Starting phenix.real_space_refine on Thu Jul 2 04:36:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vsq_65304/07_2026/9vsq_65304_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vsq_65304/07_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_65304/07_2026/9vsq_65304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vsq_65304/07_2026/9vsq_65304.map" model { file = "/net/cci-nas-00/data/ceres_data/9vsq_65304/07_2026/9vsq_65304_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vsq_65304/07_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 55 Ad-hoc single atom residues: {' K': 4} Unusual residues: {'CLR': 1, 'YN9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 4 Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 55 Ad-hoc single atom residues: {' K': 3} Unusual residues: {'CLR': 1, 'YN9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 3 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: 1.36, per 1000 atoms: 0.21 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: 0.58 Conformation dependent library (CDL) restraints added in 265.0 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: 0.21 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: 0.71 Time building geometry restraints manager: 0.67 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.110 Find NCS groups from input model: 0.070 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:5.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 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/Z covalent geometry : bond 0.00460 / 0.22 ( 6668) covalent geometry : angle 0.61157 / 0.33 ( 9100) hydrogen bonds : bond 0.11301 / 7.21 ( 532) hydrogen bonds : angle 4.98242 / 3.64 ( 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 : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 121 average time/residue: 0.4734 time to fit residues: 60.1206 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 : 0.145 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3611 r_free = 0.3611 target = 0.137320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.095072 restraints weight = 6927.629| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.85 r_work: 0.2906 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.0864 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= 0.139 Angle : 0.555 7.881 9100 Z= 0.278 Chirality : 0.039 0.124 1120 Planarity : 0.005 0.050 1094 Dihedral : 9.747 87.762 1042 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.18 % Allowed : 13.15 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.40 (0.29), residues: 812 helix: 2.49 (0.19), residues: 720 sheet: None (None), residues: 0 loop : 0.22 (0.64), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.019 0.002 TYR A 359 PHE 0.011 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/Z covalent geometry : bond 0.00303 / 0.14 ( 6668) covalent geometry : angle 0.55514 / 0.28 ( 9100) hydrogen bonds : bond 0.05057 / 3.42 ( 532) hydrogen bonds : angle 4.09858 / 2.94 ( 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 139 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7692 (mm110) cc_final: 0.7478 (mm110) REVERT: A 181 TYR cc_start: 0.7947 (m-80) cc_final: 0.6957 (t80) REVERT: A 212 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7509 (mp) REVERT: B 71 GLN cc_start: 0.7685 (mm110) cc_final: 0.7448 (mm110) REVERT: B 181 TYR cc_start: 0.7942 (m-80) cc_final: 0.6894 (t80) REVERT: B 212 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7526 (mp) outliers start: 22 outliers final: 6 residues processed: 128 average time/residue: 0.3929 time to fit residues: 53.2671 Evaluate side-chains 120 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 LEU 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 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: 3.9990 chunk 3 optimal weight: 9.9990 chunk 73 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.138392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.096132 restraints weight = 6897.136| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.84 r_work: 0.2921 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6668 Z= 0.131 Angle : 0.520 6.959 9100 Z= 0.260 Chirality : 0.039 0.121 1120 Planarity : 0.005 0.050 1094 Dihedral : 8.828 86.016 1038 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.89 % Allowed : 14.88 % 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 : -0.08 (0.59), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.016 0.002 TYR A 359 PHE 0.012 0.001 PHE B 99 TRP 0.011 0.002 TRP B 324 HIS 0.002 0.000 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 6668) covalent geometry : angle 0.51980 / 0.26 ( 9100) hydrogen bonds : bond 0.04538 / 3.09 ( 532) hydrogen bonds : angle 3.91281 / 2.81 ( 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 130 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7665 (mm110) cc_final: 0.7434 (mm110) REVERT: A 212 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7463 (mp) REVERT: B 71 GLN cc_start: 0.7676 (mm110) cc_final: 0.7427 (mm110) REVERT: B 212 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7494 (mp) outliers start: 20 outliers final: 9 residues processed: 115 average time/residue: 0.3551 time to fit residues: 43.2265 Evaluate side-chains 114 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 339 ARG 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: 0.0070 chunk 77 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.097414 restraints weight = 6960.637| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.85 r_work: 0.2941 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1449 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= 0.116 Angle : 0.496 7.345 9100 Z= 0.247 Chirality : 0.038 0.116 1120 Planarity : 0.005 0.051 1094 Dihedral : 8.507 85.231 1038 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.18 % Allowed : 15.46 % Favored : 81.36 % 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: 3.64 (0.29), residues: 812 helix: 2.72 (0.19), residues: 710 sheet: None (None), residues: 0 loop : -0.02 (0.58), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 375 TYR 0.019 0.002 TYR A 359 PHE 0.011 0.001 PHE A 99 TRP 0.010 0.001 TRP B 324 HIS 0.002 0.000 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 6668) covalent geometry : angle 0.49551 / 0.25 ( 9100) hydrogen bonds : bond 0.04210 / 2.87 ( 532) hydrogen bonds : angle 3.81662 / 2.74 ( 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 137 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7670 (mm110) cc_final: 0.7415 (mm110) REVERT: A 181 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.6983 (t80) REVERT: A 212 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7444 (mp) REVERT: B 71 GLN cc_start: 0.7665 (mm110) cc_final: 0.7386 (mm110) REVERT: B 181 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.6934 (t80) REVERT: B 212 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7491 (mp) outliers start: 22 outliers final: 11 residues processed: 122 average time/residue: 0.3728 time to fit residues: 48.2407 Evaluate side-chains 119 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 339 ARG Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 426 TYR 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 426 TYR 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: 4.9990 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3638 r_free = 0.3638 target = 0.139352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.097053 restraints weight = 7029.800| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.85 r_work: 0.2938 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6668 Z= 0.119 Angle : 0.489 6.693 9100 Z= 0.246 Chirality : 0.038 0.116 1120 Planarity : 0.005 0.051 1094 Dihedral : 8.420 84.382 1038 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.89 % Allowed : 16.76 % Favored : 80.35 % 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: 3.73 (0.29), residues: 812 helix: 2.80 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -0.10 (0.58), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.019 0.002 TYR B 359 PHE 0.013 0.001 PHE A 99 TRP 0.010 0.001 TRP A 324 HIS 0.002 0.000 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 6668) covalent geometry : angle 0.48919 / 0.25 ( 9100) hydrogen bonds : bond 0.04199 / 2.86 ( 532) hydrogen bonds : angle 3.79422 / 2.72 ( 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 132 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7680 (mm110) cc_final: 0.7425 (mm110) REVERT: A 212 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7488 (mp) REVERT: A 214 MET cc_start: 0.8285 (mtm) cc_final: 0.8010 (mtp) REVERT: B 71 GLN cc_start: 0.7669 (mm110) cc_final: 0.7388 (mm110) REVERT: B 191 GLN cc_start: 0.8343 (tt0) cc_final: 0.8025 (tt0) REVERT: B 212 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7512 (mp) REVERT: B 214 MET cc_start: 0.8290 (mtm) cc_final: 0.8025 (mtp) outliers start: 20 outliers final: 9 residues processed: 121 average time/residue: 0.3777 time to fit residues: 48.3824 Evaluate side-chains 117 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 426 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 399 LEU Chi-restraints excluded: chain B residue 403 GLU 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: 1.9990 chunk 46 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.139750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.097323 restraints weight = 7017.890| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.85 r_work: 0.2944 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6668 Z= 0.117 Angle : 0.486 6.326 9100 Z= 0.245 Chirality : 0.038 0.117 1120 Planarity : 0.004 0.050 1094 Dihedral : 8.328 83.010 1038 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 4.05 % Allowed : 15.32 % 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: 3.80 (0.29), residues: 812 helix: 2.83 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 0.04 (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 0.012 0.001 PHE A 99 TRP 0.010 0.001 TRP B 324 HIS 0.002 0.000 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 6668) covalent geometry : angle 0.48595 / 0.25 ( 9100) hydrogen bonds : bond 0.04123 / 2.82 ( 532) hydrogen bonds : angle 3.76754 / 2.71 ( 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 136 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7674 (mm110) cc_final: 0.7415 (mm110) REVERT: A 181 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.7026 (t80) REVERT: A 212 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7433 (mp) REVERT: A 214 MET cc_start: 0.8314 (mtm) cc_final: 0.8024 (mtp) REVERT: B 71 GLN cc_start: 0.7666 (mm110) cc_final: 0.7384 (mm110) REVERT: B 181 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.6966 (t80) REVERT: B 212 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7490 (mp) REVERT: B 214 MET cc_start: 0.8301 (mtm) cc_final: 0.8037 (mtp) outliers start: 28 outliers final: 13 residues processed: 120 average time/residue: 0.3427 time to fit residues: 43.6392 Evaluate side-chains 117 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 339 ARG 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 373 LEU 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: 0.6980 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3641 r_free = 0.3641 target = 0.139446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.097233 restraints weight = 6956.449| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.85 r_work: 0.2937 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1736 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= 0.120 Angle : 0.485 6.102 9100 Z= 0.245 Chirality : 0.038 0.119 1120 Planarity : 0.004 0.050 1094 Dihedral : 8.249 81.482 1038 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.03 % Allowed : 16.47 % 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: 3.82 (0.29), residues: 812 helix: 2.81 (0.19), residues: 710 sheet: None (None), residues: 0 loop : 0.30 (0.60), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 309 TYR 0.021 0.002 TYR B 359 PHE 0.014 0.001 PHE A 99 TRP 0.010 0.001 TRP B 324 HIS 0.002 0.000 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 6668) covalent geometry : angle 0.48499 / 0.25 ( 9100) hydrogen bonds : bond 0.04118 / 2.81 ( 532) hydrogen bonds : angle 3.76419 / 2.71 ( 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: 21 poor density : 104 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7669 (mm110) cc_final: 0.7405 (mm110) REVERT: A 212 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7439 (mp) REVERT: A 214 MET cc_start: 0.8302 (mtm) cc_final: 0.8081 (mtp) REVERT: B 71 GLN cc_start: 0.7651 (mm110) cc_final: 0.7370 (mm110) REVERT: B 181 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.6974 (t80) REVERT: B 212 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7458 (mp) REVERT: B 214 MET cc_start: 0.8288 (mtm) cc_final: 0.7995 (mtp) outliers start: 21 outliers final: 13 residues processed: 112 average time/residue: 0.3780 time to fit residues: 44.9370 Evaluate side-chains 116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 339 ARG 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 339 ARG Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 373 LEU 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: 5.9990 chunk 80 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3643 r_free = 0.3643 target = 0.139502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.097292 restraints weight = 6980.300| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.84 r_work: 0.2941 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1777 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= 0.117 Angle : 0.484 5.943 9100 Z= 0.244 Chirality : 0.038 0.118 1120 Planarity : 0.004 0.050 1094 Dihedral : 8.128 79.436 1038 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.60 % Allowed : 16.76 % 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: 3.87 (0.29), residues: 812 helix: 2.83 (0.19), residues: 710 sheet: None (None), residues: 0 loop : 0.40 (0.61), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 260 TYR 0.020 0.002 TYR A 359 PHE 0.012 0.001 PHE A 99 TRP 0.010 0.001 TRP B 324 HIS 0.002 0.000 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 6668) covalent geometry : angle 0.48367 / 0.24 ( 9100) hydrogen bonds : bond 0.04075 / 2.78 ( 532) hydrogen bonds : angle 3.75323 / 2.70 ( 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 123 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7677 (mm110) cc_final: 0.7407 (mm110) REVERT: A 181 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7003 (t80) REVERT: A 212 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7451 (mp) REVERT: A 214 MET cc_start: 0.8310 (mtm) cc_final: 0.8087 (mtp) REVERT: B 71 GLN cc_start: 0.7656 (mm110) cc_final: 0.7371 (mm110) REVERT: B 181 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.6979 (t80) REVERT: B 212 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7441 (mp) REVERT: B 214 MET cc_start: 0.8269 (mtm) cc_final: 0.8047 (mtp) REVERT: B 404 THR cc_start: 0.9089 (m) cc_final: 0.8803 (p) REVERT: B 450 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7877 (mm) outliers start: 18 outliers final: 10 residues processed: 111 average time/residue: 0.3832 time to fit residues: 45.0957 Evaluate side-chains 116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 67 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 0.0070 chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3668 r_free = 0.3668 target = 0.141497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.099351 restraints weight = 6998.160| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.85 r_work: 0.2968 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1940 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= 0.103 Angle : 0.470 5.838 9100 Z= 0.236 Chirality : 0.037 0.117 1120 Planarity : 0.004 0.050 1094 Dihedral : 7.911 75.974 1038 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.03 % Allowed : 16.33 % 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: 4.13 (0.29), residues: 812 helix: 3.08 (0.19), residues: 698 sheet: None (None), residues: 0 loop : 0.30 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 260 TYR 0.014 0.001 TYR B 359 PHE 0.011 0.001 PHE A 99 TRP 0.010 0.001 TRP A 324 HIS 0.002 0.000 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 6668) covalent geometry : angle 0.46974 / 0.24 ( 9100) hydrogen bonds : bond 0.03734 / 2.55 ( 532) hydrogen bonds : angle 3.72181 / 2.68 ( 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 127 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7663 (mm110) cc_final: 0.7399 (mm110) REVERT: A 212 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7429 (mp) REVERT: A 214 MET cc_start: 0.8230 (mtm) cc_final: 0.8008 (mtp) REVERT: B 71 GLN cc_start: 0.7622 (mm110) cc_final: 0.7335 (mm110) REVERT: B 181 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.6972 (t80) REVERT: B 212 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7421 (mp) REVERT: B 214 MET cc_start: 0.8238 (mtm) cc_final: 0.8002 (mtp) REVERT: B 404 THR cc_start: 0.9079 (m) cc_final: 0.8794 (p) outliers start: 21 outliers final: 12 residues processed: 115 average time/residue: 0.4041 time to fit residues: 49.0364 Evaluate side-chains 114 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 339 ARG 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 373 LEU 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: 0.6980 chunk 34 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 70 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3662 r_free = 0.3662 target = 0.140847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.099436 restraints weight = 6848.022| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.81 r_work: 0.2963 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2006 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= 0.107 Angle : 0.473 5.814 9100 Z= 0.238 Chirality : 0.037 0.117 1120 Planarity : 0.004 0.050 1094 Dihedral : 7.715 71.918 1038 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.75 % Allowed : 16.91 % Favored : 80.35 % 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: 4.16 (0.29), residues: 812 helix: 3.05 (0.19), residues: 702 sheet: None (None), residues: 0 loop : 0.53 (0.59), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 260 TYR 0.017 0.001 TYR A 359 PHE 0.012 0.001 PHE A 99 TRP 0.010 0.001 TRP A 324 HIS 0.002 0.000 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 6668) covalent geometry : angle 0.47292 / 0.24 ( 9100) hydrogen bonds : bond 0.03823 / 2.62 ( 532) hydrogen bonds : angle 3.70199 / 2.66 ( 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 121 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 GLN cc_start: 0.7674 (mm110) cc_final: 0.7411 (mm110) REVERT: A 212 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7460 (mp) REVERT: A 214 MET cc_start: 0.8258 (mtm) cc_final: 0.8014 (mtp) REVERT: B 71 GLN cc_start: 0.7621 (mm110) cc_final: 0.7331 (mm110) REVERT: B 181 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.6987 (t80) REVERT: B 214 MET cc_start: 0.8253 (mtm) cc_final: 0.8015 (mtp) REVERT: B 404 THR cc_start: 0.9074 (m) cc_final: 0.8831 (p) outliers start: 19 outliers final: 12 residues processed: 111 average time/residue: 0.3975 time to fit residues: 46.4571 Evaluate side-chains 117 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 339 ARG 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 218 ILE Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 373 LEU 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: 0.9980 chunk 64 optimal weight: 0.0020 chunk 56 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3629 r_free = 0.3629 target = 0.138059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.095954 restraints weight = 6892.592| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.82 r_work: 0.2917 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1895 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= 0.141 Angle : 0.508 5.848 9100 Z= 0.256 Chirality : 0.039 0.125 1120 Planarity : 0.005 0.050 1094 Dihedral : 7.755 70.554 1038 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.60 % Allowed : 17.05 % Favored : 80.35 % 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: 4.01 (0.29), residues: 812 helix: 2.96 (0.19), residues: 696 sheet: None (None), residues: 0 loop : 0.58 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 35 TYR 0.017 0.002 TYR B 359 PHE 0.014 0.001 PHE A 99 TRP 0.010 0.002 TRP B 324 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 6668) covalent geometry : angle 0.50816 / 0.26 ( 9100) hydrogen bonds : bond 0.04389 / 3.00 ( 532) hydrogen bonds : angle 3.76847 / 2.71 ( 1578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1816.35 seconds wall clock time: 31 minutes 38.35 seconds (1898.35 seconds total)