Mon 24 Dec 00:15:36 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 1vme-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vme-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vme-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vme-4.0-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/1vme-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vme-4.0-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 ============================================================ Mon 24 Dec 00:15:41 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/1vme-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vme-4.0-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 581 and 0 Target number of residues in the AU: 581 Target solvent content: 0.6690 Checking the provided sequence file Detected sequence length: 410 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 820 Adjusted target solvent content: 0.53 Input MTZ file: 1vme-4.0-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: 4 Cell parameters: 55.242 95.831 90.130 90.000 95.426 90.000 Input sequence file: 1vme-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6560 target number of atoms Had to go as low as 0.75 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: 48.998 4.000 Wilson plot Bfac: 91.38 7991 reflections ( 99.75 % complete ) and 0 restraints for refining 7221 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3331 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3208 (Rfree = 0.000) for 7221 atoms. Found 34 (34 requested) and removed 98 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.80 3.65 Search for helices and strands: 0 residues in 0 chains, 7271 seeds are put forward NCS extension: 0 residues added, 7271 seeds are put forward Round 1: 312 peptides, 64 chains. Longest chain 10 peptides. Score 0.281 Round 2: 381 peptides, 66 chains. Longest chain 10 peptides. Score 0.390 Round 3: 417 peptides, 63 chains. Longest chain 15 peptides. Score 0.471 Round 4: 405 peptides, 62 chains. Longest chain 13 peptides. Score 0.459 Round 5: 423 peptides, 61 chains. Longest chain 15 peptides. Score 0.493 Taking the results from Round 5 Chains 61, Residues 362, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 13762 restraints for refining 5923 atoms. 12347 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2731 (Rfree = 0.000) for 5923 atoms. Found 26 (28 requested) and removed 58 (14 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2475 (Rfree = 0.000) for 5803 atoms. Found 19 (27 requested) and removed 38 (13 requested) atoms. Cycle 3: After refmac, R = 0.2041 (Rfree = 0.000) for 5726 atoms. Found 8 (27 requested) and removed 41 (13 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.1906 (Rfree = 0.000) for 5667 atoms. Found 5 (27 requested) and removed 24 (13 requested) atoms. Cycle 5: After refmac, R = 0.1833 (Rfree = 0.000) for 5635 atoms. Found 1 (26 requested) and removed 27 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.78 3.63 Search for helices and strands: 0 residues in 0 chains, 5820 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 5837 seeds are put forward Round 1: 374 peptides, 64 chains. Longest chain 14 peptides. Score 0.393 Round 2: 410 peptides, 62 chains. Longest chain 13 peptides. Score 0.466 Round 3: 414 peptides, 59 chains. Longest chain 14 peptides. Score 0.493 Round 4: 435 peptides, 57 chains. Longest chain 15 peptides. Score 0.537 Round 5: 440 peptides, 58 chains. Longest chain 23 peptides. Score 0.538 Taking the results from Round 5 Chains 60, Residues 382, Estimated correctness of the model 0.0 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 13332 restraints for refining 5924 atoms. 11754 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2576 (Rfree = 0.000) for 5924 atoms. Found 26 (28 requested) and removed 69 (14 requested) atoms. Cycle 7: After refmac, R = 0.2333 (Rfree = 0.000) for 5829 atoms. Found 21 (27 requested) and removed 52 (13 requested) atoms. Cycle 8: After refmac, R = 0.2322 (Rfree = 0.000) for 5764 atoms. Found 23 (27 requested) and removed 34 (13 requested) atoms. Cycle 9: After refmac, R = 0.2187 (Rfree = 0.000) for 5736 atoms. Found 17 (27 requested) and removed 28 (13 requested) atoms. Cycle 10: After refmac, R = 0.1813 (Rfree = 0.000) for 5700 atoms. Found 5 (27 requested) and removed 25 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.79 3.64 Search for helices and strands: 0 residues in 0 chains, 5877 seeds are put forward NCS extension: 15 residues added (3 deleted due to clashes), 5892 seeds are put forward Round 1: 367 peptides, 63 chains. Longest chain 14 peptides. Score 0.389 Round 2: 396 peptides, 62 chains. Longest chain 15 peptides. Score 0.444 Round 3: 425 peptides, 61 chains. Longest chain 17 peptides. Score 0.496 Round 4: 416 peptides, 61 chains. Longest chain 15 peptides. Score 0.483 Round 5: 421 peptides, 58 chains. Longest chain 27 peptides. Score 0.510 Taking the results from Round 5 Chains 60, Residues 363, Estimated correctness of the model 0.0 % 2 chains (49 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 12959 restraints for refining 5922 atoms. 11344 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2307 (Rfree = 0.000) for 5922 atoms. Found 24 (28 requested) and removed 56 (14 requested) atoms. Cycle 12: After refmac, R = 0.2322 (Rfree = 0.000) for 5851 atoms. Found 27 (27 requested) and removed 46 (13 requested) atoms. Cycle 13: After refmac, R = 0.2205 (Rfree = 0.000) for 5816 atoms. Found 14 (27 requested) and removed 54 (13 requested) atoms. Cycle 14: After refmac, R = 0.2162 (Rfree = 0.000) for 5760 atoms. Found 20 (27 requested) and removed 28 (13 requested) atoms. Cycle 15: After refmac, R = 0.2078 (Rfree = 0.000) for 5740 atoms. Found 20 (27 requested) and removed 28 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.81 3.66 Search for helices and strands: 0 residues in 0 chains, 5891 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 5913 seeds are put forward Round 1: 367 peptides, 64 chains. Longest chain 11 peptides. Score 0.381 Round 2: 419 peptides, 70 chains. Longest chain 14 peptides. Score 0.425 Round 3: 417 peptides, 62 chains. Longest chain 20 peptides. Score 0.477 Round 4: 440 peptides, 67 chains. Longest chain 25 peptides. Score 0.479 Round 5: 431 peptides, 64 chains. Longest chain 13 peptides. Score 0.485 Taking the results from Round 5 Chains 64, Residues 367, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 13486 restraints for refining 5923 atoms. 12077 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2771 (Rfree = 0.000) for 5923 atoms. Found 28 (28 requested) and removed 38 (14 requested) atoms. Cycle 17: After refmac, R = 0.2424 (Rfree = 0.000) for 5882 atoms. Found 28 (28 requested) and removed 37 (14 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2279 (Rfree = 0.000) for 5844 atoms. Found 24 (27 requested) and removed 32 (13 requested) atoms. Cycle 19: After refmac, R = 0.1936 (Rfree = 0.000) for 5805 atoms. Found 11 (27 requested) and removed 25 (13 requested) atoms. Cycle 20: After refmac, R = 0.1976 (Rfree = 0.000) for 5781 atoms. Found 19 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.81 3.66 Search for helices and strands: 0 residues in 0 chains, 5959 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 5976 seeds are put forward Round 1: 318 peptides, 66 chains. Longest chain 12 peptides. Score 0.276 Round 2: 356 peptides, 67 chains. Longest chain 10 peptides. Score 0.339 Round 3: 371 peptides, 64 chains. Longest chain 17 peptides. Score 0.388 Round 4: 394 peptides, 65 chains. Longest chain 17 peptides. Score 0.420 Round 5: 382 peptides, 61 chains. Longest chain 15 peptides. Score 0.429 Taking the results from Round 5 Chains 61, Residues 321, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 13597 restraints for refining 5924 atoms. 12314 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2369 (Rfree = 0.000) for 5924 atoms. Found 26 (28 requested) and removed 32 (14 requested) atoms. Cycle 22: After refmac, R = 0.2216 (Rfree = 0.000) for 5883 atoms. Found 23 (28 requested) and removed 28 (14 requested) atoms. Cycle 23: After refmac, R = 0.1943 (Rfree = 0.000) for 5856 atoms. Found 4 (27 requested) and removed 30 (13 requested) atoms. Cycle 24: After refmac, R = 0.1899 (Rfree = 0.000) for 5814 atoms. Found 13 (27 requested) and removed 20 (13 requested) atoms. Cycle 25: After refmac, R = 0.1802 (Rfree = 0.000) for 5800 atoms. Found 4 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.80 3.65 Search for helices and strands: 0 residues in 0 chains, 5940 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 5958 seeds are put forward Round 1: 327 peptides, 68 chains. Longest chain 9 peptides. Score 0.277 Round 2: 345 peptides, 59 chains. Longest chain 18 peptides. Score 0.380 Round 3: 366 peptides, 65 chains. Longest chain 12 peptides. Score 0.372 Round 4: 369 peptides, 65 chains. Longest chain 14 peptides. Score 0.377 Round 5: 378 peptides, 65 chains. Longest chain 14 peptides. Score 0.393 Taking the results from Round 5 Chains 65, Residues 313, Estimated correctness of the model 0.0 % 6 chains (30 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 13740 restraints for refining 5921 atoms. 12457 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2433 (Rfree = 0.000) for 5921 atoms. Found 28 (28 requested) and removed 47 (14 requested) atoms. Cycle 27: After refmac, R = 0.2405 (Rfree = 0.000) for 5874 atoms. Found 28 (28 requested) and removed 28 (14 requested) atoms. Cycle 28: After refmac, R = 0.1949 (Rfree = 0.000) for 5845 atoms. Found 12 (27 requested) and removed 27 (13 requested) atoms. Cycle 29: After refmac, R = 0.2019 (Rfree = 0.000) for 5817 atoms. Found 25 (27 requested) and removed 28 (13 requested) atoms. Cycle 30: After refmac, R = 0.2246 (Rfree = 0.000) for 5805 atoms. Found 27 (27 requested) and removed 25 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.77 3.62 Search for helices and strands: 0 residues in 0 chains, 5946 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 5959 seeds are put forward Round 1: 278 peptides, 59 chains. Longest chain 10 peptides. Score 0.255 Round 2: 323 peptides, 60 chains. Longest chain 15 peptides. Score 0.333 Round 3: 329 peptides, 58 chains. Longest chain 16 peptides. Score 0.360 Round 4: 319 peptides, 58 chains. Longest chain 14 peptides. Score 0.342 Round 5: 325 peptides, 57 chains. Longest chain 15 peptides. Score 0.360 Taking the results from Round 5 Chains 58, Residues 268, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 14061 restraints for refining 5923 atoms. 12982 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2452 (Rfree = 0.000) for 5923 atoms. Found 28 (28 requested) and removed 34 (14 requested) atoms. Cycle 32: After refmac, R = 0.2301 (Rfree = 0.000) for 5882 atoms. Found 28 (28 requested) and removed 34 (14 requested) atoms. Cycle 33: After refmac, R = 0.1877 (Rfree = 0.000) for 5848 atoms. Found 16 (27 requested) and removed 27 (13 requested) atoms. Cycle 34: After refmac, R = 0.1713 (Rfree = 0.000) for 5824 atoms. Found 6 (27 requested) and removed 18 (13 requested) atoms. Cycle 35: After refmac, R = 0.1669 (Rfree = 0.000) for 5805 atoms. Found 10 (27 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.81 3.66 Search for helices and strands: 0 residues in 0 chains, 5953 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 5966 seeds are put forward Round 1: 281 peptides, 60 chains. Longest chain 11 peptides. Score 0.253 Round 2: 318 peptides, 61 chains. Longest chain 11 peptides. Score 0.316 Round 3: 328 peptides, 59 chains. Longest chain 11 peptides. Score 0.350 Round 4: 326 peptides, 56 chains. Longest chain 15 peptides. Score 0.370 Round 5: 327 peptides, 58 chains. Longest chain 12 peptides. Score 0.356 Taking the results from Round 4 Chains 56, Residues 270, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 14251 restraints for refining 5923 atoms. 13221 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2489 (Rfree = 0.000) for 5923 atoms. Found 28 (28 requested) and removed 30 (14 requested) atoms. Cycle 37: After refmac, R = 0.2440 (Rfree = 0.000) for 5898 atoms. Found 28 (28 requested) and removed 28 (14 requested) atoms. Cycle 38: After refmac, R = 0.2342 (Rfree = 0.000) for 5867 atoms. Found 28 (28 requested) and removed 26 (14 requested) atoms. Cycle 39: After refmac, R = 0.2430 (Rfree = 0.000) for 5857 atoms. Found 27 (27 requested) and removed 34 (13 requested) atoms. Cycle 40: After refmac, R = 0.2274 (Rfree = 0.000) for 5836 atoms. Found 27 (27 requested) and removed 29 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.83 3.68 Search for helices and strands: 0 residues in 0 chains, 6015 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 6028 seeds are put forward Round 1: 250 peptides, 53 chains. Longest chain 9 peptides. Score 0.249 Round 2: 273 peptides, 49 chains. Longest chain 14 peptides. Score 0.329 Round 3: 277 peptides, 53 chains. Longest chain 11 peptides. Score 0.303 Round 4: 262 peptides, 48 chains. Longest chain 17 peptides. Score 0.316 Round 5: 277 peptides, 50 chains. Longest chain 14 peptides. Score 0.328 Taking the results from Round 2 Chains 49, Residues 224, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence ------------------------------------------------------ 7991 reflections ( 99.75 % complete ) and 14075 restraints for refining 5886 atoms. 13174 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2436 (Rfree = 0.000) for 5886 atoms. Found 27 (27 requested) and removed 43 (13 requested) atoms. Cycle 42: After refmac, R = 0.2203 (Rfree = 0.000) for 5840 atoms. Found 27 (27 requested) and removed 33 (13 requested) atoms. Cycle 43: After refmac, R = 0.2242 (Rfree = 0.000) for 5810 atoms. Found 27 (27 requested) and removed 34 (13 requested) atoms. Cycle 44: After refmac, R = 0.2123 (Rfree = 0.000) for 5789 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. Cycle 45: After refmac, R = 0.2120 (Rfree = 0.000) for 5778 atoms. Found 27 (27 requested) and removed 28 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.78 3.63 Search for helices and strands: 0 residues in 0 chains, 5896 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5915 seeds are put forward Round 1: 246 peptides, 54 chains. Longest chain 10 peptides. Score 0.232 Round 2: 286 peptides, 56 chains. Longest chain 12 peptides. Score 0.296 Round 3: 303 peptides, 53 chains. Longest chain 13 peptides. Score 0.352 Round 4: 304 peptides, 53 chains. Longest chain 13 peptides. Score 0.354 Round 5: 283 peptides, 51 chains. Longest chain 13 peptides. Score 0.331 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 53, Residues 251, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vme-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7991 reflections ( 99.75 % complete ) and 14001 restraints for refining 5922 atoms. 13027 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2314 (Rfree = 0.000) for 5922 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.2186 (Rfree = 0.000) for 5874 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2134 (Rfree = 0.000) for 5844 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2079 (Rfree = 0.000) for 5818 atoms. TimeTaking 63.8