null Sun 23 Dec 22:22:50 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 2o62-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o62-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o62-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o62-3.2-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/2o62-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o62-3.2-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 22:23:00 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/2o62-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o62-3.2-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 419 and 0 Target number of residues in the AU: 419 Target solvent content: 0.6113 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: 2o62-3.2-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: 2o62-3.2-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 3.200 Wilson plot Bfac: 57.41 10009 reflections ( 98.68 % complete ) and 0 restraints for refining 4826 atoms. Observations/parameters ratio is 0.52 ------------------------------------------------------ Starting model: R = 0.3743 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3669 (Rfree = 0.000) for 4826 atoms. Found 30 (43 requested) and removed 97 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.11 3.11 Search for helices and strands: 0 residues in 0 chains, 4765 seeds are put forward NCS extension: 0 residues added, 4765 seeds are put forward Round 1: 154 peptides, 35 chains. Longest chain 6 peptides. Score 0.216 Round 2: 190 peptides, 39 chains. Longest chain 11 peptides. Score 0.280 Round 3: 236 peptides, 46 chains. Longest chain 11 peptides. Score 0.330 Round 4: 242 peptides, 44 chains. Longest chain 15 peptides. Score 0.371 Round 5: 231 peptides, 40 chains. Longest chain 11 peptides. Score 0.388 Taking the results from Round 5 Chains 40, Residues 191, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 10009 reflections ( 98.68 % complete ) and 8898 restraints for refining 3944 atoms. 8114 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3156 (Rfree = 0.000) for 3944 atoms. Found 19 (35 requested) and removed 47 (17 requested) atoms. Cycle 2: After refmac, R = 0.3062 (Rfree = 0.000) for 3872 atoms. Found 16 (35 requested) and removed 29 (17 requested) atoms. Cycle 3: After refmac, R = 0.3135 (Rfree = 0.000) for 3837 atoms. Found 24 (34 requested) and removed 25 (17 requested) atoms. Cycle 4: After refmac, R = 0.3173 (Rfree = 0.000) for 3811 atoms. Found 28 (34 requested) and removed 36 (17 requested) atoms. Cycle 5: After refmac, R = 0.3144 (Rfree = 0.000) for 3796 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.99 2.99 Search for helices and strands: 0 residues in 0 chains, 3862 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 3874 seeds are put forward Round 1: 179 peptides, 38 chains. Longest chain 8 peptides. Score 0.258 Round 2: 206 peptides, 39 chains. Longest chain 10 peptides. Score 0.329 Round 3: 220 peptides, 41 chains. Longest chain 10 peptides. Score 0.345 Round 4: 218 peptides, 40 chains. Longest chain 14 peptides. Score 0.351 Round 5: 245 peptides, 44 chains. Longest chain 12 peptides. Score 0.379 Taking the results from Round 5 Chains 44, Residues 201, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10009 reflections ( 98.68 % complete ) and 8635 restraints for refining 3863 atoms. 7849 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3113 (Rfree = 0.000) for 3863 atoms. Found 22 (34 requested) and removed 48 (17 requested) atoms. Cycle 7: After refmac, R = 0.3031 (Rfree = 0.000) for 3803 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. Cycle 8: After refmac, R = 0.2797 (Rfree = 0.000) for 3787 atoms. Found 31 (34 requested) and removed 25 (17 requested) atoms. Cycle 9: After refmac, R = 0.2747 (Rfree = 0.000) for 3775 atoms. Found 27 (34 requested) and removed 24 (17 requested) atoms. Cycle 10: After refmac, R = 0.2373 (Rfree = 0.000) for 3768 atoms. Found 17 (33 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.04 3.04 Search for helices and strands: 0 residues in 0 chains, 3854 seeds are put forward NCS extension: 0 residues added, 3854 seeds are put forward Round 1: 177 peptides, 38 chains. Longest chain 8 peptides. Score 0.251 Round 2: 234 peptides, 46 chains. Longest chain 9 peptides. Score 0.324 Round 3: 238 peptides, 43 chains. Longest chain 14 peptides. Score 0.372 Round 4: 235 peptides, 39 chains. Longest chain 14 peptides. Score 0.411 Round 5: 235 peptides, 42 chains. Longest chain 14 peptides. Score 0.375 Taking the results from Round 4 Chains 40, Residues 196, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 10009 reflections ( 98.68 % complete ) and 8656 restraints for refining 3837 atoms. 7883 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2712 (Rfree = 0.000) for 3837 atoms. Found 26 (34 requested) and removed 47 (17 requested) atoms. Cycle 12: After refmac, R = 0.2617 (Rfree = 0.000) for 3802 atoms. Found 19 (34 requested) and removed 30 (17 requested) atoms. Cycle 13: After refmac, R = 0.2593 (Rfree = 0.000) for 3784 atoms. Found 25 (34 requested) and removed 24 (17 requested) atoms. Cycle 14: After refmac, R = 0.2483 (Rfree = 0.000) for 3776 atoms. Found 20 (33 requested) and removed 21 (16 requested) atoms. Cycle 15: After refmac, R = 0.2399 (Rfree = 0.000) for 3771 atoms. Found 14 (33 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.04 3.04 Search for helices and strands: 0 residues in 0 chains, 3795 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3814 seeds are put forward Round 1: 200 peptides, 40 chains. Longest chain 11 peptides. Score 0.298 Round 2: 201 peptides, 39 chains. Longest chain 11 peptides. Score 0.313 Round 3: 229 peptides, 42 chains. Longest chain 11 peptides. Score 0.358 Round 4: 240 peptides, 44 chains. Longest chain 10 peptides. Score 0.365 Round 5: 236 peptides, 41 chains. Longest chain 10 peptides. Score 0.390 Taking the results from Round 5 Chains 41, Residues 195, Estimated correctness of the model 0.0 % 5 chains (34 residues) have been docked in sequence ------------------------------------------------------ 10009 reflections ( 98.68 % complete ) and 8569 restraints for refining 3944 atoms. 7717 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3070 (Rfree = 0.000) for 3944 atoms. Found 35 (35 requested) and removed 42 (17 requested) atoms. Cycle 17: After refmac, R = 0.2657 (Rfree = 0.000) for 3907 atoms. Found 35 (35 requested) and removed 26 (17 requested) atoms. Cycle 18: After refmac, R = 0.2702 (Rfree = 0.000) for 3898 atoms. Found 35 (35 requested) and removed 28 (17 requested) atoms. Cycle 19: After refmac, R = 0.2723 (Rfree = 0.000) for 3893 atoms. Found 35 (35 requested) and removed 32 (17 requested) atoms. Cycle 20: After refmac, R = 0.2707 (Rfree = 0.000) for 3866 atoms. Found 34 (34 requested) and removed 31 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 3.08 Search for helices and strands: 0 residues in 0 chains, 3907 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3919 seeds are put forward Round 1: 177 peptides, 39 chains. Longest chain 8 peptides. Score 0.238 Round 2: 219 peptides, 42 chains. Longest chain 13 peptides. Score 0.329 Round 3: 220 peptides, 37 chains. Longest chain 14 peptides. Score 0.394 Round 4: 221 peptides, 38 chains. Longest chain 11 peptides. Score 0.385 Round 5: 235 peptides, 39 chains. Longest chain 16 peptides. Score 0.411 Taking the results from Round 5 Chains 41, Residues 196, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 10009 reflections ( 98.68 % complete ) and 8592 restraints for refining 3944 atoms. 7800 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2774 (Rfree = 0.000) for 3944 atoms. Found 31 (35 requested) and removed 47 (17 requested) atoms. Cycle 22: After refmac, R = 0.2466 (Rfree = 0.000) for 3910 atoms. Found 26 (35 requested) and removed 29 (17 requested) atoms. Cycle 23: After refmac, R = 0.2390 (Rfree = 0.000) for 3888 atoms. Found 34 (35 requested) and removed 28 (17 requested) atoms. Cycle 24: After refmac, R = 0.2290 (Rfree = 0.000) for 3883 atoms. Found 25 (34 requested) and removed 21 (17 requested) atoms. Cycle 25: After refmac, R = 0.2245 (Rfree = 0.000) for 3880 atoms. Found 23 (34 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.07 3.07 Search for helices and strands: 0 residues in 0 chains, 3946 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3957 seeds are put forward Round 1: 181 peptides, 39 chains. Longest chain 8 peptides. Score 0.251 Round 2: 225 peptides, 39 chains. Longest chain 16 peptides. Score 0.384 Round 3: 219 peptides, 38 chains. Longest chain 11 peptides. Score 0.379 Round 4: 218 peptides, 35 chains. Longest chain 13 peptides. Score 0.413 Round 5: 223 peptides, 39 chains. Longest chain 14 peptides. Score 0.378 Taking the results from Round 4 Chains 35, Residues 183, Estimated correctness of the model 0.0 % 4 chains (14 residues) have been docked in sequence ------------------------------------------------------ 10009 reflections ( 98.68 % complete ) and 8723 restraints for refining 3944 atoms. 8003 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2389 (Rfree = 0.000) for 3944 atoms. Found 25 (35 requested) and removed 23 (17 requested) atoms. Cycle 27: After refmac, R = 0.2236 (Rfree = 0.000) for 3935 atoms. Found 23 (35 requested) and removed 20 (17 requested) atoms. Cycle 28: After refmac, R = 0.2296 (Rfree = 0.000) for 3931 atoms. Found 26 (35 requested) and removed 22 (17 requested) atoms. Cycle 29: After refmac, R = 0.2205 (Rfree = 0.000) for 3930 atoms. Found 31 (35 requested) and removed 19 (17 requested) atoms. Cycle 30: After refmac, R = 0.2285 (Rfree = 0.000) for 3940 atoms. Found 26 (35 requested) and removed 24 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.07 3.07 Search for helices and strands: 0 residues in 0 chains, 3957 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3976 seeds are put forward Round 1: 203 peptides, 43 chains. Longest chain 9 peptides. Score 0.268 Round 2: 229 peptides, 42 chains. Longest chain 13 peptides. Score 0.358 Round 3: 241 peptides, 44 chains. Longest chain 14 peptides. Score 0.368 Round 4: 224 peptides, 37 chains. Longest chain 14 peptides. Score 0.405 Round 5: 206 peptides, 36 chains. Longest chain 10 peptides. Score 0.366 Taking the results from Round 4 Chains 37, Residues 187, Estimated correctness of the model 0.0 % 7 chains (33 residues) have been docked in sequence ------------------------------------------------------ 10009 reflections ( 98.68 % complete ) and 8719 restraints for refining 3943 atoms. 7919 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2376 (Rfree = 0.000) for 3943 atoms. Found 21 (35 requested) and removed 23 (17 requested) atoms. Cycle 32: After refmac, R = 0.2352 (Rfree = 0.000) for 3928 atoms. Found 22 (35 requested) and removed 20 (17 requested) atoms. Cycle 33: After refmac, R = 0.2745 (Rfree = 0.000) for 3923 atoms. Found 35 (35 requested) and removed 20 (17 requested) atoms. Cycle 34: After refmac, R = 0.2348 (Rfree = 0.000) for 3927 atoms. Found 21 (35 requested) and removed 18 (17 requested) atoms. Cycle 35: After refmac, R = 0.2210 (Rfree = 0.000) for 3928 atoms. Found 10 (35 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.03 3.03 Search for helices and strands: 0 residues in 0 chains, 3942 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3959 seeds are put forward Round 1: 205 peptides, 43 chains. Longest chain 10 peptides. Score 0.274 Round 2: 217 peptides, 41 chains. Longest chain 9 peptides. Score 0.336 Round 3: 234 peptides, 42 chains. Longest chain 12 peptides. Score 0.373 Round 4: 233 peptides, 39 chains. Longest chain 12 peptides. Score 0.406 Round 5: 212 peptides, 36 chains. Longest chain 11 peptides. Score 0.384 Taking the results from Round 4 Chains 39, Residues 194, Estimated correctness of the model 0.0 % 9 chains (43 residues) have been docked in sequence ------------------------------------------------------ 10009 reflections ( 98.68 % complete ) and 8378 restraints for refining 3942 atoms. 7506 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2506 (Rfree = 0.000) for 3942 atoms. Found 33 (35 requested) and removed 31 (17 requested) atoms. Cycle 37: After refmac, R = 0.2532 (Rfree = 0.000) for 3932 atoms. Found 35 (35 requested) and removed 24 (17 requested) atoms. Cycle 38: After refmac, R = 0.2346 (Rfree = 0.000) for 3934 atoms. Found 27 (35 requested) and removed 19 (17 requested) atoms. Cycle 39: After refmac, R = 0.2308 (Rfree = 0.000) for 3931 atoms. Found 18 (35 requested) and removed 22 (17 requested) atoms. Cycle 40: After refmac, R = 0.2238 (Rfree = 0.000) for 3919 atoms. Found 16 (35 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.09 3.09 Search for helices and strands: 0 residues in 0 chains, 3952 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 3967 seeds are put forward Round 1: 198 peptides, 42 chains. Longest chain 7 peptides. Score 0.265 Round 2: 208 peptides, 39 chains. Longest chain 9 peptides. Score 0.334 Round 3: 224 peptides, 40 chains. Longest chain 10 peptides. Score 0.369 Round 4: 231 peptides, 40 chains. Longest chain 10 peptides. Score 0.388 Round 5: 234 peptides, 44 chains. Longest chain 10 peptides. Score 0.348 Taking the results from Round 4 Chains 40, Residues 191, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 10009 reflections ( 98.68 % complete ) and 8781 restraints for refining 3944 atoms. 8047 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2290 (Rfree = 0.000) for 3944 atoms. Found 20 (35 requested) and removed 19 (17 requested) atoms. Cycle 42: After refmac, R = 0.2229 (Rfree = 0.000) for 3942 atoms. Found 18 (35 requested) and removed 19 (17 requested) atoms. Cycle 43: After refmac, R = 0.2211 (Rfree = 0.000) for 3939 atoms. Found 14 (35 requested) and removed 19 (17 requested) atoms. Cycle 44: After refmac, R = 0.2194 (Rfree = 0.000) for 3932 atoms. Found 14 (35 requested) and removed 21 (17 requested) atoms. Cycle 45: After refmac, R = 0.2289 (Rfree = 0.000) for 3924 atoms. Found 33 (35 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.08 3.08 Search for helices and strands: 0 residues in 0 chains, 3979 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 3991 seeds are put forward Round 1: 197 peptides, 40 chains. Longest chain 11 peptides. Score 0.288 Round 2: 203 peptides, 35 chains. Longest chain 14 peptides. Score 0.370 Round 3: 198 peptides, 35 chains. Longest chain 12 peptides. Score 0.356 Round 4: 203 peptides, 36 chains. Longest chain 13 peptides. Score 0.358 Round 5: 198 peptides, 35 chains. Longest chain 8 peptides. Score 0.356 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 168, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2o62-3_warpNtrace.pdb as input Building loops using Loopy2018 35 chains (168 residues) following loop building 2 chains (7 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10009 reflections ( 98.68 % complete ) and 8843 restraints for refining 3944 atoms. 8193 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2453 (Rfree = 0.000) for 3944 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2378 (Rfree = 0.000) for 3918 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.2242 (Rfree = 0.000) for 3893 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.2618 (Rfree = 0.000) for 3875 atoms. Found 0 (34 requested) and removed 17 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:21:40 GMT 2018 Job finished. TimeTaking 58.85 Used memory is bytes: 19877776