Starting phenix.real_space_refine on Sat May 10 22:46:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fht_29103/05_2025/8fht_29103.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fht_29103/05_2025/8fht_29103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fht_29103/05_2025/8fht_29103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fht_29103/05_2025/8fht_29103.map" model { file = "/net/cci-nas-00/data/ceres_data/8fht_29103/05_2025/8fht_29103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fht_29103/05_2025/8fht_29103.cif" } resolution = 3.02 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= -0.001 sd= 0.045 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: 6 Type Number sf(0) Gaussians S 42 5.16 5 Cl 2 4.86 5 Na 2 4.78 5 C 4618 2.51 5 N 1106 2.21 5 O 1236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7006 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3501 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 18, 'TRANS': 449} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3501 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 18, 'TRANS': 449} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.55, per 1000 atoms: 0.65 Number of scatterers: 7006 At special positions: 0 Unit cell: (105.78, 81.7, 94.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 42 16.00 Na 2 11.00 O 1236 8.00 N 1106 7.00 C 4618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 421 " distance=2.06 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 436 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 421 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 436 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.65 Conformation dependent library (CDL) restraints added in 923.8 milliseconds 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1700 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 80.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 152 through 158 removed outlier: 4.145A pdb=" N TYR A 156 " --> pdb=" O GLY A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 195 removed outlier: 6.748A pdb=" N ILE A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N VAL A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 212 removed outlier: 4.175A pdb=" N PHE A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 250 removed outlier: 4.418A pdb=" N SER A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 278 Processing helix chain 'A' and resid 279 through 306 removed outlier: 4.734A pdb=" N VAL A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 315 Processing helix chain 'A' and resid 321 through 329 Processing helix chain 'A' and resid 339 through 348 Processing helix chain 'A' and resid 349 through 352 removed outlier: 3.573A pdb=" N THR A 352 " --> pdb=" O PRO A 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 349 through 352' Processing helix chain 'A' and resid 355 through 360 removed outlier: 4.345A pdb=" N ILE A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 removed outlier: 3.547A pdb=" N LEU A 364 " --> pdb=" O SER A 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 364' Processing helix chain 'A' and resid 366 through 395 Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 427 through 434 Processing helix chain 'A' and resid 445 through 451 removed outlier: 3.509A pdb=" N MET A 449 " --> pdb=" O GLN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 486 removed outlier: 3.872A pdb=" N ILE A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 486 " --> pdb=" O CYS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 496 removed outlier: 3.504A pdb=" N PHE A 494 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 521 Processing helix chain 'A' and resid 524 through 554 Proline residue: A 530 - end of helix Processing helix chain 'A' and resid 566 through 585 Processing helix chain 'A' and resid 585 through 606 Processing helix chain 'B' and resid 142 through 151 Processing helix chain 'B' and resid 152 through 158 removed outlier: 4.132A pdb=" N TYR B 156 " --> pdb=" O GLY B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 195 removed outlier: 6.942A pdb=" N ILE B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N VAL B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 212 removed outlier: 4.164A pdb=" N PHE B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 250 removed outlier: 4.430A pdb=" N SER B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 278 Processing helix chain 'B' and resid 279 through 306 removed outlier: 4.740A pdb=" N VAL B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU B 288 " --> pdb=" O LYS B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 315 Processing helix chain 'B' and resid 321 through 329 Processing helix chain 'B' and resid 339 through 348 Processing helix chain 'B' and resid 349 through 352 removed outlier: 3.559A pdb=" N THR B 352 " --> pdb=" O PRO B 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 349 through 352' Processing helix chain 'B' and resid 355 through 360 removed outlier: 4.315A pdb=" N ILE B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 364 removed outlier: 3.536A pdb=" N LEU B 364 " --> pdb=" O SER B 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 361 through 364' Processing helix chain 'B' and resid 366 through 395 Proline residue: B 372 - end of helix Processing helix chain 'B' and resid 427 through 434 removed outlier: 3.600A pdb=" N THR B 431 " --> pdb=" O PHE B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 451 removed outlier: 3.608A pdb=" N MET B 449 " --> pdb=" O GLN B 445 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 451 " --> pdb=" O MET B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 486 removed outlier: 3.858A pdb=" N ILE B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP B 486 " --> pdb=" O CYS B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 496 removed outlier: 3.510A pdb=" N PHE B 494 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 521 Processing helix chain 'B' and resid 524 through 554 Proline residue: B 530 - end of helix Processing helix chain 'B' and resid 566 through 585 Processing helix chain 'B' and resid 585 through 606 535 hydrogen bonds defined for protein. 1584 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: 1.82 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1078 1.31 - 1.44: 2024 1.44 - 1.57: 4014 1.57 - 1.71: 0 1.71 - 1.84: 62 Bond restraints: 7178 Sorted by residual: bond pdb=" C LEU A 601 " pdb=" O LEU A 601 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.18e-02 7.18e+03 2.10e+01 bond pdb=" CA TYR A 602 " pdb=" C TYR A 602 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.27e-02 6.20e+03 1.49e+01 bond pdb=" CA TYR B 602 " pdb=" C TYR B 602 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.32e-02 5.74e+03 1.36e+01 bond pdb=" N LEU A 601 " pdb=" CA LEU A 601 " ideal model delta sigma weight residual 1.459 1.419 0.040 1.23e-02 6.61e+03 1.05e+01 bond pdb=" CA TYR A 602 " pdb=" CB TYR A 602 " ideal model delta sigma weight residual 1.529 1.480 0.049 1.55e-02 4.16e+03 9.81e+00 ... (remaining 7173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 9678 2.46 - 4.92: 110 4.92 - 7.38: 16 7.38 - 9.83: 1 9.83 - 12.29: 1 Bond angle restraints: 9806 Sorted by residual: angle pdb=" N CYS B 416 " pdb=" CA CYS B 416 " pdb=" C CYS B 416 " ideal model delta sigma weight residual 108.90 121.19 -12.29 1.63e+00 3.76e-01 5.69e+01 angle pdb=" N LEU A 419 " pdb=" CA LEU A 419 " pdb=" C LEU A 419 " ideal model delta sigma weight residual 111.36 115.92 -4.56 1.09e+00 8.42e-01 1.75e+01 angle pdb=" N CYS A 416 " pdb=" CA CYS A 416 " pdb=" C CYS A 416 " ideal model delta sigma weight residual 108.52 115.27 -6.75 1.63e+00 3.76e-01 1.72e+01 angle pdb=" N ALA A 420 " pdb=" CA ALA A 420 " pdb=" C ALA A 420 " ideal model delta sigma weight residual 111.37 117.81 -6.44 1.65e+00 3.67e-01 1.52e+01 angle pdb=" CA GLY A 414 " pdb=" C GLY A 414 " pdb=" N ALA A 415 " ideal model delta sigma weight residual 114.67 118.78 -4.11 1.11e+00 8.12e-01 1.37e+01 ... (remaining 9801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 3734 16.26 - 32.51: 278 32.51 - 48.77: 73 48.77 - 65.02: 17 65.02 - 81.28: 6 Dihedral angle restraints: 4108 sinusoidal: 1440 harmonic: 2668 Sorted by residual: dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 436 " pdb=" CB CYS A 436 " ideal model delta sinusoidal sigma weight residual 93.00 172.85 -79.85 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS A 416 " pdb=" SG CYS A 416 " pdb=" SG CYS A 421 " pdb=" CB CYS A 421 " ideal model delta sinusoidal sigma weight residual -86.00 -32.42 -53.58 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" C VAL B 603 " pdb=" N VAL B 603 " pdb=" CA VAL B 603 " pdb=" CB VAL B 603 " ideal model delta harmonic sigma weight residual -122.00 -131.87 9.87 0 2.50e+00 1.60e-01 1.56e+01 ... (remaining 4105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1017 0.063 - 0.126: 131 0.126 - 0.188: 12 0.188 - 0.251: 4 0.251 - 0.314: 4 Chirality restraints: 1168 Sorted by residual: chirality pdb=" CA VAL B 603 " pdb=" N VAL B 603 " pdb=" C VAL B 603 " pdb=" CB VAL B 603 " both_signs ideal model delta sigma weight residual False 2.44 2.13 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA CYS B 416 " pdb=" N CYS B 416 " pdb=" C CYS B 416 " pdb=" CB CYS B 416 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA VAL A 603 " pdb=" N VAL A 603 " pdb=" C VAL A 603 " pdb=" CB VAL A 603 " both_signs ideal model delta sigma weight residual False 2.44 2.16 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 1165 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 602 " -0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C TYR B 602 " 0.065 2.00e-02 2.50e+03 pdb=" O TYR B 602 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL B 603 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 602 " 0.019 2.00e-02 2.50e+03 3.65e-02 1.34e+01 pdb=" C TYR A 602 " -0.063 2.00e-02 2.50e+03 pdb=" O TYR A 602 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL A 603 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 601 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C LEU A 601 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU A 601 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR A 602 " 0.013 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1166 2.76 - 3.29: 7025 3.29 - 3.83: 12038 3.83 - 4.36: 12922 4.36 - 4.90: 23686 Nonbonded interactions: 56837 Sorted by model distance: nonbonded pdb=" O TRP B 151 " pdb="NA NA B1101 " model vdw 2.220 2.470 nonbonded pdb=" O TRP A 151 " pdb="NA NA A1101 " model vdw 2.228 2.470 nonbonded pdb=" O SER B 345 " pdb=" OG SER B 533 " model vdw 2.297 3.040 nonbonded pdb=" OG SER A 468 " pdb="NA NA A1101 " model vdw 2.299 2.470 nonbonded pdb=" O SER A 345 " pdb=" OG SER A 533 " model vdw 2.309 3.040 ... (remaining 56832 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.350 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 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 0.054 7182 Z= 0.218 Angle : 0.636 12.293 9814 Z= 0.366 Chirality : 0.047 0.314 1168 Planarity : 0.004 0.037 1206 Dihedral : 12.982 81.279 2396 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.96 % Allowed : 0.96 % Favored : 98.07 % Cbeta Deviations : 0.35 % 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: 2.06 (0.28), residues: 932 helix: 2.22 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -0.94 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 586 HIS 0.002 0.001 HIS B 234 PHE 0.025 0.002 PHE B 238 TYR 0.018 0.001 TYR A 602 ARG 0.002 0.000 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.11214 ( 535) hydrogen bonds : angle 4.63120 ( 1584) SS BOND : bond 0.01436 ( 4) SS BOND : angle 2.23185 ( 8) covalent geometry : bond 0.00374 ( 7178) covalent geometry : angle 0.63304 ( 9806) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.722 Fit side-chains REVERT: B 417 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7170 (mt-10) outliers start: 7 outliers final: 0 residues processed: 117 average time/residue: 0.1843 time to fit residues: 29.2281 Evaluate side-chains 101 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.0470 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 0.0000 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.200632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.155753 restraints weight = 7348.334| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.29 r_work: 0.3698 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7182 Z= 0.128 Angle : 0.490 4.783 9814 Z= 0.268 Chirality : 0.039 0.165 1168 Planarity : 0.004 0.036 1206 Dihedral : 4.152 50.918 991 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.24 % Allowed : 6.89 % Favored : 91.87 % 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: 2.29 (0.28), residues: 932 helix: 2.44 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.88 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 586 HIS 0.002 0.001 HIS A 549 PHE 0.017 0.002 PHE A 598 TYR 0.011 0.001 TYR A 602 ARG 0.001 0.000 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 535) hydrogen bonds : angle 3.97465 ( 1584) SS BOND : bond 0.00412 ( 4) SS BOND : angle 1.33729 ( 8) covalent geometry : bond 0.00271 ( 7178) covalent geometry : angle 0.48844 ( 9806) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7964 (t) cc_final: 0.7618 (p) REVERT: B 309 SER cc_start: 0.7949 (t) cc_final: 0.7628 (p) REVERT: B 416 CYS cc_start: 0.3659 (OUTLIER) cc_final: 0.2907 (t) outliers start: 9 outliers final: 5 residues processed: 117 average time/residue: 0.1783 time to fit residues: 28.5185 Evaluate side-chains 106 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 35 optimal weight: 0.0020 chunk 10 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.199325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.154092 restraints weight = 7380.079| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.28 r_work: 0.3678 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7182 Z= 0.131 Angle : 0.481 4.658 9814 Z= 0.262 Chirality : 0.039 0.171 1168 Planarity : 0.004 0.036 1206 Dihedral : 3.487 14.979 988 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.38 % Allowed : 9.23 % Favored : 89.39 % 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: 2.26 (0.28), residues: 932 helix: 2.39 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.83 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 586 HIS 0.002 0.001 HIS A 549 PHE 0.026 0.002 PHE A 238 TYR 0.007 0.001 TYR B 605 ARG 0.001 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.04362 ( 535) hydrogen bonds : angle 3.89988 ( 1584) SS BOND : bond 0.00268 ( 4) SS BOND : angle 0.99924 ( 8) covalent geometry : bond 0.00288 ( 7178) covalent geometry : angle 0.48034 ( 9806) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7850 (t) cc_final: 0.7476 (p) REVERT: B 309 SER cc_start: 0.7909 (t) cc_final: 0.7573 (p) outliers start: 10 outliers final: 9 residues processed: 112 average time/residue: 0.1823 time to fit residues: 27.8013 Evaluate side-chains 107 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.192431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.143604 restraints weight = 7264.118| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.33 r_work: 0.3503 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7182 Z= 0.138 Angle : 0.492 4.832 9814 Z= 0.268 Chirality : 0.039 0.177 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.557 15.484 988 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.34 % Allowed : 10.33 % Favored : 87.33 % 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: 2.20 (0.27), residues: 932 helix: 2.36 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.87 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 586 HIS 0.003 0.001 HIS A 549 PHE 0.018 0.002 PHE A 238 TYR 0.017 0.001 TYR B 602 ARG 0.001 0.000 ARG B 158 Details of bonding type rmsd hydrogen bonds : bond 0.04382 ( 535) hydrogen bonds : angle 3.91808 ( 1584) SS BOND : bond 0.00198 ( 4) SS BOND : angle 1.72167 ( 8) covalent geometry : bond 0.00318 ( 7178) covalent geometry : angle 0.48967 ( 9806) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7777 (t) cc_final: 0.7291 (p) REVERT: B 309 SER cc_start: 0.7893 (t) cc_final: 0.7506 (p) outliers start: 17 outliers final: 13 residues processed: 104 average time/residue: 0.1836 time to fit residues: 25.7389 Evaluate side-chains 107 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN B 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.191972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142852 restraints weight = 7202.589| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.34 r_work: 0.3496 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7182 Z= 0.139 Angle : 0.484 4.689 9814 Z= 0.267 Chirality : 0.039 0.187 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.539 15.642 988 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.48 % Allowed : 11.29 % Favored : 86.23 % 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: 2.22 (0.27), residues: 932 helix: 2.36 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.81 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 586 HIS 0.002 0.000 HIS B 549 PHE 0.018 0.002 PHE A 238 TYR 0.014 0.001 TYR B 602 ARG 0.002 0.000 ARG B 261 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 535) hydrogen bonds : angle 3.91684 ( 1584) SS BOND : bond 0.00197 ( 4) SS BOND : angle 0.90564 ( 8) covalent geometry : bond 0.00319 ( 7178) covalent geometry : angle 0.48371 ( 9806) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7664 (t) cc_final: 0.7206 (p) REVERT: B 309 SER cc_start: 0.7839 (t) cc_final: 0.7445 (p) REVERT: B 431 THR cc_start: 0.7513 (m) cc_final: 0.6957 (p) outliers start: 18 outliers final: 14 residues processed: 108 average time/residue: 0.1989 time to fit residues: 29.3562 Evaluate side-chains 104 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 53 optimal weight: 6.9990 chunk 44 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.192268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.143224 restraints weight = 7229.710| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.35 r_work: 0.3502 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7182 Z= 0.131 Angle : 0.477 4.666 9814 Z= 0.262 Chirality : 0.039 0.186 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.514 15.655 988 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.20 % Allowed : 11.71 % Favored : 86.09 % 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: 2.28 (0.28), residues: 932 helix: 2.41 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.81 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 586 HIS 0.002 0.000 HIS B 549 PHE 0.016 0.001 PHE A 238 TYR 0.016 0.001 TYR B 602 ARG 0.001 0.000 ARG B 158 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 535) hydrogen bonds : angle 3.87550 ( 1584) SS BOND : bond 0.00193 ( 4) SS BOND : angle 0.78630 ( 8) covalent geometry : bond 0.00298 ( 7178) covalent geometry : angle 0.47674 ( 9806) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7640 (t) cc_final: 0.7163 (p) REVERT: A 343 MET cc_start: 0.8054 (mmt) cc_final: 0.7483 (mmt) REVERT: B 309 SER cc_start: 0.7792 (t) cc_final: 0.7373 (p) REVERT: B 431 THR cc_start: 0.7545 (m) cc_final: 0.6991 (p) outliers start: 16 outliers final: 12 residues processed: 100 average time/residue: 0.1788 time to fit residues: 24.2368 Evaluate side-chains 100 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 91 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.189270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.140234 restraints weight = 7237.282| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.34 r_work: 0.3472 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7182 Z= 0.166 Angle : 0.521 4.940 9814 Z= 0.287 Chirality : 0.041 0.201 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.628 16.069 988 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.62 % Allowed : 11.16 % Favored : 86.23 % 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: 2.10 (0.27), residues: 932 helix: 2.25 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.80 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 586 HIS 0.004 0.001 HIS A 549 PHE 0.014 0.002 PHE A 238 TYR 0.015 0.001 TYR B 602 ARG 0.003 0.000 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.04696 ( 535) hydrogen bonds : angle 4.03464 ( 1584) SS BOND : bond 0.00253 ( 4) SS BOND : angle 0.67763 ( 8) covalent geometry : bond 0.00401 ( 7178) covalent geometry : angle 0.52132 ( 9806) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7602 (t) cc_final: 0.7088 (p) REVERT: A 343 MET cc_start: 0.8101 (mmt) cc_final: 0.7600 (mmt) REVERT: B 309 SER cc_start: 0.7705 (t) cc_final: 0.7302 (p) REVERT: B 431 THR cc_start: 0.7624 (m) cc_final: 0.7054 (p) outliers start: 19 outliers final: 12 residues processed: 105 average time/residue: 0.1962 time to fit residues: 27.6443 Evaluate side-chains 103 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.190065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.140946 restraints weight = 7335.501| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.37 r_work: 0.3479 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7182 Z= 0.145 Angle : 0.498 4.717 9814 Z= 0.275 Chirality : 0.039 0.196 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.578 15.819 988 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.07 % Allowed : 12.26 % Favored : 85.67 % 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: 2.21 (0.27), residues: 932 helix: 2.34 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.79 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 586 HIS 0.003 0.001 HIS A 549 PHE 0.014 0.001 PHE A 238 TYR 0.014 0.001 TYR B 602 ARG 0.001 0.000 ARG A 158 Details of bonding type rmsd hydrogen bonds : bond 0.04444 ( 535) hydrogen bonds : angle 3.97188 ( 1584) SS BOND : bond 0.00223 ( 4) SS BOND : angle 0.61344 ( 8) covalent geometry : bond 0.00340 ( 7178) covalent geometry : angle 0.49773 ( 9806) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7508 (t) cc_final: 0.7001 (p) REVERT: A 343 MET cc_start: 0.8078 (mmt) cc_final: 0.7610 (mmt) REVERT: B 165 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7501 (mt0) REVERT: B 309 SER cc_start: 0.7641 (t) cc_final: 0.7193 (p) outliers start: 15 outliers final: 10 residues processed: 100 average time/residue: 0.1900 time to fit residues: 25.5817 Evaluate side-chains 98 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 32 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.188333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139572 restraints weight = 7336.035| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.32 r_work: 0.3461 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7182 Z= 0.158 Angle : 0.511 4.912 9814 Z= 0.282 Chirality : 0.040 0.200 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.620 15.882 988 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.20 % Allowed : 12.26 % Favored : 85.54 % 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: 2.15 (0.27), residues: 932 helix: 2.28 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.77 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 586 HIS 0.003 0.001 HIS B 549 PHE 0.014 0.002 PHE A 238 TYR 0.007 0.001 TYR A 602 ARG 0.001 0.000 ARG B 261 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 535) hydrogen bonds : angle 4.00334 ( 1584) SS BOND : bond 0.00244 ( 4) SS BOND : angle 0.56479 ( 8) covalent geometry : bond 0.00374 ( 7178) covalent geometry : angle 0.51104 ( 9806) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7415 (t) cc_final: 0.6853 (p) REVERT: A 343 MET cc_start: 0.8104 (mmt) cc_final: 0.7658 (mmt) REVERT: B 309 SER cc_start: 0.7561 (t) cc_final: 0.7079 (p) REVERT: B 431 THR cc_start: 0.7634 (m) cc_final: 0.7072 (p) outliers start: 16 outliers final: 14 residues processed: 99 average time/residue: 0.1910 time to fit residues: 25.3216 Evaluate side-chains 103 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 0.0970 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.190662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.141805 restraints weight = 7399.199| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.36 r_work: 0.3485 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7182 Z= 0.129 Angle : 0.482 5.136 9814 Z= 0.268 Chirality : 0.039 0.197 1168 Planarity : 0.004 0.038 1206 Dihedral : 3.531 15.240 988 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.79 % Allowed : 12.67 % Favored : 85.54 % 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: 2.30 (0.28), residues: 932 helix: 2.39 (0.19), residues: 672 sheet: None (None), residues: 0 loop : -0.86 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 586 HIS 0.002 0.000 HIS A 549 PHE 0.015 0.001 PHE A 238 TYR 0.005 0.001 TYR A 249 ARG 0.001 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 535) hydrogen bonds : angle 3.90706 ( 1584) SS BOND : bond 0.00198 ( 4) SS BOND : angle 0.52638 ( 8) covalent geometry : bond 0.00289 ( 7178) covalent geometry : angle 0.48185 ( 9806) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 343 MET cc_start: 0.8065 (mmt) cc_final: 0.7619 (mmt) REVERT: B 165 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7482 (mt0) REVERT: B 431 THR cc_start: 0.7695 (m) cc_final: 0.7200 (p) outliers start: 13 outliers final: 12 residues processed: 98 average time/residue: 0.1874 time to fit residues: 24.8042 Evaluate side-chains 98 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 0.0020 chunk 13 optimal weight: 0.6980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.192576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.143830 restraints weight = 7350.163| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.36 r_work: 0.3505 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7182 Z= 0.120 Angle : 0.466 4.933 9814 Z= 0.260 Chirality : 0.038 0.186 1168 Planarity : 0.004 0.038 1206 Dihedral : 3.415 14.455 988 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.65 % Allowed : 13.09 % Favored : 85.26 % 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: 2.53 (0.28), residues: 932 helix: 2.58 (0.19), residues: 670 sheet: None (None), residues: 0 loop : -0.81 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 586 HIS 0.001 0.000 HIS B 549 PHE 0.015 0.001 PHE A 238 TYR 0.004 0.001 TYR A 249 ARG 0.001 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03916 ( 535) hydrogen bonds : angle 3.81945 ( 1584) SS BOND : bond 0.00190 ( 4) SS BOND : angle 0.51339 ( 8) covalent geometry : bond 0.00258 ( 7178) covalent geometry : angle 0.46559 ( 9806) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3307.50 seconds wall clock time: 58 minutes 10.99 seconds (3490.99 seconds total)