10 requested) atoms. Cycle 10: After refmac, R = 0.2437 (Rfree = 0.000) for 2884 atoms. Found 11 (17 requested) and removed 12 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.23 2.94 Search for helices and strands: 0 residues in 0 chains, 2956 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 2973 seeds are put forward Round 1: 266 peptides, 30 chains. Longest chain 23 peptides. Score 0.623 Round 2: 294 peptides, 28 chains. Longest chain 31 peptides. Score 0.700 Round 3: 281 peptides, 32 chains. Longest chain 22 peptides. Score 0.636 Round 4: 281 peptides, 28 chains. Longest chain 23 peptides. Score 0.675 Round 5: 279 peptides, 26 chains. Longest chain 31 peptides. Score 0.689 Taking the results from Round 2 Chains 28, Residues 266, Estimated correctness of the model 57.9 % 1 chains (20 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 6124 restraints for refining 2924 atoms. 5000 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2552 (Rfree = 0.000) for 2924 atoms. Found 18 (18 requested) and removed 14 (11 requested) atoms. Cycle 12: After refmac, R = 0.2401 (Rfree = 0.000) for 2918 atoms. Found 6 (18 requested) and removed 11 (11 requested) atoms. Cycle 13: After refmac, R = 0.2359 (Rfree = 0.000) for 2907 atoms. Found 6 (17 requested) and removed 10 (10 requested) atoms. Cycle 14: After refmac, R = 0.2308 (Rfree = 0.000) for 2900 atoms. Found 7 (17 requested) and removed 11 (10 requested) atoms. Cycle 15: After refmac, R = 0.2269 (Rfree = 0.000) for 2896 atoms. Found 10 (17 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 2.90 Search for helices and strands: 0 residues in 0 chains, 2994 seeds are put forward NCS extension: 40 residues added (7 deleted due to clashes), 3034 seeds are put forward Round 1: 270 peptides, 32 chains. Longest chain 25 peptides. Score 0.611 Round 2: 272 peptides, 33 chains. Longest chain 22 peptides. Score 0.605 Round 3: 289 peptides, 28 chains. Longest chain 21 peptides. Score 0.690 Round 4: 292 peptides, 28 chains. Longest chain 34 peptides. Score 0.696 Round 5: 285 peptides, 32 chains. Longest chain 20 peptides. Score 0.645 Taking the results from Round 4 Chains 30, Residues 264, Estimated correctness of the model 56.8 % 2 chains (49 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 5722 restraints for refining 2925 atoms. 4483 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2489 (Rfree = 0.000) for 2925 atoms. Found 18 (18 requested) and removed 17 (11 requested) atoms. Cycle 17: After refmac, R = 0.2236 (Rfree = 0.000) for 2908 atoms. Found 18 (18 requested) and removed 15 (11 requested) atoms. Cycle 18: After refmac, R = 0.2228 (Rfree = 0.000) for 2901 atoms. Found 13 (17 requested) and removed 14 (10 requested) atoms. Cycle 19: After refmac, R = 0.2131 (Rfree = 0.000) for 2896 atoms. Found 12 (17 requested) and removed 14 (10 requested) atoms. Cycle 20: After refmac, R = 0.2110 (Rfree = 0.000) for 2888 atoms. Found 13 (17 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.18 2.90 Search for helices and strands: 0 residues in 0 chains, 2956 seeds are put forward NCS extension: 25 residues added (5 deleted due to clashes), 2981 seeds are put forward Round 1: 272 peptides, 31 chains. Longest chain 34 peptides. Score 0.626 Round 2: 294 peptides, 27 chains. Longest chain 37 peptides. Score 0.708 Round 3: 300 peptides, 30 chains. Longest chain 30 peptides. Score 0.693 Round 4: 295 peptides, 29 chains. Longest chain 37 peptides. Score 0.693 Round 5: 295 peptides, 30 chains. Longest chain 31 peptides. Score 0.684 Taking the results from Round 2 Chains 29, Residues 267, Estimated correctness of the model 59.9 % 2 chains (51 residues) have been docked in sequence Building loops using Loopy2018 29 chains (267 residues) following loop building 2 chains (51 residues) in sequence following loop building ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 5627 restraints for refining 2925 atoms. 4359 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2336 (Rfree = 0.000) for 2925 atoms. Found 12 (18 requested) and removed 17 (11 requested) atoms. Cycle 22: After refmac, R = 0.2190 (Rfree = 0.000) for 2914 atoms. Found 8 (17 requested) and removed 14 (11 requested) atoms. Cycle 23: After refmac, R = 0.2108 (Rfree = 0.000) for 2905 atoms. Found 3 (16 requested) and removed 10 (10 requested) atoms. Cycle 24: After refmac, R = 0.2018 (Rfree = 0.000) for 2895 atoms. Found 1 (16 requested) and removed 10 (10 requested) atoms. Cycle 25: After refmac, R = 0.2000 (Rfree = 0.000) for 2885 atoms. Found 1 (15 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.23 2.94 Search for helices and strands: 0 residues in 0 chains, 2959 seeds are put forward NCS extension: 37 residues added (0 deleted due to clashes), 2996 seeds are put forward Round 1: 272 peptides, 35 chains. Longest chain 28 peptides. Score 0.584 Round 2: 293 peptides, 30 chains. Longest chain 34 peptides. Score 0.680 Round 3: 289 peptides, 33 chains. Longest chain 23 peptides. Score 0.643 Round 4: 304 peptides, 34 chains. Longest chain 27 peptides. Score 0.665 Round 5: 295 peptides, 25 chains. Longest chain 34 peptides. Score 0.727 Taking the results from Round 5 Chains 25, Residues 270, Estimated correctness of the model 64.5 % 3 chains (57 residues) have been docked in sequence Building loops using Loopy2018 25 chains (270 residues) following loop building 3 chains (57 residues) in sequence following loop building ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 5622 restraints for refining 2925 atoms. 4317 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2557 (Rfree = 0.000) for 2925 atoms. Found 15 (15 requested) and removed 21 (11 requested) atoms. Cycle 27: After refmac, R = 0.2483 (Rfree = 0.000) for 2910 atoms. Found 14 (15 requested) and removed 14 (11 requested) atoms. Cycle 28: After refmac, R = 0.2355 (Rfree = 0.000) for 2905 atoms. Found 13 (14 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.2327 (Rfree = 0.000) for 2907 atoms. Found 13 (13 requested) and removed 10 (10 requested) atoms. Cycle 30: After refmac, R = 0.2285 (Rfree = 0.000) for 2906 atoms. Found 13 (13 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 2985 seeds are put forward NCS extension: 25 residues added (7 deleted due to clashes), 3010 seeds are put forward Round 1: 258 peptides, 32 chains. Longest chain 23 peptides. Score 0.583 Round 2: 273 peptides, 28 chains. Longest chain 30 peptides. Score 0.658 Round 3: 266 peptides, 30 chains. Longest chain 26 peptides. Score 0.623 Round 4: 276 peptides, 34 chains. Longest chain 22 peptides. Score 0.604 Round 5: 275 peptides, 28 chains. Longest chain 38 peptides. Score 0.663 Taking the results from Round 5 Chains 28, Residues 247, Estimated correctness of the model 47.9 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 6301 restraints for refining 2925 atoms. 5323 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2587 (Rfree = 0.000) for 2925 atoms. Found 13 (13 requested) and removed 15 (11 requested) atoms. Cycle 32: After refmac, R = 0.2441 (Rfree = 0.000) for 2913 atoms. Found 13 (13 requested) and removed 12 (11 requested) atoms. Cycle 33: After refmac, R = 0.2433 (Rfree = 0.000) for 2913 atoms. Found 13 (13 requested) and removed 11 (10 requested) atoms. Cycle 34: After refmac, R = 0.2251 (Rfree = 0.000) for 2912 atoms. Found 12 (13 requested) and removed 11 (11 requested) atoms. Cycle 35: After refmac, R = 0.2328 (Rfree = 0.000) for 2912 atoms. Found 11 (13 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.20 2.91 Search for helices and strands: 0 residues in 0 chains, 3003 seeds are put forward NCS extension: 44 residues added (3 deleted due to clashes), 3047 seeds are put forward Round 1: 227 peptides, 31 chains. Longest chain 18 peptides. Score 0.515 Round 2: 263 peptides, 32 chains. Longest chain 27 peptides. Score 0.595 Round 3: 263 peptides, 29 chains. Longest chain 25 peptides. Score 0.627 Round 4: 271 peptides, 30 chains. Longest chain 22 peptides. Score 0.634 Round 5: 263 peptides, 30 chains. Longest chain 21 peptides. Score 0.616 Taking the results from Round 4 Chains 31, Residues 241, Estimated correctness of the model 39.4 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 6096 restraints for refining 2925 atoms. 5053 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2556 (Rfree = 0.000) for 2925 atoms. Found 13 (13 requested) and removed 14 (11 requested) atoms. Cycle 37: After refmac, R = 0.2468 (Rfree = 0.000) for 2914 atoms. Found 13 (13 requested) and removed 13 (11 requested) atoms. Cycle 38: After refmac, R = 0.2399 (Rfree = 0.000) for 2905 atoms. Found 13 (13 requested) and removed 11 (10 requested) atoms. Cycle 39: After refmac, R = 0.2306 (Rfree = 0.000) for 2905 atoms. Found 7 (13 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.2308 (Rfree = 0.000) for 2900 atoms. Found 2 (13 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.00 Search for helices and strands: 0 residues in 0 chains, 2962 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2975 seeds are put forward Round 1: 239 peptides, 34 chains. Longest chain 15 peptides. Score 0.511 Round 2: 252 peptides, 26 chains. Longest chain 38 peptides. Score 0.633 Round 3: 256 peptides, 27 chains. Longest chain 22 peptides. Score 0.632 Round 4: 264 peptides, 29 chains. Longest chain 25 peptides. Score 0.629 Round 5: 269 peptides, 30 chains. Longest chain 32 peptides. Score 0.630 Taking the results from Round 2 Chains 28, Residues 226, Estimated correctness of the model 39.1 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 7539 reflections ( 99.76 % complete ) and 6113 restraints for refining 2925 atoms. 5145 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2454 (Rfree = 0.000) for 2925 atoms. Found 13 (13 requested) and removed 13 (11 requested) atoms. Cycle 42: After refmac, R = 0.2290 (Rfree = 0.000) for 2916 atoms. Found 12 (13 requested) and removed 11 (11 requested) atoms. Cycle 43: After refmac, R = 0.2249 (Rfree = 0.000) for 2913 atoms. Found 6 (13 requested) and removed 11 (11 requested) atoms. Cycle 44: After refmac, R = 0.2211 (Rfree = 0.000) for 2908 atoms. Found 4 (13 requested) and removed 12 (10 requested) atoms. Cycle 45: After refmac, R = 0.2210 (Rfree = 0.000) for 2900 atoms. Found 5 (13 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 2.98 Search for helices and strands: 0 residues in 0 chains, 2961 seeds are put forward NCS extension: 48 residues added (7 deleted due to clashes), 3009 seeds are put forward Round 1: 225 peptides, 34 chains. Longest chain 16 peptides. Score 0.471 Round 2: 248 peptides, 28 chains. Longest chain 38 peptides. Score 0.603 Round 3: 256 peptides, 32 chains. Longest chain 21 peptides. Score 0.578 Round 4: 247 peptides, 28 chains. Longest chain 38 peptides. Score 0.601 Round 5: 251 peptides, 31 chains. Longest chain 21 peptides. Score 0.577 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 220, Estimated correctness of the model 29.7 % 2 chains (40 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 2p97-3_warpNtrace.pdb as input Building loops using Loopy2018 31 chains (220 residues) following loop building 2 chains (40 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7539 reflections ( 99.76 % complete ) and 6100 restraints for refining 2925 atoms. 5086 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2510 (Rfree = 0.000) for 2925 atoms. Found 0 (13 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2374 (Rfree = 0.000) for 2899 atoms. Found 0 (13 requested) and removed 10 (11 requested) atoms. Cycle 48: After refmac, R = 0.2303 (Rfree = 0.000) for 2885 atoms. Found 0 (13 requested) and removed 4 (10 requested) atoms. Cycle 49: After refmac, R = 0.2280 (Rfree = 0.000) for 2878 atoms. Found 0 (13 requested) and removed 1 (10 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:27:23 GMT 2018 Job finished. TimeTaking 59.47 Used memory is bytes: 7867896