Sun 23 Dec 22:22:49 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 2o62-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o62-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o62-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o62-3.4-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/2o62-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o62-3.4-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 ============================================================ Sun 23 Dec 22:22:59 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/2o62-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o62-3.4-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 410 and 0 Target number of residues in the AU: 410 Target solvent content: 0.6197 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: 2o62-3.4-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: 19 Cell parameters: 61.210 71.880 132.610 90.000 90.000 90.000 Input sequence file: 2o62-3.4-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 3.400 Wilson plot Bfac: 61.00 8352 reflections ( 98.43 % complete ) and 0 restraints for refining 4783 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3740 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3609 (Rfree = 0.000) for 4783 atoms. Found 36 (36 requested) and removed 92 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.23 3.23 Search for helices and strands: 0 residues in 0 chains, 4745 seeds are put forward NCS extension: 0 residues added, 4745 seeds are put forward Round 1: 165 peptides, 36 chains. Longest chain 8 peptides. Score 0.239 Round 2: 208 peptides, 42 chains. Longest chain 9 peptides. Score 0.296 Round 3: 212 peptides, 40 chains. Longest chain 9 peptides. Score 0.334 Round 4: 223 peptides, 40 chains. Longest chain 10 peptides. Score 0.366 Round 5: 228 peptides, 42 chains. Longest chain 11 peptides. Score 0.356 Taking the results from Round 4 Chains 40, Residues 183, Estimated correctness of the model 0.0 % 5 chains (18 residues) have been docked in sequence ------------------------------------------------------ 8352 reflections ( 98.43 % complete ) and 9185 restraints for refining 3928 atoms. 8455 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2791 (Rfree = 0.000) for 3928 atoms. Found 18 (29 requested) and removed 42 (14 requested) atoms. Cycle 2: After refmac, R = 0.2722 (Rfree = 0.000) for 3867 atoms. Found 14 (29 requested) and removed 31 (14 requested) atoms. Cycle 3: After refmac, R = 0.2717 (Rfree = 0.000) for 3844 atoms. Found 23 (29 requested) and removed 22 (14 requested) atoms. Cycle 4: After refmac, R = 0.2687 (Rfree = 0.000) for 3835 atoms. Found 13 (29 requested) and removed 27 (14 requested) atoms. Cycle 5: After refmac, R = 0.2604 (Rfree = 0.000) for 3811 atoms. Found 15 (28 requested) and removed 23 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 3.17 Search for helices and strands: 0 residues in 0 chains, 3846 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3858 seeds are put forward Round 1: 209 peptides, 43 chains. Longest chain 10 peptides. Score 0.286 Round 2: 237 peptides, 44 chains. Longest chain 10 peptides. Score 0.357 Round 3: 239 peptides, 39 chains. Longest chain 16 peptides. Score 0.422 Round 4: 253 peptides, 41 chains. Longest chain 11 peptides. Score 0.436 Round 5: 231 peptides, 38 chains. Longest chain 13 peptides. Score 0.412 Taking the results from Round 4 Chains 42, Residues 212, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 8352 reflections ( 98.43 % complete ) and 8847 restraints for refining 3928 atoms. 7950 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3003 (Rfree = 0.000) for 3928 atoms. Found 29 (29 requested) and removed 30 (14 requested) atoms. Cycle 7: After refmac, R = 0.2863 (Rfree = 0.000) for 3909 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. Cycle 8: After refmac, R = 0.2631 (Rfree = 0.000) for 3899 atoms. Found 16 (29 requested) and removed 23 (14 requested) atoms. Cycle 9: After refmac, R = 0.2933 (Rfree = 0.000) for 3883 atoms. Found 29 (29 requested) and removed 33 (14 requested) atoms. Cycle 10: After refmac, R = 0.2743 (Rfree = 0.000) for 3871 atoms. Found 16 (29 requested) and removed 23 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.14 3.14 Search for helices and strands: 0 residues in 0 chains, 3929 seeds are put forward NCS extension: 0 residues added, 3929 seeds are put forward Round 1: 213 peptides, 43 chains. Longest chain 10 peptides. Score 0.299 Round 2: 231 peptides, 39 chains. Longest chain 14 peptides. Score 0.400 Round 3: 237 peptides, 37 chains. Longest chain 13 peptides. Score 0.440 Round 4: 231 peptides, 35 chains. Longest chain 12 peptides. Score 0.448 Round 5: 240 peptides, 37 chains. Longest chain 15 peptides. Score 0.448 Taking the results from Round 5 Chains 38, Residues 203, Estimated correctness of the model 0.0 % 6 chains (43 residues) have been docked in sequence ------------------------------------------------------ 8352 reflections ( 98.43 % complete ) and 8544 restraints for refining 3927 atoms. 7631 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3152 (Rfree = 0.000) for 3927 atoms. Found 29 (29 requested) and removed 26 (14 requested) atoms. Cycle 12: After refmac, R = 0.2915 (Rfree = 0.000) for 3897 atoms. Found 29 (29 requested) and removed 24 (14 requested) atoms. Cycle 13: After refmac, R = 0.2491 (Rfree = 0.000) for 3870 atoms. Found 18 (29 requested) and removed 18 (14 requested) atoms. Cycle 14: After refmac, R = 0.2477 (Rfree = 0.000) for 3844 atoms. Found 7 (29 requested) and removed 18 (14 requested) atoms. Cycle 15: After refmac, R = 0.2433 (Rfree = 0.000) for 3827 atoms. Found 9 (28 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 3.17 Search for helices and strands: 0 residues in 0 chains, 3863 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3887 seeds are put forward Round 1: 205 peptides, 42 chains. Longest chain 14 peptides. Score 0.287 Round 2: 250 peptides, 44 chains. Longest chain 11 peptides. Score 0.393 Round 3: 235 peptides, 43 chains. Longest chain 11 peptides. Score 0.363 Round 4: 240 peptides, 42 chains. Longest chain 11 peptides. Score 0.389 Round 5: 243 peptides, 39 chains. Longest chain 16 peptides. Score 0.433 Taking the results from Round 5 Chains 40, Residues 204, Estimated correctness of the model 0.0 % 5 chains (33 residues) have been docked in sequence ------------------------------------------------------ 8352 reflections ( 98.43 % complete ) and 8747 restraints for refining 3928 atoms. 7871 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2644 (Rfree = 0.000) for 3928 atoms. Found 27 (29 requested) and removed 15 (14 requested) atoms. Cycle 17: After refmac, R = 0.2550 (Rfree = 0.000) for 3916 atoms. Found 29 (29 requested) and removed 19 (14 requested) atoms. Cycle 18: After refmac, R = 0.2532 (Rfree = 0.000) for 3916 atoms. Found 29 (29 requested) and removed 17 (14 requested) atoms. Cycle 19: After refmac, R = 0.2571 (Rfree = 0.000) for 3913 atoms. Found 29 (29 requested) and removed 16 (14 requested) atoms. Cycle 20: After refmac, R = 0.2425 (Rfree = 0.000) for 3914 atoms. Found 29 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 3.19 Search for helices and strands: 0 residues in 0 chains, 4003 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 4028 seeds are put forward Round 1: 187 peptides, 38 chains. Longest chain 8 peptides. Score 0.283 Round 2: 207 peptides, 39 chains. Longest chain 9 peptides. Score 0.332 Round 3: 215 peptides, 39 chains. Longest chain 10 peptides. Score 0.355 Round 4: 212 peptides, 38 chains. Longest chain 9 peptides. Score 0.359 Round 5: 228 peptides, 37 chains. Longest chain 13 peptides. Score 0.416 Taking the results from Round 5 Chains 37, Residues 191, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 8352 reflections ( 98.43 % complete ) and 8753 restraints for refining 3928 atoms. 7970 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2554 (Rfree = 0.000) for 3928 atoms. Found 29 (29 requested) and removed 27 (14 requested) atoms. Cycle 22: After refmac, R = 0.2440 (Rfree = 0.000) for 3902 atoms. Found 23 (29 requested) and removed 20 (14 requested) atoms. Cycle 23: After refmac, R = 0.2289 (Rfree = 0.000) for 3889 atoms. Found 29 (29 requested) and removed 15 (14 requested) atoms. Cycle 24: After refmac, R = 0.2220 (Rfree = 0.000) for 3897 atoms. Found 14 (29 requested) and removed 15 (14 requested) atoms. Cycle 25: After refmac, R = 0.2274 (Rfree = 0.000) for 3885 atoms. Found 22 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 3.16 Search for helices and strands: 0 residues in 0 chains, 3919 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3940 seeds are put forward Round 1: 212 peptides, 43 chains. Longest chain 14 peptides. Score 0.296 Round 2: 231 peptides, 43 chains. Longest chain 13 peptides. Score 0.352 Round 3: 236 peptides, 42 chains. Longest chain 12 peptides. Score 0.378 Round 4: 252 peptides, 44 chains. Longest chain 14 peptides. Score 0.399 Round 5: 237 peptides, 41 chains. Longest chain 13 peptides. Score 0.393 Taking the results from Round 4 Chains 44, Residues 208, Estimated correctness of the model 0.0 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ 8352 reflections ( 98.43 % complete ) and 8695 restraints for refining 3928 atoms. 7825 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2465 (Rfree = 0.000) for 3928 atoms. Found 13 (29 requested) and removed 16 (14 requested) atoms. Cycle 27: After refmac, R = 0.2297 (Rfree = 0.000) for 3906 atoms. Found 13 (29 requested) and removed 16 (14 requested) atoms. Cycle 28: After refmac, R = 0.2304 (Rfree = 0.000) for 3892 atoms. Found 16 (29 requested) and removed 18 (14 requested) atoms. Cycle 29: After refmac, R = 0.2211 (Rfree = 0.000) for 3883 atoms. Found 12 (29 requested) and removed 18 (14 requested) atoms. Cycle 30: After refmac, R = 0.2005 (Rfree = 0.000) for 3872 atoms. Found 2 (29 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.18 Search for helices and strands: 0 residues in 0 chains, 3888 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3908 seeds are put forward Round 1: 196 peptides, 40 chains. Longest chain 13 peptides. Score 0.285 Round 2: 212 peptides, 37 chains. Longest chain 14 peptides. Score 0.371 Round 3: 218 peptides, 39 chains. Longest chain 12 peptides. Score 0.364 Round 4: 221 peptides, 38 chains. Longest chain 11 peptides. Score 0.385 Round 5: 210 peptides, 34 chains. Longest chain 11 peptides. Score 0.403 Taking the results from Round 5 Chains 34, Residues 176, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 8352 reflections ( 98.43 % complete ) and 8875 restraints for refining 3928 atoms. 8157 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2400 (Rfree = 0.000) for 3928 atoms. Found 24 (29 requested) and removed 17 (14 requested) atoms. Cycle 32: After refmac, R = 0.2286 (Rfree = 0.000) for 3914 atoms. Found 26 (29 requested) and removed 16 (14 requested) atoms. Cycle 33: After refmac, R = 0.2003 (Rfree = 0.000) for 3913 atoms. Found 8 (29 requested) and removed 14 (14 requested) atoms. Cycle 34: After refmac, R = 0.1933 (Rfree = 0.000) for 3895 atoms. Found 10 (29 requested) and removed 16 (14 requested) atoms. Cycle 35: After refmac, R = 0.1933 (Rfree = 0.000) for 3887 atoms. Found 5 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 3.21 Search for helices and strands: 0 residues in 0 chains, 3894 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 3900 seeds are put forward Round 1: 197 peptides, 43 chains. Longest chain 6 peptides. Score 0.249 Round 2: 229 peptides, 46 chains. Longest chain 8 peptides. Score 0.309 Round 3: 232 peptides, 46 chains. Longest chain 11 peptides. Score 0.318 Round 4: 222 peptides, 42 chains. Longest chain 11 peptides. Score 0.338 Round 5: 211 peptides, 41 chains. Longest chain 11 peptides. Score 0.318 Taking the results from Round 4 Chains 42, Residues 180, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 8352 reflections ( 98.43 % complete ) and 8982 restraints for refining 3928 atoms. 8280 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2385 (Rfree = 0.000) for 3928 atoms. Found 15 (29 requested) and removed 16 (14 requested) atoms. Cycle 37: After refmac, R = 0.2254 (Rfree = 0.000) for 3907 atoms. Found 18 (29 requested) and removed 14 (14 requested) atoms. Cycle 38: After refmac, R = 0.2383 (Rfree = 0.000) for 3899 atoms. Found 28 (29 requested) and removed 16 (14 requested) atoms. Cycle 39: After refmac, R = 0.1999 (Rfree = 0.000) for 3904 atoms. Found 4 (29 requested) and removed 15 (14 requested) atoms. Cycle 40: After refmac, R = 0.2001 (Rfree = 0.000) for 3889 atoms. Found 7 (29 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 3.16 Search for helices and strands: 0 residues in 0 chains, 3910 seeds are put forward NCS extension: 0 residues added, 3910 seeds are put forward Round 1: 203 peptides, 45 chains. Longest chain 6 peptides. Score 0.242 Round 2: 221 peptides, 43 chains. Longest chain 8 peptides. Score 0.323 Round 3: 226 peptides, 44 chains. Longest chain 12 peptides. Score 0.325 Round 4: 222 peptides, 44 chains. Longest chain 8 peptides. Score 0.313 Round 5: 212 peptides, 40 chains. Longest chain 11 peptides. Score 0.334 Taking the results from Round 5 Chains 40, Residues 172, Estimated correctness of the model 0.0 % 5 chains (19 residues) have been docked in sequence ------------------------------------------------------ 8352 reflections ( 98.43 % complete ) and 8800 restraints for refining 3928 atoms. 8105 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2531 (Rfree = 0.000) for 3928 atoms. Found 28 (29 requested) and removed 18 (14 requested) atoms. Cycle 42: After refmac, R = 0.2444 (Rfree = 0.000) for 3919 atoms. Found 29 (29 requested) and removed 19 (14 requested) atoms. Cycle 43: After refmac, R = 0.2229 (Rfree = 0.000) for 3917 atoms. Found 24 (29 requested) and removed 16 (14 requested) atoms. Cycle 44: After refmac, R = 0.1968 (Rfree = 0.000) for 3914 atoms. Found 6 (29 requested) and removed 14 (14 requested) atoms. Cycle 45: After refmac, R = 0.2180 (Rfree = 0.000) for 3898 atoms. Found 25 (29 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 3.18 Search for helices and strands: 0 residues in 0 chains, 3951 seeds are put forward NCS extension: 0 residues added, 3951 seeds are put forward Round 1: 162 peptides, 37 chains. Longest chain 7 peptides. Score 0.215 Round 2: 176 peptides, 36 chains. Longest chain 7 peptides. Score 0.275 Round 3: 180 peptides, 35 chains. Longest chain 9 peptides. Score 0.301 Round 4: 201 peptides, 39 chains. Longest chain 8 peptides. Score 0.313 Round 5: 186 peptides, 37 chains. Longest chain 8 peptides. Score 0.293 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 162, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2o62-3_warpNtrace.pdb as input Building loops using Loopy2018 39 chains (162 residues) following loop building 2 chains (10 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8352 reflections ( 98.43 % complete ) and 8646 restraints for refining 3886 atoms. 8011 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2234 (Rfree = 0.000) for 3886 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2209 (Rfree = 0.000) for 3868 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2291 (Rfree = 0.000) for 3843 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2330 (Rfree = 0.000) for 3824 atoms. TimeTaking 57.93