Starting phenix.real_space_refine on Wed Sep 17 10:43:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7axz_11933/09_2025/7axz_11933.cif Found real_map, /net/cci-nas-00/data/ceres_data/7axz_11933/09_2025/7axz_11933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7axz_11933/09_2025/7axz_11933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7axz_11933/09_2025/7axz_11933.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7axz_11933/09_2025/7axz_11933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7axz_11933/09_2025/7axz_11933.map" } resolution = 3.2 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= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 5266 2.51 5 N 1389 2.21 5 O 1529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8225 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 4033 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 4192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4192 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 25, 'TRANS': 498} Chain breaks: 3 Time building chain proxies: 2.00, per 1000 atoms: 0.24 Number of scatterers: 8225 At special positions: 0 Unit cell: (97.464, 86.984, 119.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1529 8.00 N 1389 7.00 C 5266 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: 0.69 Conformation dependent library (CDL) restraints added in 405.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 34.2% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 58 through 77 Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 124 through 135 removed outlier: 3.532A pdb=" N MET A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 157 removed outlier: 4.238A pdb=" N VAL A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 196 removed outlier: 3.620A pdb=" N ALA A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 removed outlier: 3.563A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 330 through 334 Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 377 through 391 removed outlier: 3.625A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 468 Processing helix chain 'A' and resid 480 through 494 removed outlier: 3.680A pdb=" N GLN A 484 " --> pdb=" O ASN A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 519 Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 29 through 47 Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 87 through 94 removed outlier: 3.631A pdb=" N LEU B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 122 Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.540A pdb=" N LYS B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS B 156 " --> pdb=" O HIS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 217 Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.539A pdb=" N LEU B 221 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.707A pdb=" N LEU B 451 " --> pdb=" O THR B 447 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 500 removed outlier: 3.963A pdb=" N GLN B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 519 through 537 removed outlier: 3.776A pdb=" N THR B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) Proline residue: B 529 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 106 removed outlier: 6.364A pdb=" N VAL A 85 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP A 36 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA A 84 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU A 38 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE A 40 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N TYR A 88 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 42 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 41 " --> pdb=" O MET A 167 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS A 164 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASP A 201 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A 166 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 262 removed outlier: 4.731A pdb=" N PHE A 410 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 397 " --> pdb=" O MET A 348 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LEU A 345 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS A 260 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU A 347 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS A 262 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N GLY A 349 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 289 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 329 Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 376 Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 84 removed outlier: 6.459A pdb=" N LEU B 56 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N HIS B 82 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE B 54 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 8 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALA B 55 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 10 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL B 57 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 12 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE B 59 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N MET B 14 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 135 removed outlier: 6.232A pdb=" N ILE B 134 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE B 163 " --> pdb=" O TYR B 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 247 through 253 removed outlier: 5.461A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 316 Processing sheet with id=AB1, first strand: chain 'B' and resid 464 through 466 314 hydrogen bonds defined for protein. 855 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2676 1.34 - 1.46: 1370 1.46 - 1.57: 4273 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 8388 Sorted by residual: bond pdb=" CA THR A 472 " pdb=" CB THR A 472 " ideal model delta sigma weight residual 1.526 1.467 0.060 1.76e-02 3.23e+03 1.14e+01 bond pdb=" C ASP A 342 " pdb=" N PRO A 343 " ideal model delta sigma weight residual 1.334 1.305 0.029 1.11e-02 8.12e+03 6.68e+00 bond pdb=" CA TYR A 409 " pdb=" C TYR A 409 " ideal model delta sigma weight residual 1.526 1.499 0.027 1.36e-02 5.41e+03 3.84e+00 bond pdb=" C ARG B 271 " pdb=" N VAL B 272 " ideal model delta sigma weight residual 1.334 1.310 0.024 1.24e-02 6.50e+03 3.60e+00 bond pdb=" CB PRO A 438 " pdb=" CG PRO A 438 " ideal model delta sigma weight residual 1.492 1.398 0.094 5.00e-02 4.00e+02 3.56e+00 ... (remaining 8383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 10428 1.49 - 2.98: 736 2.98 - 4.47: 112 4.47 - 5.96: 23 5.96 - 7.45: 7 Bond angle restraints: 11306 Sorted by residual: angle pdb=" N LEU A 337 " pdb=" CA LEU A 337 " pdb=" C LEU A 337 " ideal model delta sigma weight residual 112.72 105.91 6.81 1.36e+00 5.41e-01 2.51e+01 angle pdb=" N ARG A 339 " pdb=" CA ARG A 339 " pdb=" CB ARG A 339 " ideal model delta sigma weight residual 109.51 116.70 -7.19 1.58e+00 4.01e-01 2.07e+01 angle pdb=" CG ARG A 339 " pdb=" CD ARG A 339 " pdb=" NE ARG A 339 " ideal model delta sigma weight residual 112.00 119.45 -7.45 2.20e+00 2.07e-01 1.15e+01 angle pdb=" CA LYS A 338 " pdb=" C LYS A 338 " pdb=" N ARG A 339 " ideal model delta sigma weight residual 116.84 122.56 -5.72 1.71e+00 3.42e-01 1.12e+01 angle pdb=" C GLN B 510 " pdb=" N HIS B 511 " pdb=" CA HIS B 511 " ideal model delta sigma weight residual 120.72 115.21 5.51 1.67e+00 3.59e-01 1.09e+01 ... (remaining 11301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4612 17.91 - 35.81: 468 35.81 - 53.72: 79 53.72 - 71.62: 11 71.62 - 89.53: 11 Dihedral angle restraints: 5181 sinusoidal: 2183 harmonic: 2998 Sorted by residual: dihedral pdb=" CA MET B 389 " pdb=" C MET B 389 " pdb=" N VAL B 390 " pdb=" CA VAL B 390 " ideal model delta harmonic sigma weight residual -180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA ASP A 341 " pdb=" C ASP A 341 " pdb=" N ASP A 342 " pdb=" CA ASP A 342 " ideal model delta harmonic sigma weight residual 180.00 152.83 27.17 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA GLU A 336 " pdb=" C GLU A 336 " pdb=" N LEU A 337 " pdb=" CA LEU A 337 " ideal model delta harmonic sigma weight residual 180.00 155.65 24.35 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 5178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 715 0.037 - 0.073: 368 0.073 - 0.110: 118 0.110 - 0.147: 43 0.147 - 0.183: 20 Chirality restraints: 1264 Sorted by residual: chirality pdb=" CA THR B 479 " pdb=" N THR B 479 " pdb=" C THR B 479 " pdb=" CB THR B 479 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CB VAL B 393 " pdb=" CA VAL B 393 " pdb=" CG1 VAL B 393 " pdb=" CG2 VAL B 393 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA ILE A 273 " pdb=" N ILE A 273 " pdb=" C ILE A 273 " pdb=" CB ILE A 273 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 1261 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 165 " 0.041 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO B 166 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 166 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 166 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 450 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.18e+00 pdb=" C GLN B 450 " -0.043 2.00e-02 2.50e+03 pdb=" O GLN B 450 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B 451 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 283 " 0.041 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO A 284 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " 0.033 5.00e-02 4.00e+02 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 88 2.51 - 3.11: 6623 3.11 - 3.70: 12008 3.70 - 4.30: 17374 4.30 - 4.90: 29268 Nonbonded interactions: 65361 Sorted by model distance: nonbonded pdb=" OH TYR A 274 " pdb=" OE2 GLU A 371 " model vdw 1.911 3.040 nonbonded pdb=" OE1 GLU A 491 " pdb=" OH TYR B 316 " model vdw 1.987 3.040 nonbonded pdb=" OH TYR A 409 " pdb=" OE1 GLN B 269 " model vdw 2.033 3.040 nonbonded pdb=" OE1 GLN B 509 " pdb=" NE2 HIS B 511 " model vdw 2.097 3.120 nonbonded pdb=" NH2 ARG A 325 " pdb=" O ALA B 498 " model vdw 2.128 3.120 ... (remaining 65356 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.570 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.100 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 : 0.009 0.094 8388 Z= 0.384 Angle : 0.871 7.448 11306 Z= 0.493 Chirality : 0.052 0.183 1264 Planarity : 0.006 0.063 1456 Dihedral : 14.876 89.529 3227 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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 aren not related in a simple way. whole: -2.73 (0.25), residues: 1011 helix: -0.89 (0.27), residues: 315 sheet: -2.20 (0.40), residues: 155 loop : -2.29 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 353 TYR 0.028 0.003 TYR A 400 PHE 0.020 0.003 PHE A 471 TRP 0.027 0.003 TRP B 276 HIS 0.006 0.002 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00900 ( 8388) covalent geometry : angle 0.87051 (11306) hydrogen bonds : bond 0.13737 ( 314) hydrogen bonds : angle 7.67328 ( 855) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.7074 (mmt) cc_final: 0.6819 (mmt) REVERT: A 265 LYS cc_start: 0.7524 (mtpt) cc_final: 0.7168 (mmtt) REVERT: B 40 MET cc_start: 0.7512 (ttp) cc_final: 0.7291 (ttm) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1039 time to fit residues: 13.5365 Evaluate side-chains 61 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS A 426 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN B 527 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.113167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.091913 restraints weight = 19411.268| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.01 r_work: 0.3501 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8388 Z= 0.181 Angle : 0.642 8.772 11306 Z= 0.329 Chirality : 0.045 0.156 1264 Planarity : 0.006 0.056 1456 Dihedral : 5.315 24.813 1094 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.76 % Allowed : 6.61 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.26), residues: 1011 helix: 0.08 (0.29), residues: 314 sheet: -1.49 (0.40), residues: 166 loop : -1.98 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 339 TYR 0.014 0.001 TYR A 400 PHE 0.019 0.002 PHE A 487 TRP 0.024 0.003 TRP B 247 HIS 0.005 0.001 HIS B 382 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 8388) covalent geometry : angle 0.64247 (11306) hydrogen bonds : bond 0.04194 ( 314) hydrogen bonds : angle 5.96858 ( 855) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8458 (mp) cc_final: 0.8124 (mt) REVERT: A 102 ILE cc_start: 0.8738 (mm) cc_final: 0.8436 (mt) REVERT: A 265 LYS cc_start: 0.7803 (mtpt) cc_final: 0.7311 (mmtt) REVERT: B 210 MET cc_start: 0.8416 (ttm) cc_final: 0.8047 (tmm) REVERT: B 474 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.5651 (pm20) outliers start: 7 outliers final: 1 residues processed: 87 average time/residue: 0.0922 time to fit residues: 11.4147 Evaluate side-chains 71 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 474 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 0.4980 chunk 59 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 28 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 450 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.115279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.094155 restraints weight = 19470.663| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 3.03 r_work: 0.3558 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8388 Z= 0.107 Angle : 0.534 7.755 11306 Z= 0.271 Chirality : 0.042 0.146 1264 Planarity : 0.004 0.057 1456 Dihedral : 4.593 18.637 1094 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.98 % Allowed : 9.75 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.26), residues: 1011 helix: 0.55 (0.29), residues: 322 sheet: -1.16 (0.38), residues: 172 loop : -1.58 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 258 TYR 0.011 0.001 TYR A 400 PHE 0.022 0.001 PHE B 18 TRP 0.011 0.001 TRP B 247 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8388) covalent geometry : angle 0.53448 (11306) hydrogen bonds : bond 0.03441 ( 314) hydrogen bonds : angle 5.39059 ( 855) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8381 (mp) cc_final: 0.8051 (mt) REVERT: A 102 ILE cc_start: 0.8692 (mm) cc_final: 0.8393 (mt) REVERT: A 265 LYS cc_start: 0.7872 (mtpt) cc_final: 0.7342 (mmtt) REVERT: A 446 MET cc_start: 0.8154 (mtm) cc_final: 0.7780 (mtm) REVERT: A 498 MET cc_start: 0.6590 (ttm) cc_final: 0.5910 (tpp) REVERT: B 14 MET cc_start: 0.8467 (ttp) cc_final: 0.8243 (ttp) REVERT: B 210 MET cc_start: 0.8327 (ttm) cc_final: 0.7935 (tmm) outliers start: 9 outliers final: 2 residues processed: 91 average time/residue: 0.0768 time to fit residues: 10.5015 Evaluate side-chains 80 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 16 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS B 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.110958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.089579 restraints weight = 19677.198| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 3.00 r_work: 0.3461 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8388 Z= 0.258 Angle : 0.668 11.681 11306 Z= 0.335 Chirality : 0.045 0.144 1264 Planarity : 0.005 0.061 1456 Dihedral : 5.055 20.412 1094 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.84 % Allowed : 12.13 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.26), residues: 1011 helix: 0.09 (0.28), residues: 323 sheet: -1.22 (0.39), residues: 166 loop : -1.68 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 404 TYR 0.015 0.002 TYR A 400 PHE 0.042 0.002 PHE B 59 TRP 0.030 0.003 TRP B 247 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00611 ( 8388) covalent geometry : angle 0.66823 (11306) hydrogen bonds : bond 0.04058 ( 314) hydrogen bonds : angle 5.59190 ( 855) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8841 (mm) cc_final: 0.8535 (mt) REVERT: A 265 LYS cc_start: 0.8046 (mtpt) cc_final: 0.7445 (mmtt) REVERT: B 15 ASP cc_start: 0.7335 (t70) cc_final: 0.7014 (t0) outliers start: 17 outliers final: 10 residues processed: 86 average time/residue: 0.0801 time to fit residues: 10.2195 Evaluate side-chains 80 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 414 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.110190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.088649 restraints weight = 19467.251| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.97 r_work: 0.3465 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8388 Z= 0.230 Angle : 0.639 12.208 11306 Z= 0.319 Chirality : 0.044 0.141 1264 Planarity : 0.005 0.061 1456 Dihedral : 4.991 20.373 1094 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.06 % Allowed : 13.87 % Favored : 84.07 % 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 aren not related in a simple way. whole: -1.49 (0.26), residues: 1011 helix: 0.13 (0.28), residues: 323 sheet: -1.20 (0.40), residues: 166 loop : -1.64 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 404 TYR 0.014 0.002 TYR A 400 PHE 0.026 0.002 PHE B 345 TRP 0.038 0.003 TRP B 247 HIS 0.004 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 8388) covalent geometry : angle 0.63948 (11306) hydrogen bonds : bond 0.03885 ( 314) hydrogen bonds : angle 5.54080 ( 855) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8845 (mm) cc_final: 0.8546 (mt) REVERT: A 265 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7494 (mmtt) REVERT: B 15 ASP cc_start: 0.7284 (t70) cc_final: 0.6971 (t0) REVERT: B 474 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.5629 (pm20) outliers start: 19 outliers final: 10 residues processed: 87 average time/residue: 0.0767 time to fit residues: 10.1721 Evaluate side-chains 84 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 480 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 94 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.113685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.092170 restraints weight = 19096.746| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.97 r_work: 0.3516 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8388 Z= 0.127 Angle : 0.560 9.902 11306 Z= 0.278 Chirality : 0.042 0.140 1264 Planarity : 0.005 0.061 1456 Dihedral : 4.553 17.726 1094 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.73 % Allowed : 14.30 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.26), residues: 1011 helix: 0.64 (0.29), residues: 318 sheet: -1.25 (0.37), residues: 183 loop : -1.28 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 497 TYR 0.011 0.001 TYR A 400 PHE 0.023 0.001 PHE B 59 TRP 0.041 0.003 TRP B 247 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8388) covalent geometry : angle 0.56049 (11306) hydrogen bonds : bond 0.03405 ( 314) hydrogen bonds : angle 5.26073 ( 855) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8907 (mm) cc_final: 0.8609 (mt) REVERT: A 265 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7459 (mmtt) REVERT: B 15 ASP cc_start: 0.7055 (t70) cc_final: 0.6798 (t0) REVERT: B 206 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7918 (mm-30) REVERT: B 474 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.5531 (pm20) outliers start: 16 outliers final: 9 residues processed: 93 average time/residue: 0.0852 time to fit residues: 11.6499 Evaluate side-chains 86 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 474 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 46 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.109160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.087220 restraints weight = 19684.399| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.04 r_work: 0.3435 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 8388 Z= 0.319 Angle : 0.726 12.634 11306 Z= 0.362 Chirality : 0.046 0.147 1264 Planarity : 0.005 0.061 1456 Dihedral : 5.197 21.512 1094 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.17 % Allowed : 14.73 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.26), residues: 1011 helix: -0.10 (0.27), residues: 329 sheet: -1.24 (0.38), residues: 179 loop : -1.68 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 318 TYR 0.016 0.002 TYR A 400 PHE 0.028 0.003 PHE B 345 TRP 0.041 0.004 TRP B 247 HIS 0.005 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00757 ( 8388) covalent geometry : angle 0.72624 (11306) hydrogen bonds : bond 0.04252 ( 314) hydrogen bonds : angle 5.64963 ( 855) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8879 (mm) cc_final: 0.8627 (mt) REVERT: A 265 LYS cc_start: 0.8177 (mtpt) cc_final: 0.7562 (mmtt) REVERT: B 474 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.5627 (pm20) outliers start: 20 outliers final: 15 residues processed: 90 average time/residue: 0.0826 time to fit residues: 11.0227 Evaluate side-chains 82 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 480 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.114662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.093393 restraints weight = 19064.031| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.97 r_work: 0.3530 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8388 Z= 0.113 Angle : 0.566 10.578 11306 Z= 0.282 Chirality : 0.041 0.140 1264 Planarity : 0.005 0.062 1456 Dihedral : 4.500 18.293 1094 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.84 % Allowed : 15.71 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.26), residues: 1011 helix: 0.83 (0.29), residues: 317 sheet: -1.19 (0.39), residues: 173 loop : -1.28 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 489 TYR 0.010 0.001 TYR A 400 PHE 0.036 0.001 PHE B 59 TRP 0.023 0.002 TRP B 247 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8388) covalent geometry : angle 0.56568 (11306) hydrogen bonds : bond 0.03297 ( 314) hydrogen bonds : angle 5.23425 ( 855) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8872 (mm) cc_final: 0.8576 (mt) REVERT: A 265 LYS cc_start: 0.7993 (mtpt) cc_final: 0.7520 (mmtt) REVERT: B 161 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8974 (tp) REVERT: B 247 TRP cc_start: 0.7043 (t60) cc_final: 0.6801 (t60) REVERT: B 474 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.5466 (pm20) outliers start: 17 outliers final: 10 residues processed: 97 average time/residue: 0.0806 time to fit residues: 11.6245 Evaluate side-chains 88 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 474 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 39 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 12 optimal weight: 0.0070 chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.114560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.092795 restraints weight = 19460.144| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.09 r_work: 0.3530 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8388 Z= 0.114 Angle : 0.568 9.697 11306 Z= 0.279 Chirality : 0.041 0.138 1264 Planarity : 0.005 0.063 1456 Dihedral : 4.330 18.276 1094 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.73 % Allowed : 16.03 % 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 aren not related in a simple way. whole: -0.70 (0.27), residues: 1011 helix: 1.07 (0.29), residues: 316 sheet: -1.10 (0.39), residues: 173 loop : -1.19 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 318 TYR 0.010 0.001 TYR A 400 PHE 0.032 0.002 PHE B 59 TRP 0.020 0.002 TRP B 247 HIS 0.003 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8388) covalent geometry : angle 0.56815 (11306) hydrogen bonds : bond 0.03245 ( 314) hydrogen bonds : angle 5.10027 ( 855) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 SER cc_start: 0.8632 (t) cc_final: 0.8347 (m) REVERT: A 102 ILE cc_start: 0.8858 (mm) cc_final: 0.8565 (mt) REVERT: A 265 LYS cc_start: 0.8019 (mtpt) cc_final: 0.7546 (mmtt) REVERT: B 247 TRP cc_start: 0.7044 (t60) cc_final: 0.6776 (t60) REVERT: B 474 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.5391 (pm20) outliers start: 16 outliers final: 10 residues processed: 92 average time/residue: 0.0751 time to fit residues: 10.5310 Evaluate side-chains 86 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 480 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 16 optimal weight: 7.9990 chunk 78 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 0.0670 chunk 96 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.2524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.114912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.093576 restraints weight = 19075.132| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.97 r_work: 0.3535 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8388 Z= 0.117 Angle : 0.561 9.515 11306 Z= 0.276 Chirality : 0.041 0.139 1264 Planarity : 0.004 0.063 1456 Dihedral : 4.249 18.638 1094 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.19 % Allowed : 16.79 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.27), residues: 1011 helix: 1.15 (0.29), residues: 317 sheet: -1.06 (0.39), residues: 173 loop : -1.15 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 318 TYR 0.010 0.001 TYR A 400 PHE 0.032 0.002 PHE B 107 TRP 0.019 0.002 TRP B 247 HIS 0.002 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8388) covalent geometry : angle 0.56069 (11306) hydrogen bonds : bond 0.03176 ( 314) hydrogen bonds : angle 5.04853 ( 855) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8779 (mm) cc_final: 0.8452 (mt) REVERT: A 265 LYS cc_start: 0.8021 (mtpt) cc_final: 0.7550 (mmtt) REVERT: B 210 MET cc_start: 0.8496 (ttm) cc_final: 0.7972 (tmm) REVERT: B 474 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.5310 (pm20) outliers start: 11 outliers final: 9 residues processed: 84 average time/residue: 0.0697 time to fit residues: 9.0896 Evaluate side-chains 85 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 480 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.112724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.090976 restraints weight = 19330.730| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.04 r_work: 0.3488 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8388 Z= 0.186 Angle : 0.618 10.465 11306 Z= 0.302 Chirality : 0.043 0.173 1264 Planarity : 0.005 0.062 1456 Dihedral : 4.495 19.033 1094 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.84 % Allowed : 16.79 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.26), residues: 1011 helix: 0.74 (0.28), residues: 328 sheet: -1.12 (0.39), residues: 174 loop : -1.31 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 318 TYR 0.013 0.002 TYR B 395 PHE 0.037 0.002 PHE B 107 TRP 0.039 0.003 TRP B 247 HIS 0.004 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 8388) covalent geometry : angle 0.61834 (11306) hydrogen bonds : bond 0.03517 ( 314) hydrogen bonds : angle 5.18984 ( 855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1910.57 seconds wall clock time: 33 minutes 38.64 seconds (2018.64 seconds total)