Sun 23 Dec 23:44:06 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 1vqs-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vqs-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vqs-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.8-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/1vqs-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.8-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 ============================================================ Sun 23 Dec 23:44:10 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/1vqs-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vqs-3.8-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 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-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: 97 Cell parameters: 94.778 94.778 303.043 90.000 90.000 90.000 Input sequence file: 1vqs-3.8-parrot-mrncs.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 5172 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3345 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3363 (Rfree = 0.000) for 5172 atoms. Found 28 (28 requested) and removed 24 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 3.33 Search for helices and strands: 0 residues in 0 chains, 5274 seeds are put forward NCS extension: 0 residues added, 5274 seeds are put forward Round 1: 201 peptides, 41 chains. Longest chain 11 peptides. Score 0.275 Round 2: 272 peptides, 43 chains. Longest chain 17 peptides. Score 0.432 Round 3: 289 peptides, 44 chains. Longest chain 17 peptides. Score 0.460 Round 4: 328 peptides, 45 chains. Longest chain 17 peptides. Score 0.533 Round 5: 333 peptides, 45 chains. Longest chain 18 peptides. Score 0.543 Taking the results from Round 5 Chains 45, Residues 288, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9327 restraints for refining 4195 atoms. 8220 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3092 (Rfree = 0.000) for 4195 atoms. Found 23 (23 requested) and removed 37 (11 requested) atoms. Cycle 2: After refmac, R = 0.3019 (Rfree = 0.000) for 4078 atoms. Found 22 (22 requested) and removed 37 (11 requested) atoms. Cycle 3: After refmac, R = 0.2569 (Rfree = 0.000) for 4007 atoms. Found 14 (22 requested) and removed 28 (11 requested) atoms. Cycle 4: After refmac, R = 0.2867 (Rfree = 0.000) for 3962 atoms. Found 21 (21 requested) and removed 29 (10 requested) atoms. Cycle 5: After refmac, R = 0.2874 (Rfree = 0.000) for 3921 atoms. Found 21 (21 requested) and removed 38 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.60 3.41 Search for helices and strands: 0 residues in 0 chains, 4074 seeds are put forward NCS extension: 13 residues added (4 deleted due to clashes), 4087 seeds are put forward Round 1: 259 peptides, 44 chains. Longest chain 18 peptides. Score 0.391 Round 2: 310 peptides, 43 chains. Longest chain 19 peptides. Score 0.514 Round 3: 300 peptides, 41 chains. Longest chain 25 peptides. Score 0.512 Round 4: 310 peptides, 36 chains. Longest chain 33 peptides. Score 0.577 Round 5: 302 peptides, 40 chains. Longest chain 19 peptides. Score 0.526 Taking the results from Round 4 Chains 36, Residues 274, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9378 restraints for refining 4139 atoms. 8318 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3011 (Rfree = 0.000) for 4139 atoms. Found 22 (22 requested) and removed 39 (11 requested) atoms. Cycle 7: After refmac, R = 0.2879 (Rfree = 0.000) for 4073 atoms. Found 22 (22 requested) and removed 33 (11 requested) atoms. Cycle 8: After refmac, R = 0.2984 (Rfree = 0.000) for 4021 atoms. Found 22 (22 requested) and removed 38 (11 requested) atoms. Cycle 9: After refmac, R = 0.2904 (Rfree = 0.000) for 3957 atoms. Found 21 (21 requested) and removed 32 (10 requested) atoms. Cycle 10: After refmac, R = 0.2939 (Rfree = 0.000) for 3909 atoms. Found 21 (21 requested) and removed 23 (10 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.50 3.32 Search for helices and strands: 0 residues in 0 chains, 4074 seeds are put forward NCS extension: 36 residues added (1 deleted due to clashes), 4110 seeds are put forward Round 1: 251 peptides, 44 chains. Longest chain 18 peptides. Score 0.372 Round 2: 270 peptides, 40 chains. Longest chain 22 peptides. Score 0.457 Round 3: 272 peptides, 37 chains. Longest chain 20 peptides. Score 0.491 Round 4: 286 peptides, 34 chains. Longest chain 22 peptides. Score 0.548 Round 5: 297 peptides, 36 chains. Longest chain 19 peptides. Score 0.552 Taking the results from Round 5 Chains 39, Residues 261, Estimated correctness of the model 0.0 % 3 chains (44 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9047 restraints for refining 4197 atoms. 7840 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3118 (Rfree = 0.000) for 4197 atoms. Found 23 (23 requested) and removed 54 (11 requested) atoms. Cycle 12: After refmac, R = 0.2945 (Rfree = 0.000) for 4105 atoms. Found 22 (22 requested) and removed 33 (11 requested) atoms. Cycle 13: After refmac, R = 0.2883 (Rfree = 0.000) for 4046 atoms. Found 22 (22 requested) and removed 30 (11 requested) atoms. Cycle 14: After refmac, R = 0.2735 (Rfree = 0.000) for 4011 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. Cycle 15: After refmac, R = 0.2317 (Rfree = 0.000) for 3985 atoms. Found 13 (21 requested) and removed 17 (10 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.43 Search for helices and strands: 0 residues in 0 chains, 4103 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 4126 seeds are put forward Round 1: 257 peptides, 47 chains. Longest chain 18 peptides. Score 0.354 Round 2: 279 peptides, 41 chains. Longest chain 18 peptides. Score 0.467 Round 3: 283 peptides, 39 chains. Longest chain 21 peptides. Score 0.495 Round 4: 295 peptides, 42 chains. Longest chain 24 peptides. Score 0.492 Round 5: 305 peptides, 45 chains. Longest chain 20 peptides. Score 0.485 Taking the results from Round 3 Chains 41, Residues 244, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9358 restraints for refining 4186 atoms. 8358 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2910 (Rfree = 0.000) for 4186 atoms. Found 23 (23 requested) and removed 55 (11 requested) atoms. Cycle 17: After refmac, R = 0.2715 (Rfree = 0.000) for 4120 atoms. Found 22 (22 requested) and removed 41 (11 requested) atoms. Cycle 18: After refmac, R = 0.2861 (Rfree = 0.000) for 4085 atoms. Found 22 (22 requested) and removed 40 (11 requested) atoms. Cycle 19: After refmac, R = 0.2683 (Rfree = 0.000) for 4040 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. Cycle 20: After refmac, R = 0.2669 (Rfree = 0.000) for 4012 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.37 Search for helices and strands: 0 residues in 0 chains, 4150 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4168 seeds are put forward Round 1: 238 peptides, 47 chains. Longest chain 11 peptides. Score 0.306 Round 2: 280 peptides, 43 chains. Longest chain 18 peptides. Score 0.450 Round 3: 300 peptides, 47 chains. Longest chain 12 peptides. Score 0.455 Round 4: 297 peptides, 41 chains. Longest chain 19 peptides. Score 0.506 Round 5: 294 peptides, 41 chains. Longest chain 18 peptides. Score 0.500 Taking the results from Round 4 Chains 42, Residues 256, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9423 restraints for refining 4196 atoms. 8398 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2965 (Rfree = 0.000) for 4196 atoms. Found 23 (23 requested) and removed 55 (11 requested) atoms. Cycle 22: After refmac, R = 0.2883 (Rfree = 0.000) for 4129 atoms. Found 22 (22 requested) and removed 36 (11 requested) atoms. Cycle 23: After refmac, R = 0.2437 (Rfree = 0.000) for 4085 atoms. Found 16 (22 requested) and removed 23 (11 requested) atoms. Cycle 24: After refmac, R = 0.2730 (Rfree = 0.000) for 4051 atoms. Found 22 (22 requested) and removed 30 (11 requested) atoms. Cycle 25: After refmac, R = 0.2724 (Rfree = 0.000) for 4032 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.37 Search for helices and strands: 0 residues in 0 chains, 4150 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 4174 seeds are put forward Round 1: 223 peptides, 41 chains. Longest chain 10 peptides. Score 0.334 Round 2: 273 peptides, 42 chains. Longest chain 17 peptides. Score 0.444 Round 3: 272 peptides, 42 chains. Longest chain 14 peptides. Score 0.442 Round 4: 283 peptides, 41 chains. Longest chain 14 peptides. Score 0.476 Round 5: 284 peptides, 41 chains. Longest chain 15 peptides. Score 0.478 Taking the results from Round 5 Chains 41, Residues 243, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9595 restraints for refining 4195 atoms. 8664 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2853 (Rfree = 0.000) for 4195 atoms. Found 23 (23 requested) and removed 40 (11 requested) atoms. Cycle 27: After refmac, R = 0.2883 (Rfree = 0.000) for 4143 atoms. Found 22 (22 requested) and removed 38 (11 requested) atoms. Cycle 28: After refmac, R = 0.2852 (Rfree = 0.000) for 4092 atoms. Found 22 (22 requested) and removed 39 (11 requested) atoms. Cycle 29: After refmac, R = 0.2727 (Rfree = 0.000) for 4044 atoms. Found 22 (22 requested) and removed 35 (11 requested) atoms. Cycle 30: After refmac, R = 0.2780 (Rfree = 0.000) for 4009 atoms. Found 22 (22 requested) and removed 27 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.37 Search for helices and strands: 0 residues in 0 chains, 4134 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 4155 seeds are put forward Round 1: 205 peptides, 45 chains. Longest chain 7 peptides. Score 0.240 Round 2: 271 peptides, 50 chains. Longest chain 11 peptides. Score 0.357 Round 3: 257 peptides, 43 chains. Longest chain 11 peptides. Score 0.397 Round 4: 272 peptides, 44 chains. Longest chain 18 peptides. Score 0.422 Round 5: 265 peptides, 39 chains. Longest chain 21 peptides. Score 0.456 Taking the results from Round 5 Chains 39, Residues 226, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9683 restraints for refining 4197 atoms. 8818 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2843 (Rfree = 0.000) for 4197 atoms. Found 23 (23 requested) and removed 32 (11 requested) atoms. Cycle 32: After refmac, R = 0.2723 (Rfree = 0.000) for 4139 atoms. Found 23 (23 requested) and removed 35 (11 requested) atoms. Cycle 33: After refmac, R = 0.2837 (Rfree = 0.000) for 4089 atoms. Found 22 (22 requested) and removed 36 (11 requested) atoms. Cycle 34: After refmac, R = 0.2667 (Rfree = 0.000) for 4044 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. Cycle 35: After refmac, R = 0.2603 (Rfree = 0.000) for 4020 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 4113 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 4147 seeds are put forward Round 1: 181 peptides, 36 chains. Longest chain 10 peptides. Score 0.278 Round 2: 236 peptides, 40 chains. Longest chain 13 peptides. Score 0.377 Round 3: 250 peptides, 40 chains. Longest chain 16 peptides. Score 0.411 Round 4: 263 peptides, 46 chains. Longest chain 15 peptides. Score 0.380 Round 5: 251 peptides, 40 chains. Longest chain 16 peptides. Score 0.414 Taking the results from Round 5 Chains 40, Residues 211, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9725 restraints for refining 4183 atoms. 8921 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2856 (Rfree = 0.000) for 4183 atoms. Found 22 (22 requested) and removed 43 (11 requested) atoms. Cycle 37: After refmac, R = 0.2946 (Rfree = 0.000) for 4122 atoms. Found 22 (22 requested) and removed 32 (11 requested) atoms. Cycle 38: After refmac, R = 0.2917 (Rfree = 0.000) for 4074 atoms. Found 22 (22 requested) and removed 24 (11 requested) atoms. Cycle 39: After refmac, R = 0.2876 (Rfree = 0.000) for 4038 atoms. Found 22 (22 requested) and removed 16 (11 requested) atoms. Cycle 40: After refmac, R = 0.2944 (Rfree = 0.000) for 4021 atoms. Found 22 (22 requested) and removed 24 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 3.46 Search for helices and strands: 0 residues in 0 chains, 4109 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4127 seeds are put forward Round 1: 154 peptides, 33 chains. Longest chain 10 peptides. Score 0.237 Round 2: 201 peptides, 37 chains. Longest chain 14 peptides. Score 0.321 Round 3: 210 peptides, 37 chains. Longest chain 14 peptides. Score 0.345 Round 4: 218 peptides, 37 chains. Longest chain 13 peptides. Score 0.365 Round 5: 237 peptides, 41 chains. Longest chain 11 peptides. Score 0.369 Taking the results from Round 5 Chains 41, Residues 196, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7192 reflections ( 99.49 % complete ) and 9043 restraints for refining 3973 atoms. 8277 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3130 (Rfree = 0.000) for 3973 atoms. Found 21 (21 requested) and removed 27 (10 requested) atoms. Cycle 42: After refmac, R = 0.3089 (Rfree = 0.000) for 3929 atoms. Found 21 (21 requested) and removed 34 (10 requested) atoms. Cycle 43: After refmac, R = 0.3054 (Rfree = 0.000) for 3881 atoms. Found 21 (21 requested) and removed 33 (10 requested) atoms. Cycle 44: After refmac, R = 0.2962 (Rfree = 0.000) for 3832 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. Cycle 45: After refmac, R = 0.2944 (Rfree = 0.000) for 3813 atoms. Found 21 (21 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 3914 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3928 seeds are put forward Round 1: 162 peptides, 35 chains. Longest chain 7 peptides. Score 0.236 Round 2: 193 peptides, 35 chains. Longest chain 9 peptides. Score 0.323 Round 3: 199 peptides, 35 chains. Longest chain 11 peptides. Score 0.339 Round 4: 216 peptides, 37 chains. Longest chain 11 peptides. Score 0.360 Round 5: 218 peptides, 37 chains. Longest chain 14 peptides. Score 0.365 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 181, 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 8507 restraints for refining 3761 atoms. 7820 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3043 (Rfree = 0.000) for 3761 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.3068 (Rfree = 0.000) for 3726 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2681 (Rfree = 0.000) for 3694 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 49: After refmac, R = 0.2776 (Rfree = 0.000) for 3669 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Writing output files ... TimeTaking 44.77