Starting phenix.real_space_refine on Wed Feb 14 07:42:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zvt_14986/02_2024/7zvt_14986_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zvt_14986/02_2024/7zvt_14986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zvt_14986/02_2024/7zvt_14986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zvt_14986/02_2024/7zvt_14986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zvt_14986/02_2024/7zvt_14986_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zvt_14986/02_2024/7zvt_14986_updated.pdb" } resolution = 2.74 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 36 atoms to isotropic. 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 P 36 5.49 5 S 40 5.16 5 C 5549 2.51 5 N 1489 2.21 5 O 1728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 36": "OD1" <-> "OD2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 521": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8842 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 280 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "D" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3957 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 464} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 4272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4272 Unusual residues: {'IHP': 1} Classifications: {'peptide': 530, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 503, None: 1} Not linked: pdbres="LYS B 545 " pdbres="IHP B 801 " Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.38, per 1000 atoms: 0.61 Number of scatterers: 8842 At special positions: 0 Unit cell: (94.25, 86.45, 132.6, 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 40 16.00 P 36 15.00 O 1728 8.00 N 1489 7.00 C 5549 6.00 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: 3.49 Conformation dependent library (CDL) restraints added in 1.6 seconds 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 5 sheets defined 33.4% alpha, 15.4% beta 10 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 46 through 49 removed outlier: 3.782A pdb=" N PHE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 through 49' Processing helix chain 'A' and resid 59 through 76 Processing helix chain 'A' and resid 113 through 122 removed outlier: 4.056A pdb=" N PHE A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 135 Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 213 through 216 No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 239 through 250 removed outlier: 3.810A pdb=" N LYS A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 331 through 338 removed outlier: 4.018A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 378 through 392 Processing helix chain 'A' and resid 456 through 468 Processing helix chain 'A' and resid 481 through 494 Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 521 through 529 Processing helix chain 'B' and resid 18 through 21 Processing helix chain 'B' and resid 30 through 47 Processing helix chain 'B' and resid 88 through 95 Processing helix chain 'B' and resid 107 through 121 Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 199 through 215 Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.599A pdb=" N LEU B 221 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.820A pdb=" N ARG B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 348 through 350 No H-bonds generated for 'chain 'B' and resid 348 through 350' Processing helix chain 'B' and resid 353 through 355 No H-bonds generated for 'chain 'B' and resid 353 through 355' Processing helix chain 'B' and resid 371 through 386 Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'B' and resid 448 through 460 Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 479 through 481 No H-bonds generated for 'chain 'B' and resid 479 through 481' Processing helix chain 'B' and resid 485 through 499 Processing helix chain 'B' and resid 510 through 515 Processing helix chain 'B' and resid 520 through 536 removed outlier: 3.675A pdb=" N GLN B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) Proline residue: B 529 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 199 through 204 removed outlier: 3.827A pdb=" N THR A 170 " --> pdb=" O MET A 203 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER A 37 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N MET A 167 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 39 " --> pdb=" O MET A 167 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N PHE A 169 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 41 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU A 82 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N PHE A 40 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALA A 84 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL A 42 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A 86 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE A 87 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL A 104 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 257 through 262 removed outlier: 3.622A pdb=" N SER A 257 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG A 399 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU A 347 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR A 401 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU A 345 " --> pdb=" O THR A 401 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 77 through 81 removed outlier: 6.491A pdb=" N LEU B 56 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS B 129 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL B 11 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N HIS B 131 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N CYS B 13 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU B 133 " --> pdb=" O CYS B 13 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ASP B 15 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE B 135 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 247 through 252 removed outlier: 6.641A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N GLN B 360 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLN B 423 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 9.936A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL B 405 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG B 394 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL B 342 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ALA B 396 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N PHE B 340 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 313 through 316 283 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2733 1.34 - 1.46: 1590 1.46 - 1.58: 4624 1.58 - 1.70: 64 1.70 - 1.82: 67 Bond restraints: 9078 Sorted by residual: bond pdb=" O14 IHP B 801 " pdb=" P4 IHP B 801 " ideal model delta sigma weight residual 1.671 1.604 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O12 IHP B 801 " pdb=" P2 IHP B 801 " ideal model delta sigma weight residual 1.675 1.610 0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" O16 IHP B 801 " pdb=" P6 IHP B 801 " ideal model delta sigma weight residual 1.672 1.614 0.058 2.00e-02 2.50e+03 8.33e+00 bond pdb=" O15 IHP B 801 " pdb=" P5 IHP B 801 " ideal model delta sigma weight residual 1.675 1.618 0.057 2.00e-02 2.50e+03 8.22e+00 bond pdb=" C5 IHP B 801 " pdb=" O15 IHP B 801 " ideal model delta sigma weight residual 1.389 1.440 -0.051 2.00e-02 2.50e+03 6.60e+00 ... (remaining 9073 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.01: 385 106.01 - 113.00: 4945 113.00 - 119.99: 3066 119.99 - 126.98: 3832 126.98 - 133.98: 150 Bond angle restraints: 12378 Sorted by residual: angle pdb=" CB MET A 161 " pdb=" CG MET A 161 " pdb=" SD MET A 161 " ideal model delta sigma weight residual 112.70 124.50 -11.80 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CB GLN B 330 " pdb=" CG GLN B 330 " pdb=" CD GLN B 330 " ideal model delta sigma weight residual 112.60 118.59 -5.99 1.70e+00 3.46e-01 1.24e+01 angle pdb=" CB LYS B 442 " pdb=" CG LYS B 442 " pdb=" CD LYS B 442 " ideal model delta sigma weight residual 111.30 118.57 -7.27 2.30e+00 1.89e-01 9.98e+00 angle pdb=" CA GLN B 330 " pdb=" CB GLN B 330 " pdb=" CG GLN B 330 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.86e+00 angle pdb=" CA GLU B 329 " pdb=" CB GLU B 329 " pdb=" CG GLU B 329 " ideal model delta sigma weight residual 114.10 120.30 -6.20 2.00e+00 2.50e-01 9.60e+00 ... (remaining 12373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.85: 5171 32.85 - 65.70: 345 65.70 - 98.55: 12 98.55 - 131.40: 0 131.40 - 164.25: 1 Dihedral angle restraints: 5529 sinusoidal: 2533 harmonic: 2996 Sorted by residual: dihedral pdb=" C4' DT C 8 " pdb=" C3' DT C 8 " pdb=" O3' DT C 8 " pdb=" P DA C 9 " ideal model delta sinusoidal sigma weight residual 220.00 55.75 164.25 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" CB GLU A 524 " pdb=" CG GLU A 524 " pdb=" CD GLU A 524 " pdb=" OE1 GLU A 524 " ideal model delta sinusoidal sigma weight residual 0.00 -89.03 89.03 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU B 49 " pdb=" CG GLU B 49 " pdb=" CD GLU B 49 " pdb=" OE1 GLU B 49 " ideal model delta sinusoidal sigma weight residual 0.00 86.91 -86.91 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 5526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1143 0.050 - 0.100: 193 0.100 - 0.150: 48 0.150 - 0.201: 3 0.201 - 0.251: 1 Chirality restraints: 1388 Sorted by residual: chirality pdb=" C1 IHP B 801 " pdb=" C2 IHP B 801 " pdb=" C6 IHP B 801 " pdb=" O11 IHP B 801 " both_signs ideal model delta sigma weight residual False 2.32 2.57 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C3 IHP B 801 " pdb=" C2 IHP B 801 " pdb=" C4 IHP B 801 " pdb=" O13 IHP B 801 " both_signs ideal model delta sigma weight residual False -2.34 -2.54 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CG LEU A 147 " pdb=" CB LEU A 147 " pdb=" CD1 LEU A 147 " pdb=" CD2 LEU A 147 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.35e-01 ... (remaining 1385 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 329 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" CD GLU B 329 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU B 329 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 329 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 189 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.75e+00 pdb=" N PRO B 190 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 190 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 190 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 141 " 0.095 9.50e-02 1.11e+02 4.32e-02 1.63e+00 pdb=" NE ARG B 141 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 141 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 141 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 141 " -0.001 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 582 2.73 - 3.28: 8550 3.28 - 3.82: 14896 3.82 - 4.36: 18077 4.36 - 4.90: 30313 Nonbonded interactions: 72418 Sorted by model distance: nonbonded pdb=" N GLU A 450 " pdb=" OE1 GLU A 450 " model vdw 2.192 2.520 nonbonded pdb=" N GLN A 126 " pdb=" OE1 GLN A 126 " model vdw 2.219 2.520 nonbonded pdb=" N GLN A 158 " pdb=" OE1 GLN A 158 " model vdw 2.227 2.520 nonbonded pdb=" N GLU A 240 " pdb=" OE1 GLU A 240 " model vdw 2.270 2.520 nonbonded pdb=" O ILE B 118 " pdb=" OG1 THR B 122 " model vdw 2.279 2.440 ... (remaining 72413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 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: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 11.920 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.230 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 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 : 0.004 0.067 9078 Z= 0.277 Angle : 0.573 11.803 12378 Z= 0.276 Chirality : 0.041 0.251 1388 Planarity : 0.003 0.043 1478 Dihedral : 19.189 164.252 3577 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.94 % Allowed : 24.81 % Favored : 72.25 % 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: 1.55 (0.27), residues: 1012 helix: 2.04 (0.29), residues: 343 sheet: 0.69 (0.42), residues: 161 loop : 0.55 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 247 HIS 0.004 0.001 HIS A 163 PHE 0.010 0.001 PHE B 409 TYR 0.008 0.001 TYR A 88 ARG 0.012 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 1.182 Fit side-chains REVERT: A 448 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7537 (p90) outliers start: 27 outliers final: 20 residues processed: 110 average time/residue: 1.1577 time to fit residues: 136.7572 Evaluate side-chains 106 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 472 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.0430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9078 Z= 0.229 Angle : 0.496 9.818 12378 Z= 0.251 Chirality : 0.040 0.143 1388 Planarity : 0.003 0.054 1478 Dihedral : 17.331 165.709 1497 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.16 % Allowed : 23.39 % Favored : 73.45 % 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 (0.27), residues: 1012 helix: 2.09 (0.29), residues: 343 sheet: 0.55 (0.41), residues: 155 loop : 0.52 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 247 HIS 0.003 0.001 HIS B 511 PHE 0.015 0.001 PHE B 409 TYR 0.006 0.001 TYR A 88 ARG 0.012 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 89 time to evaluate : 1.031 Fit side-chains REVERT: A 135 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7613 (tpt) REVERT: A 391 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8205 (tp30) REVERT: A 448 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7574 (p90) REVERT: B 53 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: B 243 HIS cc_start: 0.7732 (OUTLIER) cc_final: 0.7097 (p90) REVERT: B 434 MET cc_start: 0.8846 (tpt) cc_final: 0.8609 (tpt) outliers start: 29 outliers final: 8 residues processed: 108 average time/residue: 1.2829 time to fit residues: 148.0098 Evaluate side-chains 98 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 311 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 94 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 HIS A 232 HIS B 432 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.0585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9078 Z= 0.222 Angle : 0.490 8.878 12378 Z= 0.248 Chirality : 0.039 0.142 1388 Planarity : 0.003 0.033 1478 Dihedral : 17.151 165.332 1475 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.70 % Allowed : 23.50 % Favored : 72.80 % 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: 1.49 (0.27), residues: 1012 helix: 2.09 (0.29), residues: 343 sheet: 0.54 (0.41), residues: 155 loop : 0.48 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 247 HIS 0.002 0.001 HIS B 511 PHE 0.014 0.001 PHE B 409 TYR 0.006 0.001 TYR A 400 ARG 0.006 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 83 time to evaluate : 1.056 Fit side-chains REVERT: A 92 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8658 (mtmp) REVERT: A 163 HIS cc_start: 0.7508 (m90) cc_final: 0.6605 (m170) REVERT: A 391 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8204 (tp30) REVERT: A 448 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7691 (p90) REVERT: B 53 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: B 243 HIS cc_start: 0.7719 (OUTLIER) cc_final: 0.7042 (p90) outliers start: 34 outliers final: 7 residues processed: 106 average time/residue: 1.2545 time to fit residues: 142.2107 Evaluate side-chains 98 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 481 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 9078 Z= 0.298 Angle : 0.525 11.819 12378 Z= 0.263 Chirality : 0.041 0.145 1388 Planarity : 0.003 0.032 1478 Dihedral : 17.197 165.033 1468 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.13 % Allowed : 23.29 % Favored : 72.58 % 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 (0.27), residues: 1012 helix: 2.06 (0.29), residues: 344 sheet: 0.52 (0.41), residues: 155 loop : 0.46 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 247 HIS 0.005 0.001 HIS A 163 PHE 0.014 0.001 PHE B 409 TYR 0.006 0.001 TYR B 421 ARG 0.005 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 86 time to evaluate : 1.073 Fit side-chains REVERT: A 92 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8655 (mtmp) REVERT: A 391 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8209 (tp30) REVERT: A 448 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7911 (p90) REVERT: B 53 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: B 243 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.7065 (p90) REVERT: B 434 MET cc_start: 0.8910 (tpt) cc_final: 0.8655 (tpt) outliers start: 38 outliers final: 9 residues processed: 108 average time/residue: 1.2533 time to fit residues: 144.9737 Evaluate side-chains 99 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 311 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.2980 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 25 optimal weight: 0.0670 chunk 33 optimal weight: 0.8980 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9078 Z= 0.196 Angle : 0.493 10.539 12378 Z= 0.249 Chirality : 0.039 0.149 1388 Planarity : 0.003 0.063 1478 Dihedral : 17.101 165.140 1468 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.37 % Allowed : 24.37 % Favored : 72.25 % 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: 1.46 (0.27), residues: 1012 helix: 2.07 (0.28), residues: 345 sheet: 0.53 (0.41), residues: 155 loop : 0.46 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 247 HIS 0.002 0.000 HIS B 511 PHE 0.013 0.001 PHE B 409 TYR 0.008 0.001 TYR A 103 ARG 0.014 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 88 time to evaluate : 0.869 Fit side-chains REVERT: A 92 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8619 (mtmp) REVERT: A 391 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8217 (tp30) REVERT: A 448 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7937 (p90) REVERT: B 53 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: B 243 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.7022 (p90) outliers start: 31 outliers final: 13 residues processed: 106 average time/residue: 1.3016 time to fit residues: 146.9652 Evaluate side-chains 104 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 481 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9078 Z= 0.198 Angle : 0.496 10.467 12378 Z= 0.250 Chirality : 0.039 0.142 1388 Planarity : 0.003 0.034 1478 Dihedral : 17.000 165.211 1465 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.48 % Allowed : 24.92 % Favored : 71.60 % 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: 1.46 (0.27), residues: 1012 helix: 2.07 (0.29), residues: 346 sheet: 0.50 (0.41), residues: 155 loop : 0.46 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 247 HIS 0.004 0.001 HIS A 163 PHE 0.012 0.001 PHE B 409 TYR 0.005 0.001 TYR A 400 ARG 0.008 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 88 time to evaluate : 1.138 Fit side-chains REVERT: A 92 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8587 (mtmp) REVERT: A 163 HIS cc_start: 0.7555 (OUTLIER) cc_final: 0.6973 (m170) REVERT: A 391 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8221 (tp30) REVERT: A 448 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.8028 (p90) REVERT: B 44 ARG cc_start: 0.8716 (ttt90) cc_final: 0.8431 (tpp80) REVERT: B 53 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: B 141 ARG cc_start: 0.7748 (ttp80) cc_final: 0.7315 (ttp80) REVERT: B 243 HIS cc_start: 0.7681 (OUTLIER) cc_final: 0.7039 (p90) outliers start: 32 outliers final: 12 residues processed: 106 average time/residue: 1.2553 time to fit residues: 142.4592 Evaluate side-chains 103 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 481 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 0.1980 chunk 100 optimal weight: 0.0970 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9078 Z= 0.154 Angle : 0.489 9.967 12378 Z= 0.246 Chirality : 0.039 0.144 1388 Planarity : 0.003 0.035 1478 Dihedral : 16.925 165.337 1465 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.37 % Allowed : 24.70 % Favored : 71.93 % 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 (0.27), residues: 1012 helix: 2.10 (0.29), residues: 346 sheet: 0.63 (0.43), residues: 146 loop : 0.46 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 247 HIS 0.009 0.001 HIS A 163 PHE 0.017 0.001 PHE B 183 TYR 0.005 0.001 TYR A 400 ARG 0.005 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 89 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8565 (mtmp) REVERT: A 134 MET cc_start: 0.8872 (ppp) cc_final: 0.8611 (ppp) REVERT: A 391 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8212 (tp30) REVERT: A 421 ASP cc_start: 0.8174 (t0) cc_final: 0.7957 (t0) REVERT: A 448 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.8004 (p90) REVERT: B 44 ARG cc_start: 0.8687 (ttt90) cc_final: 0.8407 (tpp80) REVERT: B 53 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: B 243 HIS cc_start: 0.7669 (OUTLIER) cc_final: 0.7034 (p90) outliers start: 31 outliers final: 14 residues processed: 105 average time/residue: 1.2261 time to fit residues: 138.0092 Evaluate side-chains 108 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 311 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 163 HIS ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9078 Z= 0.232 Angle : 0.515 10.155 12378 Z= 0.258 Chirality : 0.040 0.141 1388 Planarity : 0.004 0.068 1478 Dihedral : 16.966 165.508 1465 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.37 % Allowed : 24.48 % Favored : 72.14 % 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 (0.27), residues: 1012 helix: 2.13 (0.29), residues: 345 sheet: 0.50 (0.41), residues: 155 loop : 0.49 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 247 HIS 0.002 0.000 HIS B 511 PHE 0.012 0.001 PHE B 59 TYR 0.008 0.001 TYR A 103 ARG 0.021 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 92 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8565 (mtmp) REVERT: A 134 MET cc_start: 0.8923 (ppp) cc_final: 0.8606 (ppp) REVERT: A 163 HIS cc_start: 0.7253 (OUTLIER) cc_final: 0.6703 (m170) REVERT: A 391 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8213 (tp30) REVERT: A 421 ASP cc_start: 0.8191 (t0) cc_final: 0.7968 (t0) REVERT: A 448 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.8079 (p90) REVERT: B 44 ARG cc_start: 0.8729 (ttt90) cc_final: 0.8446 (tpp80) REVERT: B 53 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: B 243 HIS cc_start: 0.7652 (OUTLIER) cc_final: 0.7022 (p90) outliers start: 31 outliers final: 15 residues processed: 108 average time/residue: 1.2354 time to fit residues: 142.8664 Evaluate side-chains 111 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 HIS Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 357 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 40 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9078 Z= 0.227 Angle : 0.535 11.170 12378 Z= 0.266 Chirality : 0.040 0.188 1388 Planarity : 0.003 0.034 1478 Dihedral : 16.950 165.189 1465 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.83 % Allowed : 25.24 % Favored : 71.93 % 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: 1.50 (0.27), residues: 1012 helix: 2.08 (0.28), residues: 345 sheet: 0.54 (0.41), residues: 155 loop : 0.51 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 247 HIS 0.006 0.001 HIS A 163 PHE 0.012 0.001 PHE B 59 TYR 0.005 0.001 TYR A 400 ARG 0.007 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 90 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8567 (mtmp) REVERT: A 391 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8213 (tp30) REVERT: A 421 ASP cc_start: 0.8190 (t0) cc_final: 0.7966 (t0) REVERT: A 448 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8149 (p90) REVERT: B 44 ARG cc_start: 0.8722 (ttt90) cc_final: 0.8449 (tpp80) REVERT: B 53 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: B 243 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.7186 (p90) outliers start: 26 outliers final: 14 residues processed: 104 average time/residue: 1.2271 time to fit residues: 136.9668 Evaluate side-chains 107 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 339 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.7980 chunk 68 optimal weight: 0.0770 chunk 103 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9078 Z= 0.176 Angle : 0.534 11.348 12378 Z= 0.264 Chirality : 0.039 0.154 1388 Planarity : 0.003 0.067 1478 Dihedral : 16.848 165.409 1464 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.18 % Allowed : 25.79 % Favored : 72.03 % 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: 1.62 (0.27), residues: 1012 helix: 2.21 (0.29), residues: 337 sheet: 0.67 (0.43), residues: 146 loop : 0.56 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 247 HIS 0.002 0.000 HIS A 163 PHE 0.018 0.001 PHE B 183 TYR 0.006 0.001 TYR A 400 ARG 0.016 0.000 ARG A 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8595 (mtmp) REVERT: A 391 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8216 (tp30) REVERT: A 421 ASP cc_start: 0.8179 (t0) cc_final: 0.7978 (t0) REVERT: A 448 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8271 (p90) REVERT: B 44 ARG cc_start: 0.8697 (ttt90) cc_final: 0.8349 (tpp80) REVERT: B 53 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: B 243 HIS cc_start: 0.7585 (OUTLIER) cc_final: 0.7269 (p90) outliers start: 20 outliers final: 9 residues processed: 97 average time/residue: 1.2668 time to fit residues: 131.7209 Evaluate side-chains 99 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 339 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.0570 chunk 12 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.110332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.071829 restraints weight = 13768.727| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.74 r_work: 0.2757 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9078 Z= 0.175 Angle : 0.518 11.191 12378 Z= 0.257 Chirality : 0.039 0.148 1388 Planarity : 0.003 0.035 1478 Dihedral : 16.804 165.565 1464 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.18 % Allowed : 25.90 % Favored : 71.93 % 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: 1.54 (0.27), residues: 1012 helix: 2.10 (0.29), residues: 344 sheet: 0.71 (0.43), residues: 146 loop : 0.49 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 247 HIS 0.005 0.001 HIS A 163 PHE 0.011 0.001 PHE B 59 TYR 0.007 0.001 TYR A 103 ARG 0.004 0.000 ARG B 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3252.50 seconds wall clock time: 59 minutes 28.06 seconds (3568.06 seconds total)