Starting phenix.real_space_refine on Thu Jun 5 17:56:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n0x_48797/06_2025/9n0x_48797.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n0x_48797/06_2025/9n0x_48797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n0x_48797/06_2025/9n0x_48797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n0x_48797/06_2025/9n0x_48797.map" model { file = "/net/cci-nas-00/data/ceres_data/9n0x_48797/06_2025/9n0x_48797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n0x_48797/06_2025/9n0x_48797.cif" } resolution = 3.3 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= 0.004 sd= 0.021 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 Ca 2 9.91 5 P 6 5.49 5 S 40 5.16 5 C 4432 2.51 5 N 1008 2.21 5 O 1100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6588 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3181 Classifications: {'peptide': 380} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 358} Chain: "B" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3181 Classifications: {'peptide': 380} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 358} Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {' CA': 1, 'RXY': 1} Classifications: {'peptide': 2, 'undetermined': 2} Link IDs: {'TRANS': 1, None: 2} Not linked: pdbres="P5S A 502 " pdbres=" CA A 503 " Not linked: pdbres=" CA A 503 " pdbres="RXY A 504 " Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {' CA': 1, 'RXY': 1} Classifications: {'peptide': 2, 'undetermined': 2} Link IDs: {'TRANS': 1, None: 2} Not linked: pdbres="P5S B 502 " pdbres=" CA B 503 " Not linked: pdbres=" CA B 503 " pdbres="RXY B 504 " Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Time building chain proxies: 6.69, per 1000 atoms: 1.02 Number of scatterers: 6588 At special positions: 0 Unit cell: (107.748, 118.818, 69.372, 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) Ca 2 19.99 S 40 16.00 P 6 15.00 O 1100 8.00 N 1008 7.00 C 4432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 174 " - pdb=" SG CYS A 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 174 " - pdb=" SG CYS B 241 " distance=2.03 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: 2.03 Conformation dependent library (CDL) restraints added in 842.8 milliseconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1448 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 73.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 65 through 82 Processing helix chain 'A' and resid 88 through 112 removed outlier: 3.851A pdb=" N LYS A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 144 removed outlier: 3.950A pdb=" N TRP A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 186 through 193 removed outlier: 4.047A pdb=" N ASP A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 212 removed outlier: 3.663A pdb=" N LEU A 202 " --> pdb=" O PRO A 198 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 231 removed outlier: 3.509A pdb=" N CYS A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 256 through 269 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 311 through 338 removed outlier: 3.609A pdb=" N GLU A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 371 removed outlier: 3.613A pdb=" N LEU A 348 " --> pdb=" O HIS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 400 removed outlier: 3.558A pdb=" N ASP A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 removed outlier: 3.605A pdb=" N LEU A 404 " --> pdb=" O ASP A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 437 removed outlier: 3.874A pdb=" N CYS A 415 " --> pdb=" O TYR A 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 82 Processing helix chain 'B' and resid 88 through 112 removed outlier: 3.916A pdb=" N LYS B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 144 removed outlier: 3.953A pdb=" N TRP B 125 " --> pdb=" O HIS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 186 through 193 removed outlier: 4.013A pdb=" N ASP B 191 " --> pdb=" O HIS B 187 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 212 removed outlier: 3.548A pdb=" N PHE B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 202 " --> pdb=" O PRO B 198 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 231 removed outlier: 3.513A pdb=" N CYS B 217 " --> pdb=" O ASP B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 256 through 269 Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 311 through 338 removed outlier: 3.607A pdb=" N GLU B 328 " --> pdb=" O PHE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 370 removed outlier: 3.632A pdb=" N LEU B 348 " --> pdb=" O HIS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 400 removed outlier: 3.560A pdb=" N ASP B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 removed outlier: 3.618A pdb=" N LEU B 404 " --> pdb=" O ASP B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 437 removed outlier: 3.875A pdb=" N CYS B 415 " --> pdb=" O TYR B 411 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1212 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: 1.62 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 950 1.30 - 1.43: 2022 1.43 - 1.56: 3766 1.56 - 1.69: 18 1.69 - 1.81: 60 Bond restraints: 6816 Sorted by residual: bond pdb=" CBJ RXY A 504 " pdb=" CBK RXY A 504 " ideal model delta sigma weight residual 1.533 1.317 0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" CBJ RXY B 504 " pdb=" CBK RXY B 504 " ideal model delta sigma weight residual 1.533 1.318 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" CBG RXY B 504 " pdb=" CBH RXY B 504 " ideal model delta sigma weight residual 1.525 1.318 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" CBG RXY A 504 " pdb=" CBH RXY A 504 " ideal model delta sigma weight residual 1.525 1.318 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" CAK RXY A 504 " pdb=" CAL RXY A 504 " ideal model delta sigma weight residual 1.333 1.529 -0.196 2.00e-02 2.50e+03 9.59e+01 ... (remaining 6811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 9088 2.82 - 5.64: 130 5.64 - 8.47: 34 8.47 - 11.29: 14 11.29 - 14.11: 8 Bond angle restraints: 9274 Sorted by residual: angle pdb=" CAK RXY B 504 " pdb=" CAL RXY B 504 " pdb=" CAM RXY B 504 " ideal model delta sigma weight residual 126.11 112.00 14.11 3.00e+00 1.11e-01 2.21e+01 angle pdb=" CAK RXY A 504 " pdb=" CAL RXY A 504 " pdb=" CAM RXY A 504 " ideal model delta sigma weight residual 126.11 112.03 14.08 3.00e+00 1.11e-01 2.20e+01 angle pdb=" OAB RXY A 504 " pdb=" PAZ RXY A 504 " pdb=" OBX RXY A 504 " ideal model delta sigma weight residual 123.18 109.25 13.93 3.00e+00 1.11e-01 2.16e+01 angle pdb=" OAB RXY B 504 " pdb=" PAZ RXY B 504 " pdb=" OBX RXY B 504 " ideal model delta sigma weight residual 123.18 109.29 13.89 3.00e+00 1.11e-01 2.14e+01 angle pdb=" CAJ RXY A 504 " pdb=" CAK RXY A 504 " pdb=" CAL RXY A 504 " ideal model delta sigma weight residual 125.80 112.37 13.43 3.00e+00 1.11e-01 2.00e+01 ... (remaining 9269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 3752 35.80 - 71.60: 180 71.60 - 107.40: 24 107.40 - 143.20: 7 143.20 - 179.00: 11 Dihedral angle restraints: 3974 sinusoidal: 1732 harmonic: 2242 Sorted by residual: dihedral pdb=" C38 P5S A 502 " pdb=" C39 P5S A 502 " pdb=" C40 P5S A 502 " pdb=" C41 P5S A 502 " ideal model delta sinusoidal sigma weight residual 64.51 -114.49 179.00 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C38 P5S B 502 " pdb=" C39 P5S B 502 " pdb=" C40 P5S B 502 " pdb=" C41 P5S B 502 " ideal model delta sinusoidal sigma weight residual 64.51 -114.47 178.98 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CBF RXY B 504 " pdb=" CBG RXY B 504 " pdb=" CBH RXY B 504 " pdb=" CBI RXY B 504 " ideal model delta sinusoidal sigma weight residual 178.53 -0.14 178.67 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 3971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 841 0.056 - 0.112: 132 0.112 - 0.167: 9 0.167 - 0.223: 2 0.223 - 0.279: 2 Chirality restraints: 986 Sorted by residual: chirality pdb=" CAW RXY B 504 " pdb=" CAV RXY B 504 " pdb=" CAX RXY B 504 " pdb=" OBW RXY B 504 " both_signs ideal model delta sigma weight residual False 2.21 2.49 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CAW RXY A 504 " pdb=" CAV RXY A 504 " pdb=" CAX RXY A 504 " pdb=" OBW RXY A 504 " both_signs ideal model delta sigma weight residual False 2.21 2.49 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA P5S B 501 " pdb=" N P5S B 501 " pdb=" C P5S B 501 " pdb=" CB P5S B 501 " both_signs ideal model delta sigma weight residual False 2.40 2.59 -0.19 2.00e-01 2.50e+01 9.09e-01 ... (remaining 983 not shown) Planarity restraints: 1108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAJ RXY B 504 " -0.142 2.00e-02 2.50e+03 2.39e-01 5.73e+02 pdb=" CAK RXY B 504 " 0.308 2.00e-02 2.50e+03 pdb=" CAL RXY B 504 " -0.307 2.00e-02 2.50e+03 pdb=" CAM RXY B 504 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAJ RXY A 504 " 0.141 2.00e-02 2.50e+03 2.37e-01 5.62e+02 pdb=" CAK RXY A 504 " -0.305 2.00e-02 2.50e+03 pdb=" CAL RXY A 504 " 0.304 2.00e-02 2.50e+03 pdb=" CAM RXY A 504 " -0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 296 " 0.048 5.00e-02 4.00e+02 7.13e-02 8.13e+00 pdb=" N PRO B 297 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 297 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 297 " 0.040 5.00e-02 4.00e+02 ... (remaining 1105 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 781 2.75 - 3.29: 6415 3.29 - 3.82: 11099 3.82 - 4.36: 11856 4.36 - 4.90: 21679 Nonbonded interactions: 51830 Sorted by model distance: nonbonded pdb=" O PHE B 293 " pdb=" OG1 THR B 296 " model vdw 2.210 3.040 nonbonded pdb=" O PHE A 293 " pdb=" OG1 THR A 296 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR A 331 " pdb=" NH1 ARG A 350 " model vdw 2.276 3.120 nonbonded pdb=" OG1 THR B 331 " pdb=" NH1 ARG B 350 " model vdw 2.277 3.120 nonbonded pdb=" O LEU A 268 " pdb=" OH TYR A 273 " model vdw 2.284 3.040 ... (remaining 51825 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: 0.03 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: 19.230 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.180 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 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 : 0.008 0.216 6818 Z= 0.405 Angle : 0.961 14.112 9278 Z= 0.399 Chirality : 0.041 0.279 986 Planarity : 0.011 0.239 1108 Dihedral : 23.177 178.998 2520 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.29 % Allowed : 15.84 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.30), residues: 756 helix: 2.05 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -2.00 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 204 HIS 0.004 0.001 HIS A 64 PHE 0.008 0.001 PHE A 303 TYR 0.019 0.001 TYR B 366 ARG 0.002 0.001 ARG B 119 Details of bonding type rmsd hydrogen bonds : bond 0.09318 ( 404) hydrogen bonds : angle 4.62007 ( 1212) SS BOND : bond 0.00227 ( 2) SS BOND : angle 0.67024 ( 4) covalent geometry : bond 0.00812 ( 6816) covalent geometry : angle 0.96130 ( 9274) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.655 Fit side-chains REVERT: A 224 PHE cc_start: 0.6820 (t80) cc_final: 0.6572 (t80) REVERT: B 224 PHE cc_start: 0.6909 (t80) cc_final: 0.6588 (t80) outliers start: 2 outliers final: 2 residues processed: 55 average time/residue: 0.1548 time to fit residues: 12.8686 Evaluate side-chains 56 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain B residue 188 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 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 = 0.4557 r_free = 0.4557 target = 0.214840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.4160 r_free = 0.4160 target = 0.175079 restraints weight = 8502.212| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 1.88 r_work: 0.3982 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3867 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.0659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6818 Z= 0.129 Angle : 0.535 6.287 9278 Z= 0.270 Chirality : 0.039 0.133 986 Planarity : 0.005 0.048 1108 Dihedral : 23.647 176.024 1059 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.89 % Allowed : 15.41 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.30), residues: 756 helix: 1.95 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -1.83 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 204 HIS 0.004 0.001 HIS B 233 PHE 0.008 0.001 PHE A 303 TYR 0.017 0.001 TYR A 366 ARG 0.003 0.001 ARG B 126 Details of bonding type rmsd hydrogen bonds : bond 0.05040 ( 404) hydrogen bonds : angle 4.15834 ( 1212) SS BOND : bond 0.00229 ( 2) SS BOND : angle 0.62250 ( 4) covalent geometry : bond 0.00283 ( 6816) covalent geometry : angle 0.53519 ( 9274) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 1.062 Fit side-chains REVERT: A 224 PHE cc_start: 0.7003 (t80) cc_final: 0.6651 (t80) REVERT: A 260 CYS cc_start: 0.7844 (m) cc_final: 0.7221 (m) REVERT: B 223 MET cc_start: 0.6882 (mmm) cc_final: 0.6602 (mmm) outliers start: 13 outliers final: 12 residues processed: 66 average time/residue: 0.2122 time to fit residues: 21.9463 Evaluate side-chains 65 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 264 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 47 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.0670 chunk 12 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.4562 r_free = 0.4562 target = 0.215700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.173563 restraints weight = 8521.512| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 1.92 r_work: 0.3958 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6818 Z= 0.114 Angle : 0.487 5.982 9278 Z= 0.251 Chirality : 0.038 0.126 986 Planarity : 0.004 0.038 1108 Dihedral : 20.314 169.597 1056 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.33 % Allowed : 15.55 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.30), residues: 756 helix: 2.09 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.71 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 204 HIS 0.004 0.001 HIS A 233 PHE 0.006 0.001 PHE A 303 TYR 0.016 0.001 TYR A 366 ARG 0.002 0.000 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.04669 ( 404) hydrogen bonds : angle 4.10583 ( 1212) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.68132 ( 4) covalent geometry : bond 0.00238 ( 6816) covalent geometry : angle 0.48678 ( 9274) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.707 Fit side-chains REVERT: A 223 MET cc_start: 0.6700 (mmm) cc_final: 0.6393 (mmm) REVERT: A 224 PHE cc_start: 0.6873 (t80) cc_final: 0.6607 (t80) REVERT: A 260 CYS cc_start: 0.7646 (m) cc_final: 0.6950 (m) REVERT: B 224 PHE cc_start: 0.6852 (t80) cc_final: 0.6531 (t80) REVERT: B 231 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7330 (mp) REVERT: B 234 GLN cc_start: 0.7079 (mt0) cc_final: 0.6858 (mt0) REVERT: B 260 CYS cc_start: 0.7765 (m) cc_final: 0.6861 (m) outliers start: 16 outliers final: 11 residues processed: 66 average time/residue: 0.1606 time to fit residues: 16.2924 Evaluate side-chains 68 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 42 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 75 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4553 r_free = 0.4553 target = 0.220069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.180295 restraints weight = 8927.231| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 1.69 r_work: 0.3942 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3823 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6818 Z= 0.124 Angle : 0.493 6.262 9278 Z= 0.252 Chirality : 0.038 0.128 986 Planarity : 0.004 0.034 1108 Dihedral : 19.443 167.595 1056 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.76 % Allowed : 16.72 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.30), residues: 756 helix: 2.05 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -1.66 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 204 HIS 0.004 0.001 HIS A 233 PHE 0.010 0.001 PHE B 354 TYR 0.014 0.001 TYR B 366 ARG 0.004 0.000 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.04936 ( 404) hydrogen bonds : angle 4.12250 ( 1212) SS BOND : bond 0.00057 ( 2) SS BOND : angle 0.45787 ( 4) covalent geometry : bond 0.00270 ( 6816) covalent geometry : angle 0.49303 ( 9274) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.780 Fit side-chains REVERT: A 224 PHE cc_start: 0.7046 (t80) cc_final: 0.6751 (t80) REVERT: A 260 CYS cc_start: 0.7868 (m) cc_final: 0.7219 (m) REVERT: B 224 PHE cc_start: 0.7055 (t80) cc_final: 0.6747 (t80) REVERT: B 231 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7375 (mp) REVERT: B 234 GLN cc_start: 0.7169 (mt0) cc_final: 0.6937 (mt0) REVERT: B 324 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.7901 (t80) outliers start: 19 outliers final: 15 residues processed: 70 average time/residue: 0.1748 time to fit residues: 19.1846 Evaluate side-chains 71 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 63 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 2 optimal weight: 0.0000 chunk 3 optimal weight: 0.0060 chunk 7 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 overall best weight: 0.3800 ------------------------------------------------------------------------------- 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 = 0.4577 r_free = 0.4577 target = 0.216677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.176545 restraints weight = 8567.268| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 1.97 r_work: 0.4008 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3906 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6818 Z= 0.101 Angle : 0.466 7.386 9278 Z= 0.237 Chirality : 0.037 0.125 986 Planarity : 0.004 0.035 1108 Dihedral : 19.125 167.559 1056 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.33 % Allowed : 17.30 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.31), residues: 756 helix: 2.27 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -1.58 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 204 HIS 0.004 0.001 HIS A 233 PHE 0.006 0.001 PHE A 354 TYR 0.014 0.001 TYR B 366 ARG 0.005 0.000 ARG B 119 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 404) hydrogen bonds : angle 4.02856 ( 1212) SS BOND : bond 0.00157 ( 2) SS BOND : angle 0.62608 ( 4) covalent geometry : bond 0.00210 ( 6816) covalent geometry : angle 0.46572 ( 9274) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.829 Fit side-chains REVERT: A 224 PHE cc_start: 0.6852 (t80) cc_final: 0.6607 (t80) REVERT: A 260 CYS cc_start: 0.7728 (m) cc_final: 0.7048 (m) REVERT: A 324 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.7847 (t80) REVERT: B 224 PHE cc_start: 0.6844 (t80) cc_final: 0.6494 (t80) REVERT: B 231 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7316 (mp) REVERT: B 234 GLN cc_start: 0.7105 (mt0) cc_final: 0.6810 (mt0) REVERT: B 260 CYS cc_start: 0.7829 (m) cc_final: 0.6927 (m) REVERT: B 324 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.7850 (t80) outliers start: 16 outliers final: 10 residues processed: 66 average time/residue: 0.1494 time to fit residues: 14.9724 Evaluate side-chains 68 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.0070 chunk 50 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 2 optimal weight: 0.0020 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 overall best weight: 0.3606 ------------------------------------------------------------------------------- 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 = 0.4577 r_free = 0.4577 target = 0.217295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.4245 r_free = 0.4245 target = 0.181302 restraints weight = 8466.301| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 1.58 r_work: 0.4031 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3920 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6818 Z= 0.101 Angle : 0.467 7.784 9278 Z= 0.236 Chirality : 0.037 0.125 986 Planarity : 0.004 0.036 1108 Dihedral : 18.817 167.045 1056 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.20 % Allowed : 17.44 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.30), residues: 756 helix: 2.35 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -1.55 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 204 HIS 0.003 0.001 HIS A 233 PHE 0.007 0.001 PHE B 354 TYR 0.013 0.001 TYR B 366 ARG 0.006 0.000 ARG A 119 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 404) hydrogen bonds : angle 3.96277 ( 1212) SS BOND : bond 0.00087 ( 2) SS BOND : angle 0.47976 ( 4) covalent geometry : bond 0.00207 ( 6816) covalent geometry : angle 0.46667 ( 9274) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.706 Fit side-chains REVERT: A 224 PHE cc_start: 0.6829 (t80) cc_final: 0.6599 (t80) REVERT: A 238 PHE cc_start: 0.4548 (OUTLIER) cc_final: 0.4311 (m-80) REVERT: A 260 CYS cc_start: 0.7699 (m) cc_final: 0.7020 (m) REVERT: A 324 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.7815 (t80) REVERT: B 223 MET cc_start: 0.6755 (mmm) cc_final: 0.6489 (mmm) REVERT: B 224 PHE cc_start: 0.6794 (t80) cc_final: 0.6553 (t80) REVERT: B 231 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7319 (mp) REVERT: B 234 GLN cc_start: 0.7104 (mt0) cc_final: 0.6833 (mt0) REVERT: B 260 CYS cc_start: 0.7794 (m) cc_final: 0.6952 (m) outliers start: 22 outliers final: 13 residues processed: 70 average time/residue: 0.1280 time to fit residues: 13.8352 Evaluate side-chains 70 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.4533 r_free = 0.4533 target = 0.217913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.178312 restraints weight = 8813.684| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 1.74 r_work: 0.3900 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6818 Z= 0.162 Angle : 0.537 7.970 9278 Z= 0.272 Chirality : 0.040 0.139 986 Planarity : 0.004 0.032 1108 Dihedral : 19.041 164.585 1056 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.34 % Allowed : 17.15 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.30), residues: 756 helix: 1.99 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 204 HIS 0.004 0.001 HIS A 233 PHE 0.010 0.001 PHE A 127 TYR 0.011 0.001 TYR B 366 ARG 0.002 0.000 ARG A 119 Details of bonding type rmsd hydrogen bonds : bond 0.05578 ( 404) hydrogen bonds : angle 4.19568 ( 1212) SS BOND : bond 0.00152 ( 2) SS BOND : angle 0.24008 ( 4) covalent geometry : bond 0.00373 ( 6816) covalent geometry : angle 0.53728 ( 9274) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.660 Fit side-chains REVERT: A 238 PHE cc_start: 0.4812 (OUTLIER) cc_final: 0.4557 (m-80) REVERT: A 260 CYS cc_start: 0.7584 (m) cc_final: 0.6906 (m) REVERT: A 324 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.7923 (t80) REVERT: B 231 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7409 (mp) REVERT: B 234 GLN cc_start: 0.7116 (mt0) cc_final: 0.6842 (mt0) REVERT: B 260 CYS cc_start: 0.7670 (m) cc_final: 0.6800 (m) REVERT: B 324 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.7939 (t80) outliers start: 23 outliers final: 16 residues processed: 74 average time/residue: 0.1184 time to fit residues: 13.7466 Evaluate side-chains 76 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 17 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 30.0000 chunk 31 optimal weight: 0.0000 chunk 16 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 = 0.4551 r_free = 0.4551 target = 0.214191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.179969 restraints weight = 8499.879| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 1.48 r_work: 0.3995 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3889 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6818 Z= 0.118 Angle : 0.493 8.067 9278 Z= 0.249 Chirality : 0.038 0.126 986 Planarity : 0.004 0.036 1108 Dihedral : 18.767 164.728 1056 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.91 % Allowed : 18.02 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.30), residues: 756 helix: 2.13 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 204 HIS 0.003 0.001 HIS A 233 PHE 0.007 0.001 PHE B 354 TYR 0.013 0.001 TYR B 366 ARG 0.002 0.000 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.04840 ( 404) hydrogen bonds : angle 4.11409 ( 1212) SS BOND : bond 0.00067 ( 2) SS BOND : angle 0.34385 ( 4) covalent geometry : bond 0.00257 ( 6816) covalent geometry : angle 0.49276 ( 9274) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.658 Fit side-chains REVERT: A 223 MET cc_start: 0.6735 (mmm) cc_final: 0.6463 (mmm) REVERT: A 224 PHE cc_start: 0.6960 (t80) cc_final: 0.6698 (t80) REVERT: A 238 PHE cc_start: 0.4758 (OUTLIER) cc_final: 0.4523 (m-80) REVERT: A 260 CYS cc_start: 0.7623 (m) cc_final: 0.6985 (m) REVERT: A 324 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.7874 (t80) REVERT: B 224 PHE cc_start: 0.7004 (t80) cc_final: 0.6696 (t80) REVERT: B 231 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7427 (mp) REVERT: B 234 GLN cc_start: 0.7146 (mt0) cc_final: 0.6880 (mt0) REVERT: B 260 CYS cc_start: 0.7697 (m) cc_final: 0.6844 (m) REVERT: B 324 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.7882 (t80) outliers start: 20 outliers final: 13 residues processed: 71 average time/residue: 0.1231 time to fit residues: 13.6261 Evaluate side-chains 72 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 21 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 56 optimal weight: 0.0870 chunk 34 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.4560 r_free = 0.4560 target = 0.215044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.174115 restraints weight = 8551.799| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.01 r_work: 0.3975 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3860 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6818 Z= 0.112 Angle : 0.486 8.483 9278 Z= 0.244 Chirality : 0.038 0.124 986 Planarity : 0.004 0.036 1108 Dihedral : 18.454 164.610 1056 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.76 % Allowed : 18.17 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.30), residues: 756 helix: 2.19 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 204 HIS 0.003 0.001 HIS A 233 PHE 0.008 0.001 PHE A 354 TYR 0.014 0.001 TYR B 366 ARG 0.003 0.000 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.04600 ( 404) hydrogen bonds : angle 4.06526 ( 1212) SS BOND : bond 0.00102 ( 2) SS BOND : angle 0.45159 ( 4) covalent geometry : bond 0.00242 ( 6816) covalent geometry : angle 0.48579 ( 9274) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.809 Fit side-chains REVERT: A 224 PHE cc_start: 0.6949 (t80) cc_final: 0.6690 (t80) REVERT: A 238 PHE cc_start: 0.4751 (OUTLIER) cc_final: 0.4522 (m-80) REVERT: A 260 CYS cc_start: 0.7801 (m) cc_final: 0.7164 (m) REVERT: A 324 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.7878 (t80) REVERT: B 223 MET cc_start: 0.6832 (mmm) cc_final: 0.6554 (mmm) REVERT: B 224 PHE cc_start: 0.6987 (t80) cc_final: 0.6713 (t80) REVERT: B 231 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7381 (mp) REVERT: B 234 GLN cc_start: 0.7180 (mt0) cc_final: 0.6888 (mt0) REVERT: B 260 CYS cc_start: 0.7854 (m) cc_final: 0.7003 (m) REVERT: B 324 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.7945 (t80) outliers start: 19 outliers final: 14 residues processed: 69 average time/residue: 0.1453 time to fit residues: 15.4001 Evaluate side-chains 74 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 63 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4557 r_free = 0.4557 target = 0.214940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.4231 r_free = 0.4231 target = 0.180147 restraints weight = 8621.392| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 1.50 r_work: 0.4008 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6818 Z= 0.113 Angle : 0.485 8.056 9278 Z= 0.244 Chirality : 0.038 0.125 986 Planarity : 0.004 0.036 1108 Dihedral : 18.166 164.327 1056 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.62 % Allowed : 18.46 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.30), residues: 756 helix: 2.21 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -1.51 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 204 HIS 0.004 0.001 HIS B 233 PHE 0.007 0.001 PHE B 354 TYR 0.013 0.001 TYR B 366 ARG 0.003 0.000 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 404) hydrogen bonds : angle 4.05313 ( 1212) SS BOND : bond 0.00053 ( 2) SS BOND : angle 0.27359 ( 4) covalent geometry : bond 0.00245 ( 6816) covalent geometry : angle 0.48530 ( 9274) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.698 Fit side-chains REVERT: A 223 MET cc_start: 0.6647 (mmm) cc_final: 0.6396 (mmm) REVERT: A 224 PHE cc_start: 0.6894 (t80) cc_final: 0.6616 (t80) REVERT: A 238 PHE cc_start: 0.4755 (OUTLIER) cc_final: 0.4545 (m-80) REVERT: A 260 CYS cc_start: 0.7630 (m) cc_final: 0.6989 (m) REVERT: A 324 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.7856 (t80) REVERT: B 224 PHE cc_start: 0.6947 (t80) cc_final: 0.6630 (t80) REVERT: B 231 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7415 (mp) REVERT: B 234 GLN cc_start: 0.7174 (mt0) cc_final: 0.6900 (mt0) REVERT: B 260 CYS cc_start: 0.7665 (m) cc_final: 0.6810 (m) REVERT: B 324 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.7843 (t80) outliers start: 18 outliers final: 14 residues processed: 70 average time/residue: 0.1338 time to fit residues: 14.4917 Evaluate side-chains 74 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 0.0470 chunk 72 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 = 0.4557 r_free = 0.4557 target = 0.214887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.179873 restraints weight = 8563.943| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 1.45 r_work: 0.4012 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6818 Z= 0.114 Angle : 0.486 8.175 9278 Z= 0.243 Chirality : 0.038 0.125 986 Planarity : 0.004 0.035 1108 Dihedral : 17.985 164.284 1056 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.05 % Allowed : 18.02 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.30), residues: 756 helix: 2.22 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -1.51 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 204 HIS 0.003 0.001 HIS A 233 PHE 0.007 0.001 PHE A 354 TYR 0.013 0.001 TYR B 366 ARG 0.003 0.000 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 404) hydrogen bonds : angle 4.05348 ( 1212) SS BOND : bond 0.00072 ( 2) SS BOND : angle 0.45677 ( 4) covalent geometry : bond 0.00247 ( 6816) covalent geometry : angle 0.48644 ( 9274) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4287.67 seconds wall clock time: 76 minutes 35.66 seconds (4595.66 seconds total)