Starting phenix.real_space_refine on Wed Mar 12 01:51:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b0p_15791/03_2025/8b0p_15791.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b0p_15791/03_2025/8b0p_15791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b0p_15791/03_2025/8b0p_15791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b0p_15791/03_2025/8b0p_15791.map" model { file = "/net/cci-nas-00/data/ceres_data/8b0p_15791/03_2025/8b0p_15791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b0p_15791/03_2025/8b0p_15791.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3779 atoms to isotropic. 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 14 5.16 5 C 2652 2.51 5 N 655 2.21 5 O 695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4016 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3911 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 36, 'TRANS': 468} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IG7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'IG7:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.48, per 1000 atoms: 0.87 Number of scatterers: 4016 At special positions: 0 Unit cell: (57.82, 83.426, 85.904, 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 14 16.00 O 695 8.00 N 655 7.00 C 2652 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 537.3 milliseconds 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB SER B 2 " pdb=" CB LYS B 3 " Number of C-beta restraints generated: 936 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 4 sheets defined 55.3% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 9 through 24 removed outlier: 3.737A pdb=" N LEU A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 28 removed outlier: 3.544A pdb=" N PHE A 28 " --> pdb=" O THR A 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 25 through 28' Processing helix chain 'A' and resid 33 through 48 removed outlier: 3.998A pdb=" N ALA A 37 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 38 " --> pdb=" O TRP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 69 Processing helix chain 'A' and resid 74 through 82 removed outlier: 3.904A pdb=" N SER A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 116 removed outlier: 4.179A pdb=" N TYR A 104 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 126 through 140 removed outlier: 3.795A pdb=" N ALA A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 168 through 190 removed outlier: 3.572A pdb=" N ILE A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 204 removed outlier: 4.053A pdb=" N LEU A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'A' and resid 218 through 221 Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.506A pdb=" N TRP A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 254 removed outlier: 4.140A pdb=" N ASN A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 277 through 292 Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 392 through 400 Processing helix chain 'A' and resid 420 through 437 removed outlier: 3.661A pdb=" N ARG A 432 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 487 Processing helix chain 'A' and resid 488 through 507 Processing sheet with id=AA1, first strand: chain 'A' and resid 215 through 216 Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 273 removed outlier: 4.020A pdb=" N VAL A 300 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASP A 272 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ALA A 302 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 273 removed outlier: 4.020A pdb=" N VAL A 300 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASP A 272 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ALA A 302 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE A 263 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N GLY A 298 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 262 " --> pdb=" O GLN A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 375 through 376 removed outlier: 6.543A pdb=" N GLU A 381 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU A 408 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N THR A 383 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE A 410 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA A 385 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU A 407 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N SER A 443 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR A 409 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 451 " --> pdb=" O GLN A 459 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 558 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: 1.29 Time building geometry restraints manager: 1.28 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: 649 1.32 - 1.45: 1103 1.45 - 1.57: 2348 1.57 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 4126 Sorted by residual: bond pdb=" C45 IG7 B 1 " pdb=" C46 IG7 B 1 " ideal model delta sigma weight residual 1.538 1.497 0.041 2.00e-02 2.50e+03 4.30e+00 bond pdb=" C03 IG7 B 1 " pdb=" C04 IG7 B 1 " ideal model delta sigma weight residual 1.535 1.494 0.041 2.00e-02 2.50e+03 4.11e+00 bond pdb=" C42 IG7 B 1 " pdb=" O43 IG7 B 1 " ideal model delta sigma weight residual 1.428 1.458 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" C14 IG7 B 1 " pdb=" C15 IG7 B 1 " ideal model delta sigma weight residual 1.534 1.506 0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C22 IG7 B 1 " pdb=" C23 IG7 B 1 " ideal model delta sigma weight residual 1.520 1.494 0.026 2.00e-02 2.50e+03 1.63e+00 ... (remaining 4121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 5504 1.50 - 3.01: 83 3.01 - 4.51: 27 4.51 - 6.02: 7 6.02 - 7.52: 2 Bond angle restraints: 5623 Sorted by residual: angle pdb=" O LYS B 6 " pdb=" C LYS B 6 " pdb=" OXT LYS B 6 " ideal model delta sigma weight residual 118.00 125.52 -7.52 3.00e+00 1.11e-01 6.28e+00 angle pdb=" N ILE A 390 " pdb=" CA ILE A 390 " pdb=" C ILE A 390 " ideal model delta sigma weight residual 113.07 109.73 3.34 1.36e+00 5.41e-01 6.02e+00 angle pdb=" N LYS B 6 " pdb=" CA LYS B 6 " pdb=" CB LYS B 6 " ideal model delta sigma weight residual 110.50 114.14 -3.64 1.70e+00 3.46e-01 4.58e+00 angle pdb=" C42 IG7 B 1 " pdb=" C41 IG7 B 1 " pdb=" S40 IG7 B 1 " ideal model delta sigma weight residual 118.03 112.48 5.55 3.00e+00 1.11e-01 3.42e+00 angle pdb=" N LYS B 4 " pdb=" CA LYS B 4 " pdb=" CB LYS B 4 " ideal model delta sigma weight residual 110.49 113.59 -3.10 1.69e+00 3.50e-01 3.37e+00 ... (remaining 5618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 2412 35.83 - 71.66: 22 71.66 - 107.49: 6 107.49 - 143.32: 0 143.32 - 179.15: 1 Dihedral angle restraints: 2441 sinusoidal: 980 harmonic: 1461 Sorted by residual: dihedral pdb=" C04 IG7 B 1 " pdb=" C02 IG7 B 1 " pdb=" C03 IG7 B 1 " pdb=" O18 IG7 B 1 " ideal model delta sinusoidal sigma weight residual 56.62 -122.53 179.15 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA PHE A 28 " pdb=" C PHE A 28 " pdb=" N SER A 29 " pdb=" CA SER A 29 " ideal model delta harmonic sigma weight residual -180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" C23 IG7 B 1 " pdb=" C21 IG7 B 1 " pdb=" C22 IG7 B 1 " pdb=" O36 IG7 B 1 " ideal model delta sinusoidal sigma weight residual 31.18 -68.78 99.96 1 3.00e+01 1.11e-03 1.25e+01 ... (remaining 2438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.003: 632 1.003 - 2.006: 0 2.006 - 3.009: 0 3.009 - 4.012: 0 4.012 - 5.015: 3 Chirality restraints: 635 Sorted by residual: chirality pdb=" CA SER B 2 " pdb=" N SER B 2 " pdb=" C SER B 2 " pdb=" CB SER B 2 " both_signs ideal model delta sigma weight residual False 2.51 -2.50 5.01 2.00e-01 2.50e+01 6.29e+02 chirality pdb=" CA LYS B 3 " pdb=" N LYS B 3 " pdb=" C LYS B 3 " pdb=" CB LYS B 3 " both_signs ideal model delta sigma weight residual False 2.51 -2.31 4.82 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C42 IG7 B 1 " pdb=" C19 IG7 B 1 " pdb=" C41 IG7 B 1 " pdb=" O43 IG7 B 1 " both_signs ideal model delta sigma weight residual False -2.49 2.31 -4.80 2.00e-01 2.50e+01 5.76e+02 ... (remaining 632 not shown) Planarity restraints: 703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 IG7 B 1 " -0.041 2.00e-02 2.50e+03 1.14e-01 1.62e+02 pdb=" C03 IG7 B 1 " 0.103 2.00e-02 2.50e+03 pdb=" C38 IG7 B 1 " 0.137 2.00e-02 2.50e+03 pdb=" N01 IG7 B 1 " -0.183 2.00e-02 2.50e+03 pdb=" O18 IG7 B 1 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 87 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 88 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 421 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO A 422 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 422 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 422 " -0.020 5.00e-02 4.00e+02 ... (remaining 700 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 708 2.77 - 3.30: 3916 3.30 - 3.83: 6836 3.83 - 4.37: 8614 4.37 - 4.90: 14610 Nonbonded interactions: 34684 Sorted by model distance: nonbonded pdb=" OE1 GLN A 133 " pdb=" OG1 THR A 495 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR A 333 " pdb=" OE1 GLU A 389 " model vdw 2.277 3.040 nonbonded pdb=" O ALA A 98 " pdb=" OG SER A 102 " model vdw 2.309 3.040 nonbonded pdb=" O LEU A 143 " pdb=" OG1 THR A 144 " model vdw 2.330 3.040 nonbonded pdb=" ND2 ASN A 336 " pdb=" O GLY A 368 " model vdw 2.393 3.120 ... (remaining 34679 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.210 Find NCS groups from input model: 0.030 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:16.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 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 : 0.003 0.041 4126 Z= 0.223 Angle : 0.550 7.520 5623 Z= 0.267 Chirality : 0.338 5.015 635 Planarity : 0.006 0.114 703 Dihedral : 12.108 179.150 1505 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.16 % Favored : 96.64 % Rotamer: Outliers : 0.97 % Allowed : 2.68 % Favored : 96.35 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.36), residues: 506 helix: 0.31 (0.32), residues: 251 sheet: -0.62 (0.65), residues: 62 loop : -0.80 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 489 HIS 0.001 0.000 HIS A 337 PHE 0.007 0.001 PHE A 28 TYR 0.007 0.001 TYR A 313 ARG 0.001 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.451 Fit side-chains REVERT: A 82 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.5760 (p90) REVERT: A 170 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6921 (mp0) REVERT: A 331 ASP cc_start: 0.7012 (m-30) cc_final: 0.6800 (m-30) outliers start: 4 outliers final: 0 residues processed: 50 average time/residue: 0.6947 time to fit residues: 37.0330 Evaluate side-chains 39 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 223 GLN A 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115070 restraints weight = 4884.954| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.37 r_work: 0.3265 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4126 Z= 0.204 Angle : 0.608 10.285 5623 Z= 0.304 Chirality : 0.066 1.238 635 Planarity : 0.005 0.037 703 Dihedral : 12.989 169.098 614 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.16 % Favored : 96.64 % Rotamer: Outliers : 1.95 % Allowed : 5.11 % Favored : 92.94 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.38), residues: 506 helix: 0.87 (0.33), residues: 258 sheet: -0.24 (0.64), residues: 56 loop : -0.81 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 489 HIS 0.002 0.001 HIS A 425 PHE 0.011 0.001 PHE A 174 TYR 0.009 0.001 TYR A 388 ARG 0.003 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.424 Fit side-chains REVERT: A 82 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.5547 (p90) outliers start: 8 outliers final: 2 residues processed: 47 average time/residue: 0.5926 time to fit residues: 30.0515 Evaluate side-chains 41 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 0.0010 chunk 6 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.114255 restraints weight = 4866.454| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.39 r_work: 0.3253 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4126 Z= 0.171 Angle : 0.554 6.391 5623 Z= 0.275 Chirality : 0.052 0.750 635 Planarity : 0.005 0.037 703 Dihedral : 12.056 136.216 614 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.57 % Favored : 97.23 % Rotamer: Outliers : 2.43 % Allowed : 6.57 % Favored : 91.00 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.39), residues: 506 helix: 1.03 (0.33), residues: 261 sheet: -0.23 (0.63), residues: 56 loop : -0.85 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.011 0.001 PHE A 174 TYR 0.006 0.001 TYR A 104 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.410 Fit side-chains REVERT: A 50 ASN cc_start: 0.7435 (m110) cc_final: 0.6779 (t0) REVERT: A 82 PHE cc_start: 0.6543 (OUTLIER) cc_final: 0.5684 (p90) outliers start: 10 outliers final: 1 residues processed: 49 average time/residue: 0.5329 time to fit residues: 28.3120 Evaluate side-chains 37 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 0.0050 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113818 restraints weight = 4922.539| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.34 r_work: 0.3250 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4126 Z= 0.297 Angle : 0.602 6.168 5623 Z= 0.298 Chirality : 0.050 0.568 635 Planarity : 0.005 0.038 703 Dihedral : 11.851 121.043 614 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.77 % Favored : 97.04 % Rotamer: Outliers : 2.68 % Allowed : 9.00 % Favored : 88.32 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.38), residues: 506 helix: 0.91 (0.33), residues: 259 sheet: -0.43 (0.63), residues: 57 loop : -0.81 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 489 HIS 0.002 0.001 HIS A 425 PHE 0.013 0.002 PHE A 174 TYR 0.008 0.001 TYR A 104 ARG 0.003 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.434 Fit side-chains REVERT: A 50 ASN cc_start: 0.7530 (m110) cc_final: 0.6953 (t0) REVERT: A 82 PHE cc_start: 0.6778 (OUTLIER) cc_final: 0.5717 (p90) REVERT: A 121 TRP cc_start: 0.8103 (p-90) cc_final: 0.7818 (p-90) outliers start: 11 outliers final: 2 residues processed: 44 average time/residue: 0.6417 time to fit residues: 30.3356 Evaluate side-chains 38 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.0030 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.132464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119734 restraints weight = 4952.687| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.36 r_work: 0.3273 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4126 Z= 0.166 Angle : 0.536 6.048 5623 Z= 0.265 Chirality : 0.046 0.448 635 Planarity : 0.004 0.038 703 Dihedral : 11.328 112.996 614 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.46 % Allowed : 10.71 % Favored : 87.83 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.39), residues: 506 helix: 1.09 (0.34), residues: 261 sheet: -0.27 (0.63), residues: 56 loop : -0.81 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.009 0.001 PHE A 174 TYR 0.006 0.001 TYR A 406 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.431 Fit side-chains REVERT: A 50 ASN cc_start: 0.7426 (m110) cc_final: 0.6851 (t0) REVERT: A 82 PHE cc_start: 0.6674 (OUTLIER) cc_final: 0.5764 (p90) outliers start: 6 outliers final: 1 residues processed: 43 average time/residue: 0.6165 time to fit residues: 28.6363 Evaluate side-chains 37 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 287 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 0.0770 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.132361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.119663 restraints weight = 4838.350| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.34 r_work: 0.3289 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4126 Z= 0.172 Angle : 0.536 6.013 5623 Z= 0.264 Chirality : 0.045 0.383 635 Planarity : 0.004 0.037 703 Dihedral : 11.134 112.389 614 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.95 % Allowed : 11.68 % Favored : 86.37 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.39), residues: 506 helix: 1.17 (0.34), residues: 261 sheet: -0.23 (0.64), residues: 56 loop : -0.79 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.010 0.001 PHE A 28 TYR 0.006 0.001 TYR A 104 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.394 Fit side-chains REVERT: A 50 ASN cc_start: 0.7439 (m110) cc_final: 0.6866 (t0) REVERT: A 82 PHE cc_start: 0.6741 (OUTLIER) cc_final: 0.5895 (p90) outliers start: 8 outliers final: 2 residues processed: 40 average time/residue: 0.6058 time to fit residues: 26.1305 Evaluate side-chains 38 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.132314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119513 restraints weight = 4863.509| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.35 r_work: 0.3269 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4126 Z= 0.181 Angle : 0.536 6.181 5623 Z= 0.263 Chirality : 0.045 0.342 635 Planarity : 0.004 0.037 703 Dihedral : 11.027 111.557 614 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.97 % Allowed : 12.90 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.38), residues: 506 helix: 1.17 (0.34), residues: 259 sheet: -0.24 (0.65), residues: 56 loop : -0.84 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 489 HIS 0.001 0.001 HIS A 425 PHE 0.010 0.001 PHE A 174 TYR 0.006 0.001 TYR A 104 ARG 0.001 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.470 Fit side-chains REVERT: A 50 ASN cc_start: 0.7453 (m110) cc_final: 0.6848 (t0) REVERT: A 82 PHE cc_start: 0.6752 (OUTLIER) cc_final: 0.5899 (p90) outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.6431 time to fit residues: 28.4441 Evaluate side-chains 39 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.130639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.117618 restraints weight = 4817.260| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.36 r_work: 0.3268 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4126 Z= 0.177 Angle : 0.533 6.343 5623 Z= 0.264 Chirality : 0.045 0.318 635 Planarity : 0.004 0.037 703 Dihedral : 10.930 110.609 614 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.97 % Allowed : 13.14 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.38), residues: 506 helix: 1.22 (0.34), residues: 259 sheet: -0.30 (0.65), residues: 56 loop : -0.83 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.009 0.001 PHE A 174 TYR 0.006 0.001 TYR A 104 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.462 Fit side-chains REVERT: A 50 ASN cc_start: 0.7431 (m110) cc_final: 0.6803 (t0) REVERT: A 82 PHE cc_start: 0.6655 (OUTLIER) cc_final: 0.5826 (p90) outliers start: 4 outliers final: 1 residues processed: 41 average time/residue: 0.6609 time to fit residues: 29.1996 Evaluate side-chains 37 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.125806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.112282 restraints weight = 4932.141| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.38 r_work: 0.3252 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4126 Z= 0.208 Angle : 0.554 6.467 5623 Z= 0.276 Chirality : 0.045 0.306 635 Planarity : 0.004 0.037 703 Dihedral : 10.914 110.248 614 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.97 % Allowed : 13.38 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.39), residues: 506 helix: 1.19 (0.34), residues: 262 sheet: -0.47 (0.65), residues: 57 loop : -0.73 (0.47), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 489 HIS 0.001 0.001 HIS A 425 PHE 0.011 0.001 PHE A 174 TYR 0.007 0.001 TYR A 104 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.404 Fit side-chains REVERT: A 50 ASN cc_start: 0.7463 (m110) cc_final: 0.6836 (t0) REVERT: A 82 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.5789 (p90) outliers start: 4 outliers final: 1 residues processed: 38 average time/residue: 0.6048 time to fit residues: 24.9004 Evaluate side-chains 37 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 47 optimal weight: 0.3980 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.132220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119243 restraints weight = 4834.073| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.39 r_work: 0.3260 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4126 Z= 0.190 Angle : 0.542 6.459 5623 Z= 0.270 Chirality : 0.044 0.300 635 Planarity : 0.004 0.037 703 Dihedral : 10.801 109.010 614 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.73 % Allowed : 13.87 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.39), residues: 506 helix: 1.23 (0.34), residues: 262 sheet: -0.29 (0.65), residues: 56 loop : -0.76 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.010 0.001 PHE A 174 TYR 0.006 0.001 TYR A 104 ARG 0.002 0.000 ARG A 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.411 Fit side-chains REVERT: A 50 ASN cc_start: 0.7461 (m110) cc_final: 0.6981 (t0) REVERT: A 82 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.6057 (p90) outliers start: 3 outliers final: 1 residues processed: 39 average time/residue: 0.6415 time to fit residues: 26.9333 Evaluate side-chains 38 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 297 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 35 optimal weight: 0.0670 chunk 26 optimal weight: 0.8980 chunk 45 optimal weight: 0.0970 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119840 restraints weight = 4813.968| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.34 r_work: 0.3287 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4126 Z= 0.159 Angle : 0.526 6.441 5623 Z= 0.261 Chirality : 0.044 0.274 635 Planarity : 0.004 0.038 703 Dihedral : 10.604 107.796 614 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.97 % Allowed : 13.38 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.39), residues: 506 helix: 1.35 (0.34), residues: 262 sheet: -0.23 (0.65), residues: 56 loop : -0.74 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.009 0.001 PHE A 28 TYR 0.006 0.001 TYR A 406 ARG 0.002 0.000 ARG A 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2549.14 seconds wall clock time: 44 minutes 25.03 seconds (2665.03 seconds total)