Sun 23 Dec 22:22:52 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 1vqs-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqs-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqs-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqs-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/1vqs-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqs-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 22:23:02 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/1vqs-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqs-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 462 and 0 Target number of residues in the AU: 462 Target solvent content: 0.6326 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 5 Adjusted target number of residues: 580 Adjusted target solvent content: 0.54 Input MTZ file: 1vqs-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: 97 Cell parameters: 94.778 94.778 303.043 90.000 90.000 90.000 Input sequence file: 1vqs-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 4640 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: 29.971 3.801 Wilson plot Bfac: 67.67 7192 reflections ( 99.49 % complete ) and 0 restraints for refining 5162 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3417 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3212 (Rfree = 0.000) for 5162 atoms. Found 23 (28 requested) and removed 41 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.76 3.56 Search for helices and strands: 0 residues in 0 chains, 5248 seeds are put forward NCS extension: 0 residues added, 5248 seeds are put forward Round 1: 206 peptides, 39 chains. Longest chain 9 peptides. Score 0.312 Round 2: 279 peptides, 40 chains. Longest chain 13 peptides. Score 0.477 Round 3: 301 peptides, 41 chains. Longest chain 14 peptides. Score 0.514 Round 4: 329 peptides, 45 chains. Longest chain 15 peptides. Score 0.535 Round 5: 317 peptides, 42 chains. Longest chain 20 peptides. Score 0.538 Taking the results from Round 5 Chains 43, Residues 275, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9366 restraints for refining 4195 atoms. 8260 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3158 (Rfree = 0.000) for 4195 atoms. Found 23 (23 requested) and removed 28 (11 requested) atoms. Cycle 2: After refmac, R = 0.3060 (Rfree = 0.000) for 4091 atoms. Found 23 (23 requested) and removed 29 (11 requested) atoms. Cycle 3: After refmac, R = 0.2971 (Rfree = 0.000) for 4025 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 4: After refmac, R = 0.2898 (Rfree = 0.000) for 3973 atoms. Found 22 (22 requested) and removed 24 (11 requested) atoms. Cycle 5: After refmac, R = 0.2917 (Rfree = 0.000) for 3941 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 3.49 Search for helices and strands: 0 residues in 0 chains, 4091 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 4117 seeds are put forward Round 1: 300 peptides, 54 chains. Longest chain 14 peptides. Score 0.386 Round 2: 313 peptides, 45 chains. Longest chain 16 peptides. Score 0.502 Round 3: 342 peptides, 50 chains. Longest chain 19 peptides. Score 0.516 Round 4: 335 peptides, 46 chains. Longest chain 24 peptides. Score 0.538 Round 5: 341 peptides, 48 chains. Longest chain 19 peptides. Score 0.532 Taking the results from Round 4 Chains 46, Residues 289, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9211 restraints for refining 4091 atoms. 8101 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3202 (Rfree = 0.000) for 4091 atoms. Found 22 (22 requested) and removed 52 (11 requested) atoms. Cycle 7: After refmac, R = 0.2978 (Rfree = 0.000) for 4025 atoms. Found 22 (22 requested) and removed 41 (11 requested) atoms. Cycle 8: After refmac, R = 0.2580 (Rfree = 0.000) for 3979 atoms. Found 17 (22 requested) and removed 32 (11 requested) atoms. Cycle 9: After refmac, R = 0.2876 (Rfree = 0.000) for 3940 atoms. Found 21 (21 requested) and removed 32 (10 requested) atoms. Cycle 10: After refmac, R = 0.2827 (Rfree = 0.000) for 3907 atoms. Found 21 (21 requested) and removed 34 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.75 3.56 Search for helices and strands: 0 residues in 0 chains, 4024 seeds are put forward NCS extension: 33 residues added (4 deleted due to clashes), 4057 seeds are put forward Round 1: 284 peptides, 48 chains. Longest chain 17 peptides. Score 0.409 Round 2: 287 peptides, 47 chains. Longest chain 13 peptides. Score 0.426 Round 3: 294 peptides, 47 chains. Longest chain 13 peptides. Score 0.442 Round 4: 300 peptides, 46 chains. Longest chain 15 peptides. Score 0.465 Round 5: 304 peptides, 44 chains. Longest chain 19 peptides. Score 0.493 Taking the results from Round 5 Chains 44, Residues 260, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9744 restraints for refining 4197 atoms. 8748 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3013 (Rfree = 0.000) for 4197 atoms. Found 23 (23 requested) and removed 40 (11 requested) atoms. Cycle 12: After refmac, R = 0.2781 (Rfree = 0.000) for 4123 atoms. Found 22 (22 requested) and removed 42 (11 requested) atoms. Cycle 13: After refmac, R = 0.2745 (Rfree = 0.000) for 4061 atoms. Found 22 (22 requested) and removed 36 (11 requested) atoms. Cycle 14: After refmac, R = 0.2675 (Rfree = 0.000) for 4014 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 15: After refmac, R = 0.2605 (Rfree = 0.000) for 3983 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.52 3.34 Search for helices and strands: 0 residues in 0 chains, 4093 seeds are put forward NCS extension: 24 residues added (5 deleted due to clashes), 4117 seeds are put forward Round 1: 262 peptides, 49 chains. Longest chain 12 peptides. Score 0.346 Round 2: 284 peptides, 46 chains. Longest chain 14 peptides. Score 0.429 Round 3: 297 peptides, 47 chains. Longest chain 17 peptides. Score 0.449 Round 4: 296 peptides, 47 chains. Longest chain 15 peptides. Score 0.447 Round 5: 291 peptides, 44 chains. Longest chain 18 peptides. Score 0.465 Taking the results from Round 5 Chains 44, Residues 247, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9692 restraints for refining 4197 atoms. 8748 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2783 (Rfree = 0.000) for 4197 atoms. Found 23 (23 requested) and removed 38 (11 requested) atoms. Cycle 17: After refmac, R = 0.2517 (Rfree = 0.000) for 4134 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. Cycle 18: After refmac, R = 0.2526 (Rfree = 0.000) for 4098 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. Cycle 19: After refmac, R = 0.2402 (Rfree = 0.000) for 4061 atoms. Found 22 (22 requested) and removed 19 (11 requested) atoms. Cycle 20: After refmac, R = 0.2423 (Rfree = 0.000) for 4045 atoms. Found 22 (22 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.49 3.31 Search for helices and strands: 0 residues in 0 chains, 4164 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 4184 seeds are put forward Round 1: 220 peptides, 46 chains. Longest chain 10 peptides. Score 0.269 Round 2: 277 peptides, 42 chains. Longest chain 19 peptides. Score 0.453 Round 3: 299 peptides, 47 chains. Longest chain 15 peptides. Score 0.453 Round 4: 284 peptides, 38 chains. Longest chain 19 peptides. Score 0.507 Round 5: 291 peptides, 39 chains. Longest chain 15 peptides. Score 0.512 Taking the results from Round 5 Chains 39, Residues 252, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9471 restraints for refining 4195 atoms. 8502 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2694 (Rfree = 0.000) for 4195 atoms. Found 23 (23 requested) and removed 28 (11 requested) atoms. Cycle 22: After refmac, R = 0.2465 (Rfree = 0.000) for 4138 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. Cycle 23: After refmac, R = 0.2374 (Rfree = 0.000) for 4099 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 24: After refmac, R = 0.2395 (Rfree = 0.000) for 4061 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. Cycle 25: After refmac, R = 0.2320 (Rfree = 0.000) for 4041 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.31 Search for helices and strands: 0 residues in 0 chains, 4172 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 4193 seeds are put forward Round 1: 220 peptides, 44 chains. Longest chain 10 peptides. Score 0.292 Round 2: 250 peptides, 39 chains. Longest chain 15 peptides. Score 0.422 Round 3: 247 peptides, 36 chains. Longest chain 12 peptides. Score 0.446 Round 4: 251 peptides, 40 chains. Longest chain 15 peptides. Score 0.414 Round 5: 273 peptides, 42 chains. Longest chain 13 peptides. Score 0.444 Taking the results from Round 3 Chains 36, Residues 211, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9261 restraints for refining 4071 atoms. 8410 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2635 (Rfree = 0.000) for 4071 atoms. Found 22 (22 requested) and removed 50 (11 requested) atoms. Cycle 27: After refmac, R = 0.2404 (Rfree = 0.000) for 4001 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. Cycle 28: After refmac, R = 0.2331 (Rfree = 0.000) for 3977 atoms. Found 21 (21 requested) and removed 17 (10 requested) atoms. Cycle 29: After refmac, R = 0.2313 (Rfree = 0.000) for 3964 atoms. Found 21 (21 requested) and removed 22 (10 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2328 (Rfree = 0.000) for 3954 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.30 Search for helices and strands: 0 residues in 0 chains, 4081 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4094 seeds are put forward Round 1: 235 peptides, 45 chains. Longest chain 13 peptides. Score 0.320 Round 2: 273 peptides, 48 chains. Longest chain 13 peptides. Score 0.383 Round 3: 272 peptides, 47 chains. Longest chain 14 peptides. Score 0.391 Round 4: 280 peptides, 47 chains. Longest chain 19 peptides. Score 0.410 Round 5: 258 peptides, 41 chains. Longest chain 12 peptides. Score 0.420 Taking the results from Round 5 Chains 41, Residues 217, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9684 restraints for refining 4197 atoms. 8857 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2661 (Rfree = 0.000) for 4197 atoms. Found 23 (23 requested) and removed 40 (11 requested) atoms. Cycle 32: After refmac, R = 0.2515 (Rfree = 0.000) for 4138 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 33: After refmac, R = 0.2513 (Rfree = 0.000) for 4115 atoms. Found 22 (22 requested) and removed 35 (11 requested) atoms. Cycle 34: After refmac, R = 0.2500 (Rfree = 0.000) for 4083 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 35: After refmac, R = 0.2537 (Rfree = 0.000) for 4069 atoms. Found 22 (22 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 3.24 Search for helices and strands: 0 residues in 0 chains, 4197 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 4211 seeds are put forward Round 1: 215 peptides, 44 chains. Longest chain 9 peptides. Score 0.279 Round 2: 253 peptides, 46 chains. Longest chain 12 peptides. Score 0.355 Round 3: 248 peptides, 45 chains. Longest chain 12 peptides. Score 0.353 Round 4: 239 peptides, 40 chains. Longest chain 11 peptides. Score 0.385 Round 5: 228 peptides, 36 chains. Longest chain 19 peptides. Score 0.401 Taking the results from Round 5 Chains 38, Residues 192, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9659 restraints for refining 4197 atoms. 8885 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2848 (Rfree = 0.000) for 4197 atoms. Found 23 (23 requested) and removed 45 (11 requested) atoms. Cycle 37: After refmac, R = 0.2628 (Rfree = 0.000) for 4136 atoms. Found 22 (22 requested) and removed 28 (11 requested) atoms. Cycle 38: After refmac, R = 0.2588 (Rfree = 0.000) for 4102 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Cycle 39: After refmac, R = 0.2518 (Rfree = 0.000) for 4078 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. Cycle 40: After refmac, R = 0.2525 (Rfree = 0.000) for 4063 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.47 3.29 Search for helices and strands: 0 residues in 0 chains, 4135 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 4151 seeds are put forward Round 1: 199 peptides, 42 chains. Longest chain 9 peptides. Score 0.258 Round 2: 227 peptides, 40 chains. Longest chain 11 peptides. Score 0.355 Round 3: 233 peptides, 39 chains. Longest chain 13 peptides. Score 0.381 Round 4: 243 peptides, 41 chains. Longest chain 10 peptides. Score 0.384 Round 5: 255 peptides, 41 chains. Longest chain 12 peptides. Score 0.413 Taking the results from Round 5 Chains 41, Residues 214, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9662 restraints for refining 4197 atoms. 8847 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2757 (Rfree = 0.000) for 4197 atoms. Found 23 (23 requested) and removed 39 (11 requested) atoms. Cycle 42: After refmac, R = 0.2685 (Rfree = 0.000) for 4150 atoms. Found 22 (22 requested) and removed 30 (11 requested) atoms. Cycle 43: After refmac, R = 0.2638 (Rfree = 0.000) for 4116 atoms. Found 22 (22 requested) and removed 20 (11 requested) atoms. Cycle 44: After refmac, R = 0.2578 (Rfree = 0.000) for 4097 atoms. Found 22 (22 requested) and removed 20 (11 requested) atoms. Cycle 45: After refmac, R = 0.2442 (Rfree = 0.000) for 4078 atoms. Found 22 (22 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 3.31 Search for helices and strands: 0 residues in 0 chains, 4201 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 4213 seeds are put forward Round 1: 194 peptides, 44 chains. Longest chain 10 peptides. Score 0.220 Round 2: 222 peptides, 42 chains. Longest chain 10 peptides. Score 0.320 Round 3: 235 peptides, 39 chains. Longest chain 13 peptides. Score 0.386 Round 4: 223 peptides, 39 chains. Longest chain 13 peptides. Score 0.356 Round 5: 228 peptides, 38 chains. Longest chain 11 peptides. Score 0.379 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 196, 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 1vqs-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7192 reflections ( 99.49 % complete ) and 9555 restraints for refining 4135 atoms. 8810 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2772 (Rfree = 0.000) for 4135 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2711 (Rfree = 0.000) for 4094 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2741 (Rfree = 0.000) for 4061 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2506 (Rfree = 0.000) for 4031 atoms. TimeTaking 66.35