null Sun 23 Dec 22:22:41 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 2o62-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o62-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o62-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o62-4.0-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/2o62-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o62-4.0-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 22:22:50 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/2o62-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o62-4.0-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 391 and 0 Target number of residues in the AU: 391 Target solvent content: 0.6373 Checking the provided sequence file Detected sequence length: 270 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 540 Adjusted target solvent content: 0.50 Input MTZ file: 2o62-4.0-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: 19 Cell parameters: 61.210 71.880 132.610 90.000 90.000 90.000 Input sequence file: 2o62-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 4320 target number of atoms Had to go as low as 0.70 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: 66.305 4.000 Wilson plot Bfac: 70.40 5176 reflections ( 97.73 % complete ) and 0 restraints for refining 4768 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3838 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3580 (Rfree = 0.000) for 4768 atoms. Found 20 (22 requested) and removed 71 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.60 3.60 Search for helices and strands: 0 residues in 0 chains, 4753 seeds are put forward NCS extension: 0 residues added, 4753 seeds are put forward Round 1: 106 peptides, 24 chains. Longest chain 7 peptides. Score 0.207 Round 2: 149 peptides, 32 chains. Longest chain 11 peptides. Score 0.242 Round 3: 161 peptides, 32 chains. Longest chain 8 peptides. Score 0.282 Round 4: 156 peptides, 30 chains. Longest chain 10 peptides. Score 0.293 Round 5: 179 peptides, 33 chains. Longest chain 11 peptides. Score 0.325 Taking the results from Round 5 Chains 33, Residues 146, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5176 reflections ( 97.73 % complete ) and 9655 restraints for refining 3901 atoms. 9104 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3329 (Rfree = 0.000) for 3901 atoms. Found 9 (18 requested) and removed 23 (9 requested) atoms. Cycle 2: After refmac, R = 0.2957 (Rfree = 0.000) for 3834 atoms. Found 12 (18 requested) and removed 29 (9 requested) atoms. Cycle 3: After refmac, R = 0.2705 (Rfree = 0.000) for 3782 atoms. Found 11 (18 requested) and removed 19 (9 requested) atoms. Cycle 4: After refmac, R = 0.2893 (Rfree = 0.000) for 3760 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 5: After refmac, R = 0.2515 (Rfree = 0.000) for 3736 atoms. Found 9 (17 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.64 3.64 Search for helices and strands: 0 residues in 0 chains, 3780 seeds are put forward NCS extension: 0 residues added, 3780 seeds are put forward Round 1: 120 peptides, 28 chains. Longest chain 7 peptides. Score 0.197 Round 2: 157 peptides, 33 chains. Longest chain 8 peptides. Score 0.254 Round 3: 177 peptides, 36 chains. Longest chain 10 peptides. Score 0.278 Round 4: 183 peptides, 34 chains. Longest chain 10 peptides. Score 0.324 Round 5: 167 peptides, 32 chains. Longest chain 10 peptides. Score 0.301 Taking the results from Round 4 Chains 34, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5176 reflections ( 97.73 % complete ) and 8089 restraints for refining 3414 atoms. 7527 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2819 (Rfree = 0.000) for 3414 atoms. Found 11 (16 requested) and removed 28 (8 requested) atoms. Cycle 7: After refmac, R = 0.2969 (Rfree = 0.000) for 3371 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 8: After refmac, R = 0.2764 (Rfree = 0.000) for 3346 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 9: After refmac, R = 0.2483 (Rfree = 0.000) for 3327 atoms. Found 14 (15 requested) and removed 12 (7 requested) atoms. Cycle 10: After refmac, R = 0.2815 (Rfree = 0.000) for 3314 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.49 Search for helices and strands: 0 residues in 0 chains, 3378 seeds are put forward NCS extension: 0 residues added, 3378 seeds are put forward Round 1: 148 peptides, 33 chains. Longest chain 7 peptides. Score 0.224 Round 2: 180 peptides, 36 chains. Longest chain 11 peptides. Score 0.288 Round 3: 186 peptides, 37 chains. Longest chain 8 peptides. Score 0.293 Round 4: 190 peptides, 37 chains. Longest chain 11 peptides. Score 0.306 Round 5: 186 peptides, 33 chains. Longest chain 16 peptides. Score 0.346 Taking the results from Round 5 Chains 33, Residues 153, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5176 reflections ( 97.73 % complete ) and 7238 restraints for refining 3248 atoms. 6644 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2776 (Rfree = 0.000) for 3248 atoms. Found 15 (15 requested) and removed 32 (7 requested) atoms. Cycle 12: After refmac, R = 0.2712 (Rfree = 0.000) for 3201 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 13: After refmac, R = 0.2669 (Rfree = 0.000) for 3186 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 14: After refmac, R = 0.2424 (Rfree = 0.000) for 3173 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. Cycle 15: After refmac, R = 0.2146 (Rfree = 0.000) for 3158 atoms. Found 7 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.49 Search for helices and strands: 0 residues in 0 chains, 3211 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3235 seeds are put forward Round 1: 146 peptides, 33 chains. Longest chain 7 peptides. Score 0.217 Round 2: 175 peptides, 32 chains. Longest chain 10 peptides. Score 0.326 Round 3: 188 peptides, 31 chains. Longest chain 14 peptides. Score 0.378 Round 4: 202 peptides, 34 chains. Longest chain 14 peptides. Score 0.380 Round 5: 198 peptides, 33 chains. Longest chain 16 peptides. Score 0.381 Taking the results from Round 5 Chains 35, Residues 165, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5176 reflections ( 97.73 % complete ) and 7124 restraints for refining 3264 atoms. 6463 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2918 (Rfree = 0.000) for 3264 atoms. Found 14 (15 requested) and removed 32 (7 requested) atoms. Cycle 17: After refmac, R = 0.2826 (Rfree = 0.000) for 3205 atoms. Found 15 (15 requested) and removed 24 (7 requested) atoms. Cycle 18: After refmac, R = 0.2718 (Rfree = 0.000) for 3178 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 19: After refmac, R = 0.2830 (Rfree = 0.000) for 3157 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 20: After refmac, R = 0.2731 (Rfree = 0.000) for 3146 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.42 3.42 Search for helices and strands: 0 residues in 0 chains, 3235 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3252 seeds are put forward Round 1: 191 peptides, 38 chains. Longest chain 12 peptides. Score 0.296 Round 2: 213 peptides, 41 chains. Longest chain 14 peptides. Score 0.324 Round 3: 221 peptides, 42 chains. Longest chain 13 peptides. Score 0.335 Round 4: 202 peptides, 34 chains. Longest chain 21 peptides. Score 0.380 Round 5: 212 peptides, 37 chains. Longest chain 11 peptides. Score 0.371 Taking the results from Round 4 Chains 34, Residues 168, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5176 reflections ( 97.73 % complete ) and 7366 restraints for refining 3295 atoms. 6728 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2986 (Rfree = 0.000) for 3295 atoms. Found 15 (15 requested) and removed 45 (7 requested) atoms. Cycle 22: After refmac, R = 0.2834 (Rfree = 0.000) for 3233 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 23: After refmac, R = 0.2584 (Rfree = 0.000) for 3210 atoms. Found 15 (15 requested) and removed 25 (7 requested) atoms. Cycle 24: After refmac, R = 0.2717 (Rfree = 0.000) for 3182 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 25: After refmac, R = 0.2131 (Rfree = 0.000) for 3169 atoms. Found 7 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 3.53 Search for helices and strands: 0 residues in 0 chains, 3224 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 3250 seeds are put forward Round 1: 181 peptides, 40 chains. Longest chain 6 peptides. Score 0.237 Round 2: 210 peptides, 40 chains. Longest chain 10 peptides. Score 0.328 Round 3: 212 peptides, 36 chains. Longest chain 12 peptides. Score 0.384 Round 4: 222 peptides, 40 chains. Longest chain 13 peptides. Score 0.363 Round 5: 225 peptides, 43 chains. Longest chain 10 peptides. Score 0.334 Taking the results from Round 3 Chains 36, Residues 176, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5176 reflections ( 97.73 % complete ) and 7198 restraints for refining 3296 atoms. 6530 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2704 (Rfree = 0.000) for 3296 atoms. Found 15 (15 requested) and removed 30 (7 requested) atoms. Cycle 27: After refmac, R = 0.2722 (Rfree = 0.000) for 3260 atoms. Found 15 (15 requested) and removed 32 (7 requested) atoms. Cycle 28: After refmac, R = 0.2626 (Rfree = 0.000) for 3222 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. Cycle 29: After refmac, R = 0.2110 (Rfree = 0.000) for 3208 atoms. Found 10 (15 requested) and removed 10 (7 requested) atoms. Cycle 30: After refmac, R = 0.2559 (Rfree = 0.000) for 3199 atoms. Found 15 (15 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 3.50 Search for helices and strands: 0 residues in 0 chains, 3276 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3287 seeds are put forward Round 1: 186 peptides, 40 chains. Longest chain 8 peptides. Score 0.254 Round 2: 191 peptides, 36 chains. Longest chain 9 peptides. Score 0.322 Round 3: 174 peptides, 30 chains. Longest chain 11 peptides. Score 0.349 Round 4: 192 peptides, 31 chains. Longest chain 16 peptides. Score 0.389 Round 5: 195 peptides, 28 chains. Longest chain 13 peptides. Score 0.435 Taking the results from Round 5 Chains 28, Residues 167, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5176 reflections ( 97.73 % complete ) and 7803 restraints for refining 3478 atoms. 7163 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2896 (Rfree = 0.000) for 3478 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 32: After refmac, R = 0.2903 (Rfree = 0.000) for 3421 atoms. Found 16 (16 requested) and removed 29 (8 requested) atoms. Cycle 33: After refmac, R = 0.2801 (Rfree = 0.000) for 3376 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 34: After refmac, R = 0.2399 (Rfree = 0.000) for 3350 atoms. Found 15 (16 requested) and removed 11 (8 requested) atoms. Cycle 35: After refmac, R = 0.2733 (Rfree = 0.000) for 3340 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 3.63 Search for helices and strands: 0 residues in 0 chains, 3390 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 3404 seeds are put forward Round 1: 126 peptides, 28 chains. Longest chain 8 peptides. Score 0.220 Round 2: 161 peptides, 29 chains. Longest chain 12 peptides. Score 0.323 Round 3: 181 peptides, 31 chains. Longest chain 13 peptides. Score 0.357 Round 4: 181 peptides, 31 chains. Longest chain 12 peptides. Score 0.357 Round 5: 192 peptides, 34 chains. Longest chain 13 peptides. Score 0.351 Taking the results from Round 4 Chains 31, Residues 150, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5176 reflections ( 97.73 % complete ) and 7353 restraints for refining 3318 atoms. 6757 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3041 (Rfree = 0.000) for 3318 atoms. Found 15 (15 requested) and removed 32 (7 requested) atoms. Cycle 37: After refmac, R = 0.2689 (Rfree = 0.000) for 3284 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 38: After refmac, R = 0.2976 (Rfree = 0.000) for 3266 atoms. Found 15 (15 requested) and removed 24 (7 requested) atoms. Cycle 39: After refmac, R = 0.2836 (Rfree = 0.000) for 3234 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 40: After refmac, R = 0.2926 (Rfree = 0.000) for 3214 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.49 3.49 Search for helices and strands: 0 residues in 0 chains, 3270 seeds are put forward NCS extension: 0 residues added, 3270 seeds are put forward Round 1: 112 peptides, 24 chains. Longest chain 8 peptides. Score 0.230 Round 2: 152 peptides, 28 chains. Longest chain 14 peptides. Score 0.308 Round 3: 176 peptides, 33 chains. Longest chain 11 peptides. Score 0.315 Round 4: 177 peptides, 32 chains. Longest chain 15 peptides. Score 0.332 Round 5: 168 peptides, 31 chains. Longest chain 9 peptides. Score 0.317 Taking the results from Round 4 Chains 32, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5176 reflections ( 97.73 % complete ) and 7328 restraints for refining 3241 atoms. 6780 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3028 (Rfree = 0.000) for 3241 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 42: After refmac, R = 0.3025 (Rfree = 0.000) for 3212 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 43: After refmac, R = 0.2429 (Rfree = 0.000) for 3188 atoms. Found 6 (15 requested) and removed 11 (7 requested) atoms. Cycle 44: After refmac, R = 0.2885 (Rfree = 0.000) for 3167 atoms. Found 15 (15 requested) and removed 12 (7 requested) atoms. Cycle 45: After refmac, R = 0.2937 (Rfree = 0.000) for 3161 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.54 3.54 Search for helices and strands: 0 residues in 0 chains, 3213 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 3241 seeds are put forward Round 1: 123 peptides, 28 chains. Longest chain 8 peptides. Score 0.209 Round 2: 135 peptides, 27 chains. Longest chain 8 peptides. Score 0.266 Round 3: 142 peptides, 26 chains. Longest chain 13 peptides. Score 0.304 Round 4: 149 peptides, 27 chains. Longest chain 10 peptides. Score 0.312 Round 5: 151 peptides, 28 chains. Longest chain 10 peptides. Score 0.305 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 122, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2o62-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5176 reflections ( 97.73 % complete ) and 6845 restraints for refining 3096 atoms. 6371 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3068 (Rfree = 0.000) for 3096 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2529 (Rfree = 0.000) for 3066 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2855 (Rfree = 0.000) for 3048 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2878 (Rfree = 0.000) for 3034 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:16:48 GMT 2018 Job finished. TimeTaking 54.12 Used memory is bytes: 4582128