Starting phenix.real_space_refine on Fri Dec 8 02:35:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q99_18272/12_2023/8q99_18272.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q99_18272/12_2023/8q99_18272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q99_18272/12_2023/8q99_18272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q99_18272/12_2023/8q99_18272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q99_18272/12_2023/8q99_18272.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q99_18272/12_2023/8q99_18272.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2046 2.51 5 N 588 2.21 5 O 606 1.98 5 H 3396 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6642 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "D" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "C" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "B" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "E" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Chain: "F" Number of atoms: 1107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Conformer: "B" Number of residues, atoms: 71, 1104 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} bond proxies already assigned to first conformer: 1110 Time building chain proxies: 5.86, per 1000 atoms: 0.88 Number of scatterers: 6642 At special positions: 0 Unit cell: (114.536, 96.408, 37.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 606 8.00 N 588 7.00 C 2046 6.00 H 3396 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.90 Conformation dependent library (CDL) restraints added in 1.3 seconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 309 through 310 removed outlier: 6.695A pdb=" N VAL A 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.710A pdb=" N VAL A 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.288A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N GLY C 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.500A pdb=" N ILE A 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.538A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLU C 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER A 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.531A pdb=" N ASP A 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.560A pdb=" N GLN A 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ILE D 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS A 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 357 through 361 removed outlier: 6.711A pdb=" N LEU A 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE C 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 368 through 377 removed outlier: 6.562A pdb=" N LYS A 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N GLU D 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N HIS D 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR A 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU D 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS A 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 309 through 310 removed outlier: 6.431A pdb=" N VAL B 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.633A pdb=" N VAL B 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 317 through 325 removed outlier: 6.319A pdb=" N VAL B 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS F 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N SER B 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLY F 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N CYS B 322 " --> pdb=" O GLY F 323 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU F 325 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N SER B 324 " --> pdb=" O LEU F 325 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 328 through 330 removed outlier: 6.654A pdb=" N ILE B 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 337 through 342 Processing sheet with id=AB6, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.614A pdb=" N ASP B 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 350 through 354 removed outlier: 6.513A pdb=" N GLN B 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ILE E 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LYS B 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 357 through 361 Processing sheet with id=AB9, first strand: chain 'E' and resid 368 through 377 removed outlier: 6.537A pdb=" N LYS B 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLU E 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE B 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N HIS E 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR B 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU E 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS B 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) 79 hydrogen bonds defined for protein. 237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 5.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 2.22: 6681 2.22 - 3.49: 3 3.49 - 4.76: 6 4.76 - 6.03: 3 6.03 - 7.29: 3 Warning: very large bond lengths. Bond restraints: 6696 Sorted by residual: bond pdb=" N LYS B 343 " pdb=" H BLYS B 343 " ideal model delta sigma weight residual 0.860 7.294 -6.434 2.00e-02 2.50e+03 1.04e+05 bond pdb=" N LYS F 343 " pdb=" H BLYS F 343 " ideal model delta sigma weight residual 0.860 7.174 -6.314 2.00e-02 2.50e+03 9.97e+04 bond pdb=" N LYS E 343 " pdb=" H BLYS E 343 " ideal model delta sigma weight residual 0.860 7.088 -6.228 2.00e-02 2.50e+03 9.70e+04 bond pdb=" N SER B 341 " pdb=" H BSER B 341 " ideal model delta sigma weight residual 0.860 5.496 -4.636 2.00e-02 2.50e+03 5.37e+04 bond pdb=" N SER F 341 " pdb=" H BSER F 341 " ideal model delta sigma weight residual 0.860 5.442 -4.582 2.00e-02 2.50e+03 5.25e+04 ... (remaining 6691 not shown) Histogram of bond angle deviations from ideal: 25.10 - 45.99: 10 45.99 - 66.88: 7 66.88 - 87.77: 7 87.77 - 108.66: 3024 108.66 - 129.55: 9174 Bond angle restraints: 12222 Sorted by residual: angle pdb=" C LYS A 340 " pdb=" N SER A 341 " pdb=" H BSER A 341 " ideal model delta sigma weight residual 123.65 25.10 98.55 3.00e+00 1.11e-01 1.08e+03 angle pdb=" C LYS D 340 " pdb=" N SER D 341 " pdb=" H BSER D 341 " ideal model delta sigma weight residual 123.65 25.59 98.06 3.00e+00 1.11e-01 1.07e+03 angle pdb=" C LYS C 340 " pdb=" N SER C 341 " pdb=" H BSER C 341 " ideal model delta sigma weight residual 123.65 30.04 93.61 3.00e+00 1.11e-01 9.74e+02 angle pdb=" C LYS E 340 " pdb=" N SER E 341 " pdb=" H BSER E 341 " ideal model delta sigma weight residual 123.65 32.01 91.64 3.00e+00 1.11e-01 9.33e+02 angle pdb=" C LYS B 340 " pdb=" N SER B 341 " pdb=" H BSER B 341 " ideal model delta sigma weight residual 123.65 35.85 87.80 3.00e+00 1.11e-01 8.57e+02 ... (remaining 12217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 2695 16.64 - 33.29: 170 33.29 - 49.93: 31 49.93 - 66.57: 56 66.57 - 83.21: 18 Dihedral angle restraints: 2970 sinusoidal: 1644 harmonic: 1326 Sorted by residual: dihedral pdb=" CA LYS E 347 " pdb=" C LYS E 347 " pdb=" N ASP E 348 " pdb=" CA ASP E 348 " ideal model delta harmonic sigma weight residual -180.00 -153.94 -26.06 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ASP A 358 " pdb=" C ASP A 358 " pdb=" N ASN A 359 " pdb=" CA ASN A 359 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ASP D 358 " pdb=" C ASP D 358 " pdb=" N ASN D 359 " pdb=" CA ASN D 359 " ideal model delta harmonic sigma weight residual 180.00 155.24 24.76 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 2967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 267 0.066 - 0.132: 165 0.132 - 0.198: 38 0.198 - 0.263: 17 0.263 - 0.329: 11 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA LEU B 325 " pdb=" N LEU B 325 " pdb=" C LEU B 325 " pdb=" CB LEU B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA GLN A 351 " pdb=" N GLN A 351 " pdb=" C GLN A 351 " pdb=" CB GLN A 351 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA LEU A 325 " pdb=" N LEU A 325 " pdb=" C LEU A 325 " pdb=" CB LEU A 325 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 495 not shown) Planarity restraints: 978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 338 " -0.240 2.00e-02 2.50e+03 2.69e-01 7.23e+02 pdb=" N VAL A 339 " 0.436 2.00e-02 2.50e+03 pdb=" CA VAL A 339 " -0.204 2.00e-02 2.50e+03 pdb=" H BVAL A 339 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 338 " -0.237 2.00e-02 2.50e+03 2.68e-01 7.16e+02 pdb=" N VAL C 339 " 0.434 2.00e-02 2.50e+03 pdb=" CA VAL C 339 " -0.203 2.00e-02 2.50e+03 pdb=" H BVAL C 339 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 338 " -0.222 2.00e-02 2.50e+03 2.65e-01 7.04e+02 pdb=" N VAL D 339 " 0.437 2.00e-02 2.50e+03 pdb=" CA VAL D 339 " -0.201 2.00e-02 2.50e+03 pdb=" H BVAL D 339 " -0.014 2.00e-02 2.50e+03 ... (remaining 975 not shown) Histogram of nonbonded interaction distances: 0.89 - 1.63: 17 1.63 - 2.38: 1491 2.38 - 3.12: 20164 3.12 - 3.86: 24635 3.86 - 4.60: 38145 Warning: very small nonbonded interaction distances. Nonbonded interactions: 84452 Sorted by model distance: nonbonded pdb=" H BSER B 341 " pdb=" C LYS E 340 " model vdw 0.892 2.750 nonbonded pdb=" C LYS B 340 " pdb=" H BSER F 341 " model vdw 1.115 2.750 nonbonded pdb=" H BSER B 341 " pdb=" CA LYS E 340 " model vdw 1.168 2.750 nonbonded pdb=" HB2 LYS A 340 " pdb=" H BSER A 341 " model vdw 1.431 2.270 nonbonded pdb=" H BLYS B 343 " pdb=" HB2 GLU E 342 " model vdw 1.443 2.270 ... (remaining 84447 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'B' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'C' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'D' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'E' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) selection = (chain 'F' and (resid 308 through 338 or resid 340 or resid 342 or resid 344 thr \ ough 378)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.170 Extract box with map and model: 11.470 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 28.510 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.033 3300 Z= 0.734 Angle : 1.825 7.507 4416 Z= 1.206 Chirality : 0.096 0.329 498 Planarity : 0.010 0.067 558 Dihedral : 11.757 83.213 1260 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.33), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 374 PHE 0.037 0.011 PHE B 346 TYR 0.123 0.037 TYR F 310 ARG 0.004 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 2.3052 time to fit residues: 251.4218 Evaluate side-chains 72 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN C 336 GLN E 327 ASN E 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3300 Z= 0.221 Angle : 0.700 9.171 4416 Z= 0.379 Chirality : 0.048 0.123 498 Planarity : 0.003 0.027 558 Dihedral : 6.530 19.516 432 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.96 % Allowed : 13.71 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.008 0.001 PHE B 346 TYR 0.014 0.003 TYR B 310 ARG 0.003 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.574 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 78 average time/residue: 2.1814 time to fit residues: 175.4693 Evaluate side-chains 63 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.6872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3300 Z= 0.184 Angle : 0.607 9.273 4416 Z= 0.338 Chirality : 0.049 0.125 498 Planarity : 0.003 0.024 558 Dihedral : 5.497 16.182 432 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.42 % Allowed : 13.98 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 362 PHE 0.009 0.001 PHE B 346 TYR 0.012 0.003 TYR F 310 ARG 0.002 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.584 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 68 average time/residue: 2.4191 time to fit residues: 169.2962 Evaluate side-chains 59 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.505 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.6100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.0980 chunk 23 optimal weight: 0.0030 chunk 0 optimal weight: 6.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3300 Z= 0.122 Angle : 0.543 9.602 4416 Z= 0.310 Chirality : 0.049 0.128 498 Planarity : 0.002 0.026 558 Dihedral : 4.946 15.326 432 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.88 % Allowed : 14.25 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.37), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 362 PHE 0.005 0.001 PHE B 346 TYR 0.008 0.002 TYR A 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.542 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 74 average time/residue: 2.2422 time to fit residues: 170.9439 Evaluate side-chains 63 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.542 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1483 time to fit residues: 0.8579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 6.9990 chunk 16 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3300 Z= 0.142 Angle : 0.544 9.790 4416 Z= 0.310 Chirality : 0.049 0.127 498 Planarity : 0.003 0.028 558 Dihedral : 4.713 15.442 432 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.61 % Allowed : 16.13 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.38), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 362 PHE 0.007 0.001 PHE E 346 TYR 0.009 0.002 TYR F 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.563 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 67 average time/residue: 2.2313 time to fit residues: 154.2272 Evaluate side-chains 67 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.1489 time to fit residues: 1.0751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.0670 chunk 29 optimal weight: 0.8980 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 368 ASN B 327 ASN B 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.5578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3300 Z= 0.165 Angle : 0.542 9.799 4416 Z= 0.310 Chirality : 0.049 0.123 498 Planarity : 0.003 0.027 558 Dihedral : 4.658 16.086 432 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.88 % Allowed : 15.32 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.38), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 362 PHE 0.007 0.001 PHE B 346 TYR 0.011 0.002 TYR F 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.567 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 62 average time/residue: 2.4616 time to fit residues: 157.2021 Evaluate side-chains 61 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.565 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.1477 time to fit residues: 1.0852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 0.0970 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3300 Z= 0.157 Angle : 0.539 9.989 4416 Z= 0.308 Chirality : 0.048 0.124 498 Planarity : 0.003 0.026 558 Dihedral : 4.549 15.504 432 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.08 % Allowed : 16.13 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.39), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 362 PHE 0.006 0.001 PHE E 346 TYR 0.009 0.002 TYR F 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.567 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 65 average time/residue: 2.4633 time to fit residues: 164.7950 Evaluate side-chains 62 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.582 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.1546 time to fit residues: 1.1241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.0050 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3300 Z= 0.146 Angle : 0.527 9.984 4416 Z= 0.303 Chirality : 0.048 0.124 498 Planarity : 0.002 0.025 558 Dihedral : 4.423 14.561 432 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.34 % Allowed : 16.13 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.39), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.005 0.001 PHE B 346 TYR 0.009 0.002 TYR F 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.610 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 62 average time/residue: 2.4056 time to fit residues: 153.5830 Evaluate side-chains 60 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.613 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.1594 time to fit residues: 0.9487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.0670 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 0.0980 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.0324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 359 ASN B 351 GLN E 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3300 Z= 0.129 Angle : 0.522 10.082 4416 Z= 0.301 Chirality : 0.049 0.123 498 Planarity : 0.002 0.025 558 Dihedral : 4.232 13.417 432 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.34 % Allowed : 15.59 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.39), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 362 PHE 0.003 0.000 PHE E 346 TYR 0.008 0.002 TYR D 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.609 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 61 average time/residue: 2.3179 time to fit residues: 145.8010 Evaluate side-chains 60 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.563 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.1483 time to fit residues: 0.8733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3300 Z= 0.114 Angle : 0.515 10.036 4416 Z= 0.296 Chirality : 0.049 0.124 498 Planarity : 0.002 0.025 558 Dihedral : 4.085 13.177 432 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.54 % Allowed : 16.40 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.39), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 362 PHE 0.003 0.000 PHE E 346 TYR 0.007 0.002 TYR A 310 ARG 0.001 0.000 ARG F 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.457 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 2.2535 time to fit residues: 141.7938 Evaluate side-chains 59 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.534 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.6526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 359 ASN E 351 GLN F 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.129795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.123425 restraints weight = 27107.614| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.04 r_work: 0.3815 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3300 Z= 0.211 Angle : 0.551 9.892 4416 Z= 0.312 Chirality : 0.049 0.121 498 Planarity : 0.003 0.026 558 Dihedral : 4.472 13.917 432 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.81 % Allowed : 15.59 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.39), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.007 0.001 PHE E 346 TYR 0.013 0.003 TYR F 310 ARG 0.001 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4312.01 seconds wall clock time: 80 minutes 2.03 seconds (4802.03 seconds total)