Starting phenix.real_space_refine on Tue Feb 3 19:54:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vsq_65304/02_2026/9vsq_65304_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vsq_65304/02_2026/9vsq_65304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vsq_65304/02_2026/9vsq_65304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vsq_65304/02_2026/9vsq_65304.map" model { file = "/net/cci-nas-00/data/ceres_data/9vsq_65304/02_2026/9vsq_65304_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vsq_65304/02_2026/9vsq_65304_neut.cif" } resolution = 2.74 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= 0.004 sd= 0.090 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 K 7 8.98 5 S 42 5.16 5 C 4334 2.51 5 N 1054 2.21 5 O 1114 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6553 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3198 Classifications: {'peptide': 412} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 3198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3198 Classifications: {'peptide': 412} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 59 Unusual residues: {' K': 4, 'CLR': 1, 'YN9': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 58 Unusual residues: {' K': 3, 'CLR': 1, 'YN9': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Time building chain proxies: 1.58, per 1000 atoms: 0.24 Number of scatterers: 6553 At special positions: 0 Unit cell: (89.816, 78.28, 78.28, 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) K 7 19.00 S 42 16.00 F 2 9.00 O 1114 8.00 N 1054 7.00 C 4334 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.76 Conformation dependent library (CDL) restraints added in 212.1 milliseconds 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 93.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 33 through 50 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 68 through 102 Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 136 through 164 removed outlier: 4.005A pdb=" N ILE A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 175 Processing helix chain 'A' and resid 177 through 204 removed outlier: 4.689A pdb=" N GLY A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Proline residue: A 193 - end of helix removed outlier: 4.163A pdb=" N LEU A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 224 removed outlier: 3.504A pdb=" N SER A 210 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 218 " --> pdb=" O MET A 214 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 257 through 284 removed outlier: 5.077A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 306 through 333 removed outlier: 3.660A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N HIS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 353 Processing helix chain 'A' and resid 354 through 365 removed outlier: 3.619A pdb=" N PHE A 365 " --> pdb=" O GLN A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 400 removed outlier: 3.898A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 440 removed outlier: 4.909A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix removed outlier: 3.520A pdb=" N CYS A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 461 removed outlier: 4.380A pdb=" N VAL A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLY A 446 " --> pdb=" O ARG A 442 " (cutoff:3.500A) Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 461 through 476 removed outlier: 3.630A pdb=" N VAL A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 50 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 68 through 102 Processing helix chain 'B' and resid 106 through 121 Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 136 through 164 removed outlier: 4.005A pdb=" N ILE B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 169 through 175 Processing helix chain 'B' and resid 177 through 204 removed outlier: 4.691A pdb=" N GLY B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Proline residue: B 193 - end of helix removed outlier: 4.163A pdb=" N LEU B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 224 removed outlier: 3.503A pdb=" N SER B 210 " --> pdb=" O PHE B 206 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 257 through 284 removed outlier: 5.076A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 306 through 333 removed outlier: 3.660A pdb=" N PHE B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 353 Processing helix chain 'B' and resid 354 through 365 removed outlier: 3.619A pdb=" N PHE B 365 " --> pdb=" O GLN B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 400 removed outlier: 3.899A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 440 removed outlier: 4.908A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix removed outlier: 3.521A pdb=" N CYS B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 461 removed outlier: 4.380A pdb=" N VAL B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLY B 446 " --> pdb=" O ARG B 442 " (cutoff:3.500A) Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 461 through 476 removed outlier: 3.629A pdb=" N VAL B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1578 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: 0.87 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 995 1.32 - 1.44: 1794 1.44 - 1.57: 3815 1.57 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 6668 Sorted by residual: bond pdb=" CA ARG B 375 " pdb=" C ARG B 375 " ideal model delta sigma weight residual 1.523 1.466 0.057 1.37e-02 5.33e+03 1.71e+01 bond pdb=" C ARG B 375 " pdb=" O ARG B 375 " ideal model delta sigma weight residual 1.236 1.199 0.037 1.29e-02 6.01e+03 8.26e+00 bond pdb=" C1 YN9 B 601 " pdb=" C3 YN9 B 601 " ideal model delta sigma weight residual 1.481 1.535 -0.054 2.00e-02 2.50e+03 7.38e+00 bond pdb=" C1 YN9 A 601 " pdb=" C3 YN9 A 601 " ideal model delta sigma weight residual 1.481 1.535 -0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" C9 YN9 B 601 " pdb=" O1 YN9 B 601 " ideal model delta sigma weight residual 1.353 1.404 -0.051 2.00e-02 2.50e+03 6.50e+00 ... (remaining 6663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 8726 1.33 - 2.66: 285 2.66 - 3.99: 73 3.99 - 5.32: 14 5.32 - 6.65: 2 Bond angle restraints: 9100 Sorted by residual: angle pdb=" C ASN B 284 " pdb=" N VAL B 285 " pdb=" CA VAL B 285 " ideal model delta sigma weight residual 122.59 120.78 1.81 7.20e-01 1.93e+00 6.32e+00 angle pdb=" C ASN A 284 " pdb=" N VAL A 285 " pdb=" CA VAL A 285 " ideal model delta sigma weight residual 122.59 120.81 1.78 7.20e-01 1.93e+00 6.13e+00 angle pdb=" CA GLY B 307 " pdb=" C GLY B 307 " pdb=" N PRO B 308 " ideal model delta sigma weight residual 119.27 117.26 2.01 8.50e-01 1.38e+00 5.59e+00 angle pdb=" CA GLY A 307 " pdb=" C GLY A 307 " pdb=" N PRO A 308 " ideal model delta sigma weight residual 119.27 117.26 2.01 8.50e-01 1.38e+00 5.59e+00 angle pdb=" O2 YN9 B 601 " pdb=" C23 YN9 B 601 " pdb=" O3 YN9 B 601 " ideal model delta sigma weight residual 126.68 120.03 6.65 3.00e+00 1.11e-01 4.91e+00 ... (remaining 9095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 3564 17.62 - 35.24: 328 35.24 - 52.86: 88 52.86 - 70.48: 20 70.48 - 88.10: 10 Dihedral angle restraints: 4010 sinusoidal: 1596 harmonic: 2414 Sorted by residual: dihedral pdb=" CA PHE B 99 " pdb=" C PHE B 99 " pdb=" N GLN B 100 " pdb=" CA GLN B 100 " ideal model delta harmonic sigma weight residual 180.00 156.08 23.92 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA PHE A 99 " pdb=" C PHE A 99 " pdb=" N GLN A 100 " pdb=" CA GLN A 100 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA ASP B 283 " pdb=" C ASP B 283 " pdb=" N ASN B 284 " pdb=" CA ASN B 284 " ideal model delta harmonic sigma weight residual 180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 4007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 864 0.042 - 0.085: 206 0.085 - 0.127: 48 0.127 - 0.170: 1 0.170 - 0.212: 1 Chirality restraints: 1120 Sorted by residual: chirality pdb=" CA ARG B 375 " pdb=" N ARG B 375 " pdb=" C ARG B 375 " pdb=" CB ARG B 375 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA VAL B 136 " pdb=" N VAL B 136 " pdb=" C VAL B 136 " pdb=" CB VAL B 136 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA VAL A 136 " pdb=" N VAL A 136 " pdb=" C VAL A 136 " pdb=" CB VAL A 136 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 1117 not shown) Planarity restraints: 1094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 71 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" CD GLN B 71 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLN B 71 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN B 71 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 71 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" CD GLN A 71 " -0.036 2.00e-02 2.50e+03 pdb=" OE1 GLN A 71 " 0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN A 71 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 192 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO B 193 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 193 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 193 " 0.026 5.00e-02 4.00e+02 ... (remaining 1091 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 2311 2.85 - 3.43: 7792 3.43 - 4.00: 12425 4.00 - 4.57: 18878 4.57 - 5.14: 25641 Nonbonded interactions: 67047 Sorted by model distance: nonbonded pdb=" O HOH A 712 " pdb=" O HOH A 718 " model vdw 2.282 3.040 nonbonded pdb=" OD2 ASP A 266 " pdb=" O HOH A 701 " model vdw 2.308 3.040 nonbonded pdb=" OG1 THR A 319 " pdb=" OH TYR A 359 " model vdw 2.333 3.040 nonbonded pdb=" OG1 THR B 319 " pdb=" OH TYR B 359 " model vdw 2.334 3.040 nonbonded pdb=" O HOH B 713 " pdb=" O HOH B 721 " model vdw 2.383 3.040 ... (remaining 67042 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 30 through 605) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.350 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 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 : 0.005 0.057 6668 Z= 0.217 Angle : 0.612 6.647 9100 Z= 0.328 Chirality : 0.038 0.212 1120 Planarity : 0.004 0.047 1094 Dihedral : 15.619 88.098 2434 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.43 % Allowed : 13.73 % Favored : 85.84 % 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 are not related in a simple way. whole: 2.94 (0.29), residues: 812 helix: 2.21 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -0.16 (0.60), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 414 TYR 0.014 0.002 TYR A 359 PHE 0.013 0.001 PHE B 99 TRP 0.010 0.002 TRP A 394 HIS 0.003 0.001 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 6668) covalent geometry : angle 0.61157 ( 9100) hydrogen bonds : bond 0.11301 ( 532) hydrogen bonds : angle 4.98242 ( 1578) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 118 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 121 average time/residue: 0.5885 time to fit residues: 74.5035 Evaluate side-chains 114 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 426 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 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 328 HIS B 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.095925 restraints weight = 7010.658| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.83 r_work: 0.2907 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6668 Z= 0.132 Angle : 0.559 7.975 9100 Z= 0.278 Chirality : 0.039 0.118 1120 Planarity : 0.005 0.050 1094 Dihedral : 9.661 87.443 1042 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.47 % Allowed : 11.85 % Favored : 84.68 % 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 are not related in a simple way. whole: 3.38 (0.29), residues: 812 helix: 2.56 (0.19), residues: 710 sheet: None (None), residues: 0 loop : -0.18 (0.60), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.020 0.002 TYR A 359 PHE 0.010 0.001 PHE A 99 TRP 0.011 0.002 TRP B 324 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6668) covalent geometry : angle 0.55865 ( 9100) hydrogen bonds : bond 0.04759 ( 532) hydrogen bonds : angle 4.04196 ( 1578) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7685 (mm110) cc_final: 0.7474 (mm110) REVERT: A 212 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7502 (mp) REVERT: A 339 ARG cc_start: 0.7095 (ptt90) cc_final: 0.6879 (ptm-80) REVERT: B 71 GLN cc_start: 0.7659 (mm110) cc_final: 0.7420 (mm110) REVERT: B 181 TYR cc_start: 0.7923 (m-80) cc_final: 0.6876 (t80) REVERT: B 212 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7513 (mp) outliers start: 24 outliers final: 5 residues processed: 128 average time/residue: 0.4711 time to fit residues: 63.8393 Evaluate side-chains 114 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN B 171 GLN B 328 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.137962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.095548 restraints weight = 6956.493| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.84 r_work: 0.2904 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6668 Z= 0.138 Angle : 0.527 7.024 9100 Z= 0.263 Chirality : 0.039 0.124 1120 Planarity : 0.005 0.051 1094 Dihedral : 8.856 86.233 1038 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.60 % Allowed : 15.17 % Favored : 82.23 % 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 are not related in a simple way. whole: 3.47 (0.29), residues: 812 helix: 2.60 (0.19), residues: 710 sheet: None (None), residues: 0 loop : -0.07 (0.59), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.009 0.002 TYR A 313 PHE 0.013 0.001 PHE A 99 TRP 0.011 0.002 TRP A 324 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6668) covalent geometry : angle 0.52651 ( 9100) hydrogen bonds : bond 0.04676 ( 532) hydrogen bonds : angle 3.91350 ( 1578) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7674 (mm110) cc_final: 0.7448 (mm110) REVERT: A 212 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7453 (mp) REVERT: A 339 ARG cc_start: 0.7053 (ptt90) cc_final: 0.6829 (ptm-80) REVERT: A 447 ILE cc_start: 0.8738 (mt) cc_final: 0.8532 (mm) REVERT: B 71 GLN cc_start: 0.7678 (mm110) cc_final: 0.7434 (mm110) REVERT: B 212 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7491 (mp) REVERT: B 278 LEU cc_start: 0.8811 (mp) cc_final: 0.8510 (mp) outliers start: 18 outliers final: 8 residues processed: 115 average time/residue: 0.5143 time to fit residues: 62.3490 Evaluate side-chains 115 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 65 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN B 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.096624 restraints weight = 7031.221| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.85 r_work: 0.2925 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6668 Z= 0.120 Angle : 0.496 7.273 9100 Z= 0.248 Chirality : 0.038 0.117 1120 Planarity : 0.005 0.051 1094 Dihedral : 8.527 85.246 1038 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.47 % Allowed : 15.03 % Favored : 81.50 % 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 are not related in a simple way. whole: 3.68 (0.29), residues: 812 helix: 2.77 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -0.16 (0.58), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.018 0.002 TYR B 359 PHE 0.012 0.001 PHE A 99 TRP 0.011 0.001 TRP A 324 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6668) covalent geometry : angle 0.49590 ( 9100) hydrogen bonds : bond 0.04262 ( 532) hydrogen bonds : angle 3.82638 ( 1578) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7692 (mm110) cc_final: 0.7447 (mm110) REVERT: A 181 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.7000 (t80) REVERT: A 212 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7459 (mp) REVERT: A 339 ARG cc_start: 0.7073 (ptt90) cc_final: 0.6844 (ptm-80) REVERT: B 71 GLN cc_start: 0.7669 (mm110) cc_final: 0.7392 (mm110) REVERT: B 181 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.6960 (t80) REVERT: B 191 GLN cc_start: 0.8374 (tt0) cc_final: 0.8074 (tt0) REVERT: B 212 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7523 (mp) outliers start: 24 outliers final: 11 residues processed: 124 average time/residue: 0.5004 time to fit residues: 65.5797 Evaluate side-chains 120 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 450 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 65 optimal weight: 0.0570 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.0970 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN B 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.140090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.097772 restraints weight = 7083.798| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.86 r_work: 0.2954 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6668 Z= 0.109 Angle : 0.480 6.641 9100 Z= 0.241 Chirality : 0.037 0.116 1120 Planarity : 0.005 0.050 1094 Dihedral : 8.389 84.030 1038 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.03 % Allowed : 16.76 % Favored : 80.20 % 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 are not related in a simple way. whole: 3.86 (0.29), residues: 812 helix: 2.89 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -0.03 (0.59), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.010 0.001 TYR B 359 PHE 0.011 0.001 PHE A 99 TRP 0.010 0.001 TRP A 324 HIS 0.003 0.000 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 6668) covalent geometry : angle 0.47967 ( 9100) hydrogen bonds : bond 0.04013 ( 532) hydrogen bonds : angle 3.77391 ( 1578) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7693 (mm110) cc_final: 0.7447 (mm110) REVERT: A 181 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.6993 (t80) REVERT: A 191 GLN cc_start: 0.8346 (tt0) cc_final: 0.8038 (tt0) REVERT: A 212 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7480 (mp) REVERT: A 214 MET cc_start: 0.8275 (mtm) cc_final: 0.8017 (mtp) REVERT: B 71 GLN cc_start: 0.7656 (mm110) cc_final: 0.7379 (mm110) REVERT: B 181 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.6949 (t80) REVERT: B 212 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7468 (mp) REVERT: B 214 MET cc_start: 0.8273 (mtm) cc_final: 0.8036 (mtp) outliers start: 21 outliers final: 10 residues processed: 119 average time/residue: 0.5057 time to fit residues: 63.6018 Evaluate side-chains 116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 450 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 72 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN B 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.096620 restraints weight = 7081.290| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.84 r_work: 0.2920 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6668 Z= 0.123 Angle : 0.489 6.353 9100 Z= 0.246 Chirality : 0.038 0.119 1120 Planarity : 0.005 0.050 1094 Dihedral : 8.329 82.851 1038 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.76 % Allowed : 16.04 % Favored : 80.20 % 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 are not related in a simple way. whole: 3.82 (0.29), residues: 812 helix: 2.84 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 0.08 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 375 TYR 0.020 0.002 TYR A 359 PHE 0.014 0.001 PHE B 99 TRP 0.010 0.001 TRP A 324 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6668) covalent geometry : angle 0.48887 ( 9100) hydrogen bonds : bond 0.04205 ( 532) hydrogen bonds : angle 3.76122 ( 1578) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7673 (mm110) cc_final: 0.7424 (mm110) REVERT: A 181 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.7012 (t80) REVERT: A 202 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7938 (m-10) REVERT: A 212 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7422 (mp) REVERT: A 214 MET cc_start: 0.8297 (mtm) cc_final: 0.8007 (mtp) REVERT: B 71 GLN cc_start: 0.7651 (mm110) cc_final: 0.7370 (mm110) REVERT: B 172 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.8103 (mt) REVERT: B 212 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7477 (mp) REVERT: B 214 MET cc_start: 0.8293 (mtm) cc_final: 0.8014 (mtp) REVERT: B 404 THR cc_start: 0.9087 (m) cc_final: 0.8798 (p) outliers start: 26 outliers final: 13 residues processed: 117 average time/residue: 0.5285 time to fit residues: 65.2980 Evaluate side-chains 116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 450 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN B 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.097217 restraints weight = 7006.154| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.84 r_work: 0.2932 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6668 Z= 0.115 Angle : 0.481 6.145 9100 Z= 0.243 Chirality : 0.037 0.118 1120 Planarity : 0.004 0.050 1094 Dihedral : 8.256 81.703 1038 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.18 % Allowed : 16.18 % Favored : 80.64 % 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 are not related in a simple way. whole: 3.89 (0.29), residues: 812 helix: 2.89 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 0.13 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 260 TYR 0.013 0.001 TYR B 359 PHE 0.013 0.001 PHE A 99 TRP 0.010 0.001 TRP B 324 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6668) covalent geometry : angle 0.48064 ( 9100) hydrogen bonds : bond 0.04060 ( 532) hydrogen bonds : angle 3.75341 ( 1578) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7692 (mm110) cc_final: 0.7442 (mm110) REVERT: A 181 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.7004 (t80) REVERT: A 212 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7407 (mp) REVERT: A 214 MET cc_start: 0.8287 (mtm) cc_final: 0.8070 (mtp) REVERT: B 71 GLN cc_start: 0.7645 (mm110) cc_final: 0.7368 (mm110) REVERT: B 181 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.6978 (t80) REVERT: B 212 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7446 (mp) REVERT: B 214 MET cc_start: 0.8272 (mtm) cc_final: 0.7977 (mtp) outliers start: 22 outliers final: 10 residues processed: 114 average time/residue: 0.5177 time to fit residues: 62.2468 Evaluate side-chains 114 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 450 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 63 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN B 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.097288 restraints weight = 7026.615| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.84 r_work: 0.2929 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6668 Z= 0.116 Angle : 0.480 5.953 9100 Z= 0.242 Chirality : 0.038 0.119 1120 Planarity : 0.004 0.050 1094 Dihedral : 8.141 79.786 1038 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.89 % Allowed : 16.04 % Favored : 81.07 % 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 are not related in a simple way. whole: 3.94 (0.29), residues: 812 helix: 2.88 (0.19), residues: 710 sheet: None (None), residues: 0 loop : 0.42 (0.61), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 309 TYR 0.017 0.002 TYR A 359 PHE 0.013 0.001 PHE B 99 TRP 0.010 0.001 TRP A 324 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6668) covalent geometry : angle 0.48023 ( 9100) hydrogen bonds : bond 0.04043 ( 532) hydrogen bonds : angle 3.74379 ( 1578) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7686 (mm110) cc_final: 0.7431 (mm110) REVERT: A 181 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7015 (t80) REVERT: A 202 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.7951 (m-10) REVERT: A 212 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7441 (mp) REVERT: A 214 MET cc_start: 0.8299 (mtm) cc_final: 0.8078 (mtp) REVERT: A 450 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7881 (mm) REVERT: B 71 GLN cc_start: 0.7645 (mm110) cc_final: 0.7367 (mm110) REVERT: B 181 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.6999 (t80) REVERT: B 212 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7504 (mp) REVERT: B 214 MET cc_start: 0.8274 (mtm) cc_final: 0.7969 (mtp) REVERT: B 404 THR cc_start: 0.9091 (m) cc_final: 0.8804 (p) REVERT: B 450 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7883 (mm) outliers start: 20 outliers final: 10 residues processed: 109 average time/residue: 0.5379 time to fit residues: 61.9610 Evaluate side-chains 116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 450 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 44 optimal weight: 0.6980 chunk 67 optimal weight: 0.0670 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN B 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.140471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.098700 restraints weight = 7069.722| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.84 r_work: 0.2948 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6668 Z= 0.106 Angle : 0.475 5.824 9100 Z= 0.238 Chirality : 0.037 0.117 1120 Planarity : 0.004 0.050 1094 Dihedral : 7.996 77.436 1038 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.18 % Allowed : 15.75 % Favored : 81.07 % 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 are not related in a simple way. whole: 4.14 (0.29), residues: 812 helix: 3.07 (0.19), residues: 698 sheet: None (None), residues: 0 loop : 0.35 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 260 TYR 0.009 0.001 TYR A 313 PHE 0.012 0.001 PHE B 99 TRP 0.010 0.001 TRP A 324 HIS 0.003 0.000 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 6668) covalent geometry : angle 0.47504 ( 9100) hydrogen bonds : bond 0.03829 ( 532) hydrogen bonds : angle 3.73306 ( 1578) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7675 (mm110) cc_final: 0.7417 (mm110) REVERT: A 181 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7017 (t80) REVERT: A 212 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7425 (mp) REVERT: A 214 MET cc_start: 0.8265 (mtm) cc_final: 0.8029 (mtp) REVERT: B 71 GLN cc_start: 0.7639 (mm110) cc_final: 0.7356 (mm110) REVERT: B 181 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.7002 (t80) REVERT: B 212 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7449 (mp) REVERT: B 214 MET cc_start: 0.8255 (mtm) cc_final: 0.8028 (mtp) outliers start: 22 outliers final: 10 residues processed: 111 average time/residue: 0.5571 time to fit residues: 65.0863 Evaluate side-chains 111 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 403 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 60 optimal weight: 0.0000 chunk 61 optimal weight: 0.0370 chunk 70 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 overall best weight: 0.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN B 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.141885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.100331 restraints weight = 6898.721| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.82 r_work: 0.2986 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6668 Z= 0.102 Angle : 0.465 5.818 9100 Z= 0.234 Chirality : 0.036 0.118 1120 Planarity : 0.004 0.050 1094 Dihedral : 7.735 72.785 1038 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.18 % Allowed : 16.04 % Favored : 80.78 % 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 are not related in a simple way. whole: 4.22 (0.29), residues: 812 helix: 3.09 (0.19), residues: 702 sheet: None (None), residues: 0 loop : 0.56 (0.59), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 97 TYR 0.013 0.001 TYR B 359 PHE 0.011 0.001 PHE B 99 TRP 0.010 0.001 TRP B 324 HIS 0.003 0.000 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 6668) covalent geometry : angle 0.46487 ( 9100) hydrogen bonds : bond 0.03640 ( 532) hydrogen bonds : angle 3.69462 ( 1578) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7676 (mm110) cc_final: 0.7417 (mm110) REVERT: A 181 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7031 (t80) REVERT: A 212 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7486 (mp) REVERT: A 214 MET cc_start: 0.8241 (mtm) cc_final: 0.8014 (mtp) REVERT: A 404 THR cc_start: 0.9069 (m) cc_final: 0.8824 (p) REVERT: B 71 GLN cc_start: 0.7624 (mm110) cc_final: 0.7341 (mm110) REVERT: B 214 MET cc_start: 0.8232 (mtm) cc_final: 0.7991 (mtp) REVERT: B 404 THR cc_start: 0.9090 (m) cc_final: 0.8849 (p) outliers start: 22 outliers final: 11 residues processed: 118 average time/residue: 0.5161 time to fit residues: 64.2597 Evaluate side-chains 117 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 403 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 41 optimal weight: 0.0870 chunk 69 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 58 optimal weight: 0.0670 chunk 46 optimal weight: 0.8980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN B 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.142050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.100307 restraints weight = 6931.056| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.82 r_work: 0.2984 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6668 Z= 0.103 Angle : 0.469 5.732 9100 Z= 0.236 Chirality : 0.037 0.118 1120 Planarity : 0.004 0.050 1094 Dihedral : 7.546 68.631 1038 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.75 % Allowed : 16.76 % Favored : 80.49 % 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 are not related in a simple way. whole: 4.26 (0.29), residues: 812 helix: 3.16 (0.19), residues: 698 sheet: None (None), residues: 0 loop : 0.36 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 260 TYR 0.009 0.001 TYR A 313 PHE 0.012 0.001 PHE A 99 TRP 0.010 0.001 TRP B 324 HIS 0.003 0.000 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 6668) covalent geometry : angle 0.46908 ( 9100) hydrogen bonds : bond 0.03635 ( 532) hydrogen bonds : angle 3.69301 ( 1578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2478.92 seconds wall clock time: 42 minutes 58.92 seconds (2578.92 seconds total)