Starting phenix.real_space_refine on Fri Aug 22 18:52:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fht_29103/08_2025/8fht_29103.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fht_29103/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fht_29103/08_2025/8fht_29103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fht_29103/08_2025/8fht_29103.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fht_29103/08_2025/8fht_29103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fht_29103/08_2025/8fht_29103.map" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'TRP:plan': 1, 'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 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: {'TRP:plan': 1, 'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 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: 1.82, per 1000 atoms: 0.26 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: 0.64 Conformation dependent library (CDL) restraints added in 421.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.13 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: 1.06 Time building geometry restraints manager: 0.85 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: 0.01 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: 2.110 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.220 Find NCS groups from input model: 0.100 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.970 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG B 243 TYR 0.018 0.001 TYR A 602 PHE 0.025 0.002 PHE B 238 TRP 0.019 0.001 TRP B 586 HIS 0.002 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 7178) covalent geometry : angle 0.63304 ( 9806) SS BOND : bond 0.01436 ( 4) SS BOND : angle 2.23185 ( 8) hydrogen bonds : bond 0.11214 ( 535) hydrogen bonds : angle 4.63120 ( 1584) *********************** 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 : 0.245 Fit side-chains REVERT: B 417 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7169 (mt-10) outliers start: 7 outliers final: 0 residues processed: 117 average time/residue: 0.0752 time to fit residues: 11.9766 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 : 0.168 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.0470 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.0000 overall best weight: 0.4482 ------------------------------------------------------------------------------- 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 = 0.4297 r_free = 0.4297 target = 0.201568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.156521 restraints weight = 7488.920| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.31 r_work: 0.3704 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7182 Z= 0.125 Angle : 0.496 6.710 9814 Z= 0.269 Chirality : 0.038 0.167 1168 Planarity : 0.004 0.036 1206 Dihedral : 4.139 50.396 991 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.24 % Allowed : 6.75 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.28), residues: 932 helix: 2.46 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.88 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 399 TYR 0.011 0.001 TYR B 605 PHE 0.015 0.001 PHE A 598 TRP 0.012 0.001 TRP B 586 HIS 0.002 0.001 HIS B 434 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7178) covalent geometry : angle 0.49536 ( 9806) SS BOND : bond 0.00552 ( 4) SS BOND : angle 1.08379 ( 8) hydrogen bonds : bond 0.04392 ( 535) hydrogen bonds : angle 3.96325 ( 1584) *********************** 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 : 0.199 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7967 (t) cc_final: 0.7617 (p) REVERT: B 309 SER cc_start: 0.7952 (t) cc_final: 0.7630 (p) REVERT: B 416 CYS cc_start: 0.3623 (OUTLIER) cc_final: 0.2928 (t) REVERT: B 417 GLU cc_start: 0.7775 (mp0) cc_final: 0.7534 (mt-10) outliers start: 9 outliers final: 6 residues processed: 117 average time/residue: 0.0674 time to fit residues: 10.8480 Evaluate side-chains 107 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 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 54 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.198767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.153555 restraints weight = 7447.676| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.30 r_work: 0.3671 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1084 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= 0.143 Angle : 0.501 7.212 9814 Z= 0.271 Chirality : 0.039 0.173 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.505 14.797 988 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.65 % Allowed : 9.23 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.27), residues: 932 helix: 2.37 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.83 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 243 TYR 0.006 0.001 TYR B 605 PHE 0.025 0.002 PHE A 238 TRP 0.014 0.001 TRP B 586 HIS 0.003 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7178) covalent geometry : angle 0.50002 ( 9806) SS BOND : bond 0.00299 ( 4) SS BOND : angle 1.05483 ( 8) hydrogen bonds : bond 0.04479 ( 535) hydrogen bonds : angle 3.93227 ( 1584) *********************** 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 118 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7865 (t) cc_final: 0.7489 (p) REVERT: B 309 SER cc_start: 0.7918 (t) cc_final: 0.7583 (p) outliers start: 12 outliers final: 10 residues processed: 112 average time/residue: 0.0729 time to fit residues: 11.1874 Evaluate side-chains 107 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 259 ASP 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 26 optimal weight: 3.9990 chunk 7 optimal weight: 0.0770 chunk 47 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.194031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.146415 restraints weight = 7408.761| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.43 r_work: 0.3519 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1277 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= 0.132 Angle : 0.477 4.754 9814 Z= 0.261 Chirality : 0.039 0.177 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.510 15.049 988 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.20 % Allowed : 10.33 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.27), residues: 932 helix: 2.42 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.86 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 158 TYR 0.016 0.001 TYR B 602 PHE 0.020 0.002 PHE A 238 TRP 0.016 0.001 TRP B 586 HIS 0.003 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7178) covalent geometry : angle 0.47706 ( 9806) SS BOND : bond 0.00226 ( 4) SS BOND : angle 0.77349 ( 8) hydrogen bonds : bond 0.04266 ( 535) hydrogen bonds : angle 3.87741 ( 1584) *********************** 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: 16 poor density : 96 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7778 (t) cc_final: 0.7307 (p) REVERT: B 309 SER cc_start: 0.7852 (t) cc_final: 0.7451 (p) outliers start: 16 outliers final: 12 residues processed: 105 average time/residue: 0.0772 time to fit residues: 10.8977 Evaluate side-chains 107 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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 259 ASP 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 165 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.191864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.142924 restraints weight = 7241.147| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.35 r_work: 0.3498 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7182 Z= 0.143 Angle : 0.495 5.928 9814 Z= 0.271 Chirality : 0.039 0.190 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.544 15.370 988 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.34 % Allowed : 11.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.27), residues: 932 helix: 2.38 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.82 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 158 TYR 0.014 0.001 TYR B 602 PHE 0.018 0.002 PHE A 238 TRP 0.011 0.001 TRP B 586 HIS 0.003 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 7178) covalent geometry : angle 0.49404 ( 9806) SS BOND : bond 0.00282 ( 4) SS BOND : angle 1.40911 ( 8) hydrogen bonds : bond 0.04427 ( 535) hydrogen bonds : angle 3.91338 ( 1584) *********************** 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 112 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7665 (t) cc_final: 0.7209 (p) REVERT: A 343 MET cc_start: 0.8106 (mmt) cc_final: 0.7594 (mmt) REVERT: B 309 SER cc_start: 0.7832 (t) cc_final: 0.7411 (p) outliers start: 17 outliers final: 13 residues processed: 105 average time/residue: 0.0894 time to fit residues: 12.5774 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 : 0.191 ------------------------------------------------------------------------------- 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 259 ASP 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 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 49 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 42 optimal weight: 0.0170 chunk 75 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.192719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.143855 restraints weight = 7301.913| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.35 r_work: 0.3509 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1572 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= 0.128 Angle : 0.473 4.631 9814 Z= 0.260 Chirality : 0.039 0.188 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.500 15.184 988 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.34 % Allowed : 11.71 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.27), residues: 932 helix: 2.50 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.81 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 261 TYR 0.016 0.001 TYR B 602 PHE 0.016 0.001 PHE A 238 TRP 0.013 0.001 TRP B 586 HIS 0.002 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7178) covalent geometry : angle 0.47192 ( 9806) SS BOND : bond 0.00217 ( 4) SS BOND : angle 0.96678 ( 8) hydrogen bonds : bond 0.04193 ( 535) hydrogen bonds : angle 3.85469 ( 1584) *********************** 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: 17 poor density : 90 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7644 (t) cc_final: 0.7168 (p) REVERT: A 343 MET cc_start: 0.8093 (mmt) cc_final: 0.7590 (mmt) REVERT: B 309 SER cc_start: 0.7794 (t) cc_final: 0.7355 (p) outliers start: 17 outliers final: 13 residues processed: 99 average time/residue: 0.0880 time to fit residues: 11.7988 Evaluate side-chains 99 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 259 ASP 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 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 13 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 76 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.189082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.140197 restraints weight = 7253.577| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.32 r_work: 0.3469 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7182 Z= 0.162 Angle : 0.514 4.889 9814 Z= 0.282 Chirality : 0.040 0.191 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.608 15.714 988 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.03 % Allowed : 10.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.27), residues: 932 helix: 2.34 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.80 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 209 TYR 0.006 0.001 TYR A 249 PHE 0.015 0.002 PHE A 548 TRP 0.010 0.001 TRP B 586 HIS 0.004 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 7178) covalent geometry : angle 0.51371 ( 9806) SS BOND : bond 0.00267 ( 4) SS BOND : angle 0.69606 ( 8) hydrogen bonds : bond 0.04636 ( 535) hydrogen bonds : angle 3.98913 ( 1584) *********************** 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 113 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7616 (t) cc_final: 0.7109 (p) REVERT: A 343 MET cc_start: 0.8122 (mmt) cc_final: 0.7658 (mmt) REVERT: B 309 SER cc_start: 0.7725 (t) cc_final: 0.7300 (p) outliers start: 22 outliers final: 13 residues processed: 105 average time/residue: 0.0803 time to fit residues: 11.4185 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 : 0.247 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 567 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 32 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.191050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.142151 restraints weight = 7365.363| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.36 r_work: 0.3490 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7182 Z= 0.132 Angle : 0.485 4.822 9814 Z= 0.267 Chirality : 0.039 0.193 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.521 15.100 988 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.93 % Allowed : 12.95 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.27), residues: 932 helix: 2.50 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.76 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 209 TYR 0.005 0.001 TYR A 602 PHE 0.018 0.001 PHE A 548 TRP 0.014 0.001 TRP B 586 HIS 0.002 0.000 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7178) covalent geometry : angle 0.48516 ( 9806) SS BOND : bond 0.00220 ( 4) SS BOND : angle 0.70659 ( 8) hydrogen bonds : bond 0.04261 ( 535) hydrogen bonds : angle 3.88732 ( 1584) *********************** 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 103 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7518 (t) cc_final: 0.7009 (p) REVERT: A 343 MET cc_start: 0.8122 (mmt) cc_final: 0.7653 (mmt) REVERT: B 309 SER cc_start: 0.7604 (t) cc_final: 0.7133 (p) outliers start: 14 outliers final: 13 residues processed: 96 average time/residue: 0.0749 time to fit residues: 9.8129 Evaluate side-chains 100 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 259 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 75 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.192334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.143769 restraints weight = 7339.052| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.35 r_work: 0.3510 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7182 Z= 0.122 Angle : 0.466 4.683 9814 Z= 0.258 Chirality : 0.038 0.188 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.418 14.325 988 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.07 % Allowed : 13.09 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.63 (0.28), residues: 932 helix: 2.69 (0.19), residues: 658 sheet: None (None), residues: 0 loop : -0.71 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 261 TYR 0.006 0.001 TYR B 564 PHE 0.019 0.001 PHE A 548 TRP 0.014 0.001 TRP B 586 HIS 0.002 0.000 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7178) covalent geometry : angle 0.46627 ( 9806) SS BOND : bond 0.00214 ( 4) SS BOND : angle 0.59656 ( 8) hydrogen bonds : bond 0.04020 ( 535) hydrogen bonds : angle 3.80085 ( 1584) *********************** 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 106 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 343 MET cc_start: 0.8158 (mmt) cc_final: 0.7699 (mmt) REVERT: B 165 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7493 (mt0) REVERT: B 309 SER cc_start: 0.7298 (t) cc_final: 0.6746 (p) outliers start: 15 outliers final: 11 residues processed: 100 average time/residue: 0.0891 time to fit residues: 12.0045 Evaluate side-chains 101 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 259 ASP 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 419 LEU Chi-restraints excluded: chain B residue 430 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 85 optimal weight: 0.8980 chunk 73 optimal weight: 0.0770 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.193451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.144696 restraints weight = 7321.632| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.38 r_work: 0.3519 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 7182 Z= 0.116 Angle : 0.455 5.112 9814 Z= 0.253 Chirality : 0.038 0.185 1168 Planarity : 0.004 0.038 1206 Dihedral : 3.345 14.065 988 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.38 % Allowed : 13.91 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.78 (0.28), residues: 932 helix: 2.81 (0.19), residues: 658 sheet: None (None), residues: 0 loop : -0.68 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 261 TYR 0.003 0.001 TYR A 249 PHE 0.015 0.001 PHE A 238 TRP 0.015 0.001 TRP B 586 HIS 0.001 0.000 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 7178) covalent geometry : angle 0.45514 ( 9806) SS BOND : bond 0.00196 ( 4) SS BOND : angle 0.56738 ( 8) hydrogen bonds : bond 0.03832 ( 535) hydrogen bonds : angle 3.75884 ( 1584) ********************** 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 104 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 343 MET cc_start: 0.8157 (mmt) cc_final: 0.7706 (mmt) REVERT: B 165 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7530 (mt0) outliers start: 10 outliers final: 9 residues processed: 99 average time/residue: 0.0713 time to fit residues: 9.5756 Evaluate side-chains 101 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 395 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 430 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 59 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.190743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.141872 restraints weight = 7319.035| |-----------------------------------------------------------------------------| r_work (start): 0.3636 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: 0.7640 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7182 Z= 0.138 Angle : 0.480 5.017 9814 Z= 0.265 Chirality : 0.039 0.188 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.426 14.546 988 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.24 % Allowed : 14.60 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.59 (0.28), residues: 932 helix: 2.63 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.67 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 243 TYR 0.005 0.001 TYR A 249 PHE 0.014 0.001 PHE A 238 TRP 0.013 0.001 TRP B 586 HIS 0.003 0.001 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 7178) covalent geometry : angle 0.48039 ( 9806) SS BOND : bond 0.00211 ( 4) SS BOND : angle 0.51640 ( 8) hydrogen bonds : bond 0.04197 ( 535) hydrogen bonds : angle 3.85100 ( 1584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1592.82 seconds wall clock time: 28 minutes 2.13 seconds (1682.13 seconds total)