Starting phenix.real_space_refine on Wed Feb 12 02:10:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b0p_15791/02_2025/8b0p_15791.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b0p_15791/02_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_15791/02_2025/8b0p_15791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b0p_15791/02_2025/8b0p_15791.map" model { file = "/net/cci-nas-00/data/ceres_data/8b0p_15791/02_2025/8b0p_15791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b0p_15791/02_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.31, per 1000 atoms: 0.82 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: 1.19 Conformation dependent library (CDL) restraints added in 486.9 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: 0.48 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: 1.18 Time building geometry restraints manager: 1.26 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.650 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:11.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.750 ------------------------------------------------------------------------------- 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 : 0.473 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: 0.7304 time to fit residues: 38.9813 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 : 0.401 ------------------------------------------------------------------------------- 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: 0.7980 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.130707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.117587 restraints weight = 4826.945| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.34 r_work: 0.3265 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4126 Z= 0.212 Angle : 0.611 10.167 5623 Z= 0.306 Chirality : 0.066 1.229 635 Planarity : 0.005 0.037 703 Dihedral : 12.945 167.893 614 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.75 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: 0.10 (0.38), residues: 506 helix: 0.86 (0.33), residues: 258 sheet: -0.26 (0.64), residues: 56 loop : -0.82 (0.47), residues: 192 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 0.012 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 : 0.419 Fit side-chains REVERT: A 82 PHE cc_start: 0.6642 (OUTLIER) cc_final: 0.5597 (p90) outliers start: 8 outliers final: 2 residues processed: 47 average time/residue: 0.6275 time to fit residues: 31.9817 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 : 0.466 ------------------------------------------------------------------------------- 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: 6.9990 chunk 35 optimal weight: 0.0050 chunk 6 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.123618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109557 restraints weight = 4941.649| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.48 r_work: 0.3249 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1530 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= 0.194 Angle : 0.566 6.359 5623 Z= 0.281 Chirality : 0.052 0.747 635 Planarity : 0.005 0.037 703 Dihedral : 12.104 137.293 614 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.57 % Favored : 97.23 % Rotamer: Outliers : 1.95 % Allowed : 7.06 % 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: 0.24 (0.38), residues: 506 helix: 1.02 (0.33), residues: 259 sheet: -0.25 (0.63), residues: 56 loop : -0.83 (0.47), 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 0.011 0.001 PHE A 174 TYR 0.007 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 50 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.441 Fit side-chains REVERT: A 50 ASN cc_start: 0.7425 (m110) cc_final: 0.6910 (t0) REVERT: A 82 PHE cc_start: 0.6754 (OUTLIER) cc_final: 0.5891 (p90) REVERT: A 403 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7937 (m-30) outliers start: 8 outliers final: 1 residues processed: 48 average time/residue: 0.6305 time to fit residues: 32.7045 Evaluate side-chains 37 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 403 ASP 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: 0.7980 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.126494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113516 restraints weight = 4926.258| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.33 r_work: 0.3242 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4126 Z= 0.306 Angle : 0.605 6.117 5623 Z= 0.300 Chirality : 0.051 0.591 635 Planarity : 0.005 0.039 703 Dihedral : 11.935 121.920 614 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.77 % Favored : 97.04 % Rotamer: Outliers : 2.92 % Allowed : 8.76 % 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: 0.08 (0.38), residues: 506 helix: 0.87 (0.33), residues: 259 sheet: -0.43 (0.63), residues: 57 loop : -0.85 (0.46), 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 49 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.406 Fit side-chains REVERT: A 50 ASN cc_start: 0.7512 (m110) cc_final: 0.6884 (t0) REVERT: A 82 PHE cc_start: 0.6772 (OUTLIER) cc_final: 0.5663 (p90) REVERT: A 121 TRP cc_start: 0.8098 (p-90) cc_final: 0.7771 (p-90) outliers start: 12 outliers final: 3 residues processed: 46 average time/residue: 0.6281 time to fit residues: 31.0819 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 : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE 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: 3.9990 chunk 5 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.126878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.113865 restraints weight = 5008.441| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.42 r_work: 0.3209 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1742 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= 0.296 Angle : 0.596 6.189 5623 Z= 0.296 Chirality : 0.049 0.510 635 Planarity : 0.005 0.040 703 Dihedral : 11.791 113.996 614 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.95 % Allowed : 9.98 % Favored : 88.08 % 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: -0.01 (0.37), residues: 506 helix: 0.82 (0.33), residues: 256 sheet: -0.43 (0.63), residues: 57 loop : -0.92 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 489 HIS 0.002 0.001 HIS A 425 PHE 0.012 0.001 PHE A 174 TYR 0.008 0.001 TYR A 104 ARG 0.003 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 48 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.442 Fit side-chains REVERT: A 50 ASN cc_start: 0.7527 (m110) cc_final: 0.7027 (t0) REVERT: A 82 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.5878 (p90) REVERT: A 121 TRP cc_start: 0.8166 (p-90) cc_final: 0.7912 (p-90) outliers start: 8 outliers final: 3 residues processed: 45 average time/residue: 0.6773 time to fit residues: 32.6276 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 : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 0.0970 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.131462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118852 restraints weight = 4831.419| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.33 r_work: 0.3260 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1879 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= 0.175 Angle : 0.544 6.153 5623 Z= 0.270 Chirality : 0.046 0.409 635 Planarity : 0.005 0.038 703 Dihedral : 11.403 112.401 614 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.70 % Allowed : 11.19 % Favored : 87.10 % 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: 0.23 (0.38), residues: 506 helix: 1.07 (0.34), residues: 261 sheet: -0.37 (0.64), residues: 57 loop : -0.90 (0.46), 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 174 TYR 0.006 0.001 TYR A 406 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 45 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.438 Fit side-chains REVERT: A 50 ASN cc_start: 0.7472 (m110) cc_final: 0.6907 (t0) REVERT: A 82 PHE cc_start: 0.6742 (OUTLIER) cc_final: 0.5750 (p90) outliers start: 7 outliers final: 1 residues processed: 43 average time/residue: 0.6785 time to fit residues: 31.2939 Evaluate side-chains 39 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 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=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: 0.9980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 0.0570 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.132108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119286 restraints weight = 4900.368| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.35 r_work: 0.3277 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4126 Z= 0.153 Angle : 0.530 6.254 5623 Z= 0.262 Chirality : 0.044 0.343 635 Planarity : 0.004 0.038 703 Dihedral : 11.150 111.463 614 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.46 % Allowed : 12.90 % 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: 0.39 (0.38), residues: 506 helix: 1.21 (0.34), residues: 262 sheet: -0.23 (0.64), residues: 56 loop : -0.89 (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 28 TYR 0.006 0.001 TYR A 406 ARG 0.001 0.000 ARG A 442 *********************** 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 45 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.437 Fit side-chains REVERT: A 50 ASN cc_start: 0.7435 (m110) cc_final: 0.6918 (t0) REVERT: A 82 PHE cc_start: 0.6796 (OUTLIER) cc_final: 0.5955 (p90) outliers start: 6 outliers final: 0 residues processed: 42 average time/residue: 0.6887 time to fit residues: 31.0888 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 : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.127041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.113877 restraints weight = 4895.225| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.34 r_work: 0.3254 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1965 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= 0.217 Angle : 0.555 6.331 5623 Z= 0.276 Chirality : 0.045 0.328 635 Planarity : 0.005 0.037 703 Dihedral : 11.175 111.481 614 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % 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: 0.33 (0.38), residues: 506 helix: 1.15 (0.34), residues: 261 sheet: -0.32 (0.64), residues: 56 loop : -0.86 (0.46), residues: 189 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 0.011 0.001 PHE A 174 TYR 0.007 0.001 TYR A 104 ARG 0.002 0.000 ARG A 193 *********************** 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 44 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.587 Fit side-chains REVERT: A 50 ASN cc_start: 0.7496 (m110) cc_final: 0.6929 (t0) REVERT: A 82 PHE cc_start: 0.6757 (OUTLIER) cc_final: 0.5836 (p90) REVERT: A 121 TRP cc_start: 0.8111 (p-90) cc_final: 0.7795 (p-90) outliers start: 4 outliers final: 0 residues processed: 42 average time/residue: 0.7012 time to fit residues: 31.8647 Evaluate side-chains 38 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 0.0040 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 = 0.132387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119617 restraints weight = 4827.182| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.34 r_work: 0.3269 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2055 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= 0.176 Angle : 0.537 6.606 5623 Z= 0.267 Chirality : 0.044 0.309 635 Planarity : 0.005 0.038 703 Dihedral : 10.985 110.039 614 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.73 % Allowed : 13.63 % 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: 0.43 (0.39), residues: 506 helix: 1.24 (0.34), residues: 262 sheet: -0.26 (0.65), residues: 56 loop : -0.83 (0.46), 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 0.010 0.001 PHE A 174 TYR 0.006 0.001 TYR A 104 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 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 39 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.373 Fit side-chains REVERT: A 50 ASN cc_start: 0.7487 (m110) cc_final: 0.6917 (t0) REVERT: A 82 PHE cc_start: 0.6710 (OUTLIER) cc_final: 0.5825 (p90) outliers start: 3 outliers final: 1 residues processed: 38 average time/residue: 0.6399 time to fit residues: 26.2602 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 : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 314 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 5 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 = 0.3416 r_free = 0.3416 target = 0.127313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.113970 restraints weight = 4937.227| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.36 r_work: 0.3265 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2053 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= 0.183 Angle : 0.539 6.481 5623 Z= 0.267 Chirality : 0.045 0.292 635 Planarity : 0.005 0.037 703 Dihedral : 10.955 110.041 614 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.49 % Allowed : 13.38 % 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: 0.46 (0.39), residues: 506 helix: 1.25 (0.34), residues: 262 sheet: -0.25 (0.65), residues: 56 loop : -0.81 (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: 2 poor density : 38 time to evaluate : 0.393 Fit side-chains REVERT: A 50 ASN cc_start: 0.7483 (m110) cc_final: 0.6907 (t0) REVERT: A 82 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.5827 (p90) outliers start: 2 outliers final: 0 residues processed: 39 average time/residue: 0.6846 time to fit residues: 28.7064 Evaluate side-chains 38 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 0.0980 chunk 32 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 35 optimal weight: 0.0270 chunk 26 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.134332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121542 restraints weight = 4803.876| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.35 r_work: 0.3295 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2204 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= 0.151 Angle : 0.520 6.529 5623 Z= 0.258 Chirality : 0.044 0.283 635 Planarity : 0.004 0.038 703 Dihedral : 10.703 108.898 614 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.24 % Allowed : 13.87 % 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: 0.61 (0.39), residues: 506 helix: 1.39 (0.34), residues: 262 sheet: -0.20 (0.65), residues: 56 loop : -0.75 (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 0.001 0.000 ARG A 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2595.87 seconds wall clock time: 46 minutes 46.37 seconds (2806.37 seconds total)