null Sun 23 Dec 22:22:56 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 2o62-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o62-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o62-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o62-3.6-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/2o62-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o62-3.6-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 22:23:05 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/2o62-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o62-3.6-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 401 and 0 Target number of residues in the AU: 401 Target solvent content: 0.6280 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: 2o62-3.6-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: 2o62-3.6-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 3.600 Wilson plot Bfac: 65.28 7057 reflections ( 98.22 % complete ) and 0 restraints for refining 4762 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3744 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2927 (Rfree = 0.000) for 4762 atoms. Found 7 (30 requested) and removed 66 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 3.32 Search for helices and strands: 0 residues in 0 chains, 4726 seeds are put forward NCS extension: 0 residues added, 4726 seeds are put forward Round 1: 165 peptides, 36 chains. Longest chain 11 peptides. Score 0.239 Round 2: 228 peptides, 42 chains. Longest chain 11 peptides. Score 0.356 Round 3: 248 peptides, 45 chains. Longest chain 14 peptides. Score 0.376 Round 4: 230 peptides, 43 chains. Longest chain 12 peptides. Score 0.349 Round 5: 224 peptides, 40 chains. Longest chain 12 peptides. Score 0.369 Taking the results from Round 3 Chains 45, Residues 203, Estimated correctness of the model 0.0 % 6 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7057 reflections ( 98.22 % complete ) and 9326 restraints for refining 3913 atoms. 8520 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2876 (Rfree = 0.000) for 3913 atoms. Found 11 (25 requested) and removed 21 (12 requested) atoms. Cycle 2: After refmac, R = 0.2732 (Rfree = 0.000) for 3885 atoms. Found 3 (25 requested) and removed 16 (12 requested) atoms. Cycle 3: After refmac, R = 0.2667 (Rfree = 0.000) for 3860 atoms. Found 4 (24 requested) and removed 12 (12 requested) atoms. Cycle 4: After refmac, R = 0.2610 (Rfree = 0.000) for 3848 atoms. Found 0 (24 requested) and removed 14 (12 requested) atoms. Cycle 5: After refmac, R = 0.2593 (Rfree = 0.000) for 3829 atoms. Found 2 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.39 Search for helices and strands: 0 residues in 0 chains, 3876 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3892 seeds are put forward Round 1: 200 peptides, 37 chains. Longest chain 14 peptides. Score 0.336 Round 2: 237 peptides, 39 chains. Longest chain 17 peptides. Score 0.417 Round 3: 235 peptides, 37 chains. Longest chain 21 peptides. Score 0.435 Round 4: 256 peptides, 39 chains. Longest chain 17 peptides. Score 0.467 Round 5: 253 peptides, 38 chains. Longest chain 16 peptides. Score 0.470 Taking the results from Round 5 Chains 39, Residues 215, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7057 reflections ( 98.22 % complete ) and 9087 restraints for refining 3914 atoms. 8208 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2824 (Rfree = 0.000) for 3914 atoms. Found 11 (25 requested) and removed 22 (12 requested) atoms. Cycle 7: After refmac, R = 0.2749 (Rfree = 0.000) for 3882 atoms. Found 7 (25 requested) and removed 22 (12 requested) atoms. Cycle 8: After refmac, R = 0.2689 (Rfree = 0.000) for 3863 atoms. Found 2 (24 requested) and removed 16 (12 requested) atoms. Cycle 9: After refmac, R = 0.2637 (Rfree = 0.000) for 3848 atoms. Found 3 (24 requested) and removed 12 (12 requested) atoms. Cycle 10: After refmac, R = 0.2610 (Rfree = 0.000) for 3836 atoms. Found 0 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.36 Search for helices and strands: 0 residues in 0 chains, 3861 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3880 seeds are put forward Round 1: 204 peptides, 39 chains. Longest chain 9 peptides. Score 0.323 Round 2: 242 peptides, 45 chains. Longest chain 13 peptides. Score 0.359 Round 3: 242 peptides, 41 chains. Longest chain 13 peptides. Score 0.407 Round 4: 241 peptides, 37 chains. Longest chain 16 peptides. Score 0.451 Round 5: 240 peptides, 36 chains. Longest chain 13 peptides. Score 0.460 Taking the results from Round 5 Chains 36, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7057 reflections ( 98.22 % complete ) and 9344 restraints for refining 3916 atoms. 8564 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2679 (Rfree = 0.000) for 3916 atoms. Found 15 (25 requested) and removed 20 (12 requested) atoms. Cycle 12: After refmac, R = 0.2676 (Rfree = 0.000) for 3891 atoms. Found 6 (25 requested) and removed 15 (12 requested) atoms. Cycle 13: After refmac, R = 0.2413 (Rfree = 0.000) for 3875 atoms. Found 5 (24 requested) and removed 18 (12 requested) atoms. Cycle 14: After refmac, R = 0.2520 (Rfree = 0.000) for 3853 atoms. Found 8 (24 requested) and removed 12 (12 requested) atoms. Cycle 15: After refmac, R = 0.2335 (Rfree = 0.000) for 3841 atoms. Found 1 (24 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.36 Search for helices and strands: 0 residues in 0 chains, 3879 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3900 seeds are put forward Round 1: 217 peptides, 44 chains. Longest chain 11 peptides. Score 0.298 Round 2: 243 peptides, 46 chains. Longest chain 13 peptides. Score 0.350 Round 3: 256 peptides, 43 chains. Longest chain 13 peptides. Score 0.421 Round 4: 238 peptides, 37 chains. Longest chain 15 peptides. Score 0.443 Round 5: 264 peptides, 43 chains. Longest chain 17 peptides. Score 0.442 Taking the results from Round 4 Chains 37, Residues 201, Estimated correctness of the model 0.0 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7057 reflections ( 98.22 % complete ) and 8943 restraints for refining 3916 atoms. 8090 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2684 (Rfree = 0.000) for 3916 atoms. Found 7 (25 requested) and removed 58 (12 requested) atoms. Cycle 17: After refmac, R = 0.2594 (Rfree = 0.000) for 3855 atoms. Found 8 (24 requested) and removed 15 (12 requested) atoms. Cycle 18: After refmac, R = 0.2539 (Rfree = 0.000) for 3839 atoms. Found 11 (24 requested) and removed 14 (12 requested) atoms. Cycle 19: After refmac, R = 0.2496 (Rfree = 0.000) for 3833 atoms. Found 3 (24 requested) and removed 18 (12 requested) atoms. Cycle 20: After refmac, R = 0.2469 (Rfree = 0.000) for 3816 atoms. Found 4 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 3.32 Search for helices and strands: 0 residues in 0 chains, 3850 seeds are put forward NCS extension: 0 residues added, 3850 seeds are put forward Round 1: 223 peptides, 45 chains. Longest chain 10 peptides. Score 0.304 Round 2: 245 peptides, 45 chains. Longest chain 11 peptides. Score 0.367 Round 3: 241 peptides, 44 chains. Longest chain 11 peptides. Score 0.368 Round 4: 238 peptides, 41 chains. Longest chain 12 peptides. Score 0.396 Round 5: 257 peptides, 46 chains. Longest chain 11 peptides. Score 0.389 Taking the results from Round 4 Chains 41, Residues 197, Estimated correctness of the model 0.0 % 4 chains (25 residues) have been docked in sequence ------------------------------------------------------ 7057 reflections ( 98.22 % complete ) and 9036 restraints for refining 3915 atoms. 8196 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2701 (Rfree = 0.000) for 3915 atoms. Found 13 (25 requested) and removed 19 (12 requested) atoms. Cycle 22: After refmac, R = 0.2581 (Rfree = 0.000) for 3906 atoms. Found 8 (25 requested) and removed 13 (12 requested) atoms. Cycle 23: After refmac, R = 0.2490 (Rfree = 0.000) for 3898 atoms. Found 4 (25 requested) and removed 14 (12 requested) atoms. Cycle 24: After refmac, R = 0.2467 (Rfree = 0.000) for 3884 atoms. Found 5 (24 requested) and removed 12 (12 requested) atoms. Cycle 25: After refmac, R = 0.2430 (Rfree = 0.000) for 3873 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.41 Search for helices and strands: 0 residues in 0 chains, 3899 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 3911 seeds are put forward Round 1: 215 peptides, 44 chains. Longest chain 10 peptides. Score 0.292 Round 2: 226 peptides, 40 chains. Longest chain 15 peptides. Score 0.374 Round 3: 233 peptides, 41 chains. Longest chain 12 peptides. Score 0.382 Round 4: 219 peptides, 37 chains. Longest chain 13 peptides. Score 0.391 Round 5: 224 peptides, 37 chains. Longest chain 13 peptides. Score 0.405 Taking the results from Round 5 Chains 37, Residues 187, Estimated correctness of the model 0.0 % 4 chains (17 residues) have been docked in sequence ------------------------------------------------------ 7057 reflections ( 98.22 % complete ) and 9332 restraints for refining 3916 atoms. 8584 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2663 (Rfree = 0.000) for 3916 atoms. Found 12 (25 requested) and removed 24 (12 requested) atoms. Cycle 27: After refmac, R = 0.2500 (Rfree = 0.000) for 3899 atoms. Found 7 (25 requested) and removed 14 (12 requested) atoms. Cycle 28: After refmac, R = 0.2438 (Rfree = 0.000) for 3889 atoms. Found 7 (24 requested) and removed 17 (12 requested) atoms. Cycle 29: After refmac, R = 0.2398 (Rfree = 0.000) for 3878 atoms. Found 3 (24 requested) and removed 15 (12 requested) atoms. Cycle 30: After refmac, R = 0.2382 (Rfree = 0.000) for 3862 atoms. Found 2 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 3.35 Search for helices and strands: 0 residues in 0 chains, 3876 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3890 seeds are put forward Round 1: 208 peptides, 47 chains. Longest chain 7 peptides. Score 0.232 Round 2: 227 peptides, 46 chains. Longest chain 10 peptides. Score 0.303 Round 3: 222 peptides, 43 chains. Longest chain 10 peptides. Score 0.326 Round 4: 245 peptides, 46 chains. Longest chain 9 peptides. Score 0.355 Round 5: 248 peptides, 45 chains. Longest chain 21 peptides. Score 0.376 Taking the results from Round 5 Chains 45, Residues 203, Estimated correctness of the model 0.0 % 8 chains (55 residues) have been docked in sequence ------------------------------------------------------ 7057 reflections ( 98.22 % complete ) and 8709 restraints for refining 3916 atoms. 7769 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2619 (Rfree = 0.000) for 3916 atoms. Found 18 (25 requested) and removed 26 (12 requested) atoms. Cycle 32: After refmac, R = 0.2476 (Rfree = 0.000) for 3899 atoms. Found 9 (25 requested) and removed 15 (12 requested) atoms. Cycle 33: After refmac, R = 0.2414 (Rfree = 0.000) for 3888 atoms. Found 6 (24 requested) and removed 16 (12 requested) atoms. Cycle 34: After refmac, R = 0.2376 (Rfree = 0.000) for 3876 atoms. Found 4 (24 requested) and removed 12 (12 requested) atoms. Cycle 35: After refmac, R = 0.2344 (Rfree = 0.000) for 3864 atoms. Found 4 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.36 Search for helices and strands: 0 residues in 0 chains, 3900 seeds are put forward NCS extension: 39 residues added (0 deleted due to clashes), 3939 seeds are put forward Round 1: 210 peptides, 46 chains. Longest chain 8 peptides. Score 0.251 Round 2: 216 peptides, 41 chains. Longest chain 10 peptides. Score 0.333 Round 3: 241 peptides, 42 chains. Longest chain 16 peptides. Score 0.392 Round 4: 215 peptides, 39 chains. Longest chain 13 peptides. Score 0.355 Round 5: 239 peptides, 39 chains. Longest chain 14 peptides. Score 0.422 Taking the results from Round 5 Chains 39, Residues 200, Estimated correctness of the model 0.0 % 4 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7057 reflections ( 98.22 % complete ) and 9124 restraints for refining 3916 atoms. 8326 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2614 (Rfree = 0.000) for 3916 atoms. Found 12 (25 requested) and removed 26 (12 requested) atoms. Cycle 37: After refmac, R = 0.2499 (Rfree = 0.000) for 3893 atoms. Found 4 (25 requested) and removed 16 (12 requested) atoms. Cycle 38: After refmac, R = 0.2450 (Rfree = 0.000) for 3876 atoms. Found 3 (24 requested) and removed 14 (12 requested) atoms. Cycle 39: After refmac, R = 0.2432 (Rfree = 0.000) for 3859 atoms. Found 6 (24 requested) and removed 13 (12 requested) atoms. Cycle 40: After refmac, R = 0.2419 (Rfree = 0.000) for 3850 atoms. Found 4 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 3.34 Search for helices and strands: 0 residues in 0 chains, 3879 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3898 seeds are put forward Round 1: 193 peptides, 39 chains. Longest chain 9 peptides. Score 0.289 Round 2: 222 peptides, 40 chains. Longest chain 11 peptides. Score 0.363 Round 3: 222 peptides, 42 chains. Longest chain 10 peptides. Score 0.338 Round 4: 202 peptides, 38 chains. Longest chain 10 peptides. Score 0.329 Round 5: 209 peptides, 40 chains. Longest chain 11 peptides. Score 0.325 Taking the results from Round 2 Chains 40, Residues 182, Estimated correctness of the model 0.0 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ 7057 reflections ( 98.22 % complete ) and 9050 restraints for refining 3916 atoms. 8274 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2616 (Rfree = 0.000) for 3916 atoms. Found 17 (25 requested) and removed 16 (12 requested) atoms. Cycle 42: After refmac, R = 0.2503 (Rfree = 0.000) for 3910 atoms. Found 3 (25 requested) and removed 13 (12 requested) atoms. Cycle 43: After refmac, R = 0.2453 (Rfree = 0.000) for 3895 atoms. Found 3 (25 requested) and removed 12 (12 requested) atoms. Cycle 44: After refmac, R = 0.2424 (Rfree = 0.000) for 3883 atoms. Found 1 (24 requested) and removed 12 (12 requested) atoms. Cycle 45: After refmac, R = 0.2396 (Rfree = 0.000) for 3872 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.33 Search for helices and strands: 0 residues in 0 chains, 3908 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3921 seeds are put forward Round 1: 183 peptides, 40 chains. Longest chain 8 peptides. Score 0.244 Round 2: 214 peptides, 42 chains. Longest chain 10 peptides. Score 0.314 Round 3: 211 peptides, 42 chains. Longest chain 8 peptides. Score 0.305 Round 4: 224 peptides, 42 chains. Longest chain 9 peptides. Score 0.344 Round 5: 212 peptides, 39 chains. Longest chain 14 peptides. Score 0.346 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 39, Residues 173, 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 2o62-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7057 reflections ( 98.22 % complete ) and 9387 restraints for refining 3915 atoms. 8734 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2625 (Rfree = 0.000) for 3915 atoms. Found 0 (25 requested) and removed 11 (12 requested) atoms. Cycle 47: After refmac, R = 0.2558 (Rfree = 0.000) for 3900 atoms. Found 0 (25 requested) and removed 1 (12 requested) atoms. Cycle 48: After refmac, R = 0.2514 (Rfree = 0.000) for 3898 atoms. Found 0 (25 requested) and removed 3 (12 requested) atoms. Cycle 49: After refmac, R = 0.2486 (Rfree = 0.000) for 3894 atoms. Found 0 (24 requested) and removed 2 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:20:38 GMT 2018 Job finished. TimeTaking 57.71 Used memory is bytes: 12351152