Starting phenix.real_space_refine on Fri Jul 19 08:03:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0p_15791/07_2024/8b0p_15791.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0p_15791/07_2024/8b0p_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0p_15791/07_2024/8b0p_15791.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0p_15791/07_2024/8b0p_15791.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0p_15791/07_2024/8b0p_15791.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0p_15791/07_2024/8b0p_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 Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 3.19, per 1000 atoms: 0.79 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 - 3.50 Amino acid : False - 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: 1.71 Conformation dependent library (CDL) restraints added in 753.6 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: 0.51 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: 1.13 Time building geometry restraints manager: 1.80 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: 100.31 - 107.04: 181 107.04 - 113.78: 2270 113.78 - 120.52: 1588 120.52 - 127.26: 1515 127.26 - 134.00: 69 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 2.440 nonbonded pdb=" OH TYR A 333 " pdb=" OE1 GLU A 389 " model vdw 2.277 2.440 nonbonded pdb=" O ALA A 98 " pdb=" OG SER A 102 " model vdw 2.309 2.440 nonbonded pdb=" O LEU A 143 " pdb=" OG1 THR A 144 " model vdw 2.330 2.440 nonbonded pdb=" ND2 ASN A 336 " pdb=" O GLY A 368 " model vdw 2.393 2.520 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.200 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.850 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.452 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: 0.6698 time to fit residues: 35.8500 Evaluate side-chains 39 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4126 Z= 0.241 Angle : 0.613 10.918 5623 Z= 0.305 Chirality : 0.067 1.283 635 Planarity : 0.005 0.037 703 Dihedral : 12.879 165.521 614 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.36 % Favored : 96.44 % Rotamer: Outliers : 2.19 % Allowed : 5.11 % Favored : 92.70 % 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: 0.83 (0.33), residues: 258 sheet: -0.32 (0.65), residues: 57 loop : -0.81 (0.46), 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 0.012 0.001 PHE A 174 TYR 0.008 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 51 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.433 Fit side-chains REVERT: A 82 PHE cc_start: 0.6689 (OUTLIER) cc_final: 0.5677 (p90) REVERT: A 121 TRP cc_start: 0.7916 (p-90) cc_final: 0.7634 (p-90) outliers start: 9 outliers final: 3 residues processed: 49 average time/residue: 0.6841 time to fit residues: 35.8140 Evaluate side-chains 42 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 0.0970 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 0.0060 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1434 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= 0.167 Angle : 0.551 6.262 5623 Z= 0.271 Chirality : 0.051 0.743 635 Planarity : 0.004 0.037 703 Dihedral : 11.993 136.732 614 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.96 % Favored : 96.84 % Rotamer: Outliers : 1.95 % Allowed : 7.30 % Favored : 90.75 % 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: 0.34 (0.38), residues: 506 helix: 1.09 (0.34), residues: 259 sheet: -0.16 (0.64), residues: 57 loop : -0.78 (0.46), residues: 190 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 406 ARG 0.002 0.000 ARG A 442 *********************** 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 49 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.454 Fit side-chains REVERT: A 50 ASN cc_start: 0.7128 (m110) cc_final: 0.6651 (t0) REVERT: A 82 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.5836 (p90) outliers start: 8 outliers final: 2 residues processed: 46 average time/residue: 0.5868 time to fit residues: 29.2968 Evaluate side-chains 40 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1637 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= 0.147 Angle : 0.525 6.042 5623 Z= 0.257 Chirality : 0.046 0.521 635 Planarity : 0.004 0.037 703 Dihedral : 11.421 115.223 614 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.70 % Allowed : 9.73 % Favored : 88.56 % 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: 0.46 (0.39), residues: 506 helix: 1.21 (0.34), residues: 262 sheet: -0.02 (0.64), residues: 56 loop : -0.80 (0.47), residues: 188 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 174 TYR 0.006 0.001 TYR A 406 ARG 0.001 0.000 ARG A 442 *********************** 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 46 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.405 Fit side-chains REVERT: A 50 ASN cc_start: 0.7070 (m110) cc_final: 0.6624 (t0) REVERT: A 82 PHE cc_start: 0.6683 (OUTLIER) cc_final: 0.6026 (p90) outliers start: 7 outliers final: 0 residues processed: 42 average time/residue: 0.6082 time to fit residues: 27.5831 Evaluate side-chains 39 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 0.0050 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4126 Z= 0.146 Angle : 0.516 6.079 5623 Z= 0.253 Chirality : 0.044 0.395 635 Planarity : 0.004 0.037 703 Dihedral : 11.172 113.854 614 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.70 % Allowed : 10.46 % 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: 0.59 (0.39), residues: 506 helix: 1.31 (0.34), residues: 262 sheet: 0.03 (0.65), residues: 56 loop : -0.73 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.009 0.001 PHE A 174 TYR 0.005 0.001 TYR A 406 ARG 0.002 0.000 ARG A 442 *********************** 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 50 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.438 Fit side-chains REVERT: A 50 ASN cc_start: 0.7063 (m110) cc_final: 0.6719 (t0) REVERT: A 82 PHE cc_start: 0.6693 (OUTLIER) cc_final: 0.6124 (p90) outliers start: 7 outliers final: 1 residues processed: 47 average time/residue: 0.6505 time to fit residues: 32.7862 Evaluate side-chains 40 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE 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 11 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4126 Z= 0.200 Angle : 0.538 6.032 5623 Z= 0.266 Chirality : 0.045 0.357 635 Planarity : 0.004 0.036 703 Dihedral : 11.139 112.693 614 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.95 % Allowed : 10.95 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.47 (0.38), residues: 506 helix: 1.22 (0.34), residues: 259 sheet: -0.10 (0.64), residues: 56 loop : -0.74 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 313 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 46 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.432 Fit side-chains REVERT: A 50 ASN cc_start: 0.7065 (m110) cc_final: 0.6709 (t0) REVERT: A 82 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.6156 (p90) outliers start: 8 outliers final: 1 residues processed: 44 average time/residue: 0.6151 time to fit residues: 29.1962 Evaluate side-chains 38 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE 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 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4126 Z= 0.209 Angle : 0.545 6.083 5623 Z= 0.269 Chirality : 0.045 0.342 635 Planarity : 0.004 0.037 703 Dihedral : 11.093 111.980 614 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.22 % Allowed : 11.68 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.50 (0.38), residues: 506 helix: 1.20 (0.34), residues: 262 sheet: -0.13 (0.65), residues: 56 loop : -0.69 (0.47), residues: 188 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 313 ARG 0.002 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 41 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.467 Fit side-chains REVERT: A 50 ASN cc_start: 0.7126 (m110) cc_final: 0.6736 (t0) outliers start: 5 outliers final: 2 residues processed: 39 average time/residue: 0.6009 time to fit residues: 25.4061 Evaluate side-chains 38 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE 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 23 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 46 optimal weight: 0.0970 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 0.0770 chunk 13 optimal weight: 0.0980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4126 Z= 0.134 Angle : 0.507 6.101 5623 Z= 0.249 Chirality : 0.043 0.293 635 Planarity : 0.004 0.038 703 Dihedral : 10.790 110.052 614 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.22 % Allowed : 11.44 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.75 (0.39), residues: 506 helix: 1.44 (0.34), residues: 262 sheet: -0.06 (0.65), residues: 56 loop : -0.60 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 489 HIS 0.000 0.000 HIS A 425 PHE 0.008 0.001 PHE A 174 TYR 0.005 0.001 TYR A 406 ARG 0.001 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 46 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.482 Fit side-chains REVERT: A 50 ASN cc_start: 0.7058 (m110) cc_final: 0.6687 (t0) outliers start: 5 outliers final: 2 residues processed: 43 average time/residue: 0.7600 time to fit residues: 34.7739 Evaluate side-chains 38 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 40 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4126 Z= 0.255 Angle : 0.560 6.171 5623 Z= 0.277 Chirality : 0.046 0.302 635 Planarity : 0.005 0.036 703 Dihedral : 10.931 112.334 614 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.97 % Allowed : 11.92 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.38), residues: 506 helix: 1.31 (0.34), residues: 259 sheet: -0.16 (0.65), residues: 56 loop : -0.66 (0.46), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 489 HIS 0.001 0.000 HIS A 425 PHE 0.014 0.001 PHE A 174 TYR 0.007 0.001 TYR A 104 ARG 0.002 0.000 ARG A 13 *********************** 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 41 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.437 Fit side-chains REVERT: A 50 ASN cc_start: 0.7116 (m110) cc_final: 0.6713 (t0) outliers start: 4 outliers final: 2 residues processed: 39 average time/residue: 0.6775 time to fit residues: 28.4168 Evaluate side-chains 37 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 4 optimal weight: 2.9990 chunk 30 optimal weight: 0.0050 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4126 Z= 0.149 Angle : 0.519 6.199 5623 Z= 0.255 Chirality : 0.043 0.289 635 Planarity : 0.004 0.038 703 Dihedral : 10.674 109.668 614 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.97 % Allowed : 12.17 % Favored : 86.86 % 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: 0.66 (0.39), residues: 506 helix: 1.34 (0.34), residues: 262 sheet: -0.07 (0.65), residues: 56 loop : -0.61 (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 0.010 0.001 PHE A 174 TYR 0.006 0.001 TYR A 313 ARG 0.001 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 fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.445 Fit side-chains REVERT: A 50 ASN cc_start: 0.7063 (m110) cc_final: 0.6681 (t0) outliers start: 4 outliers final: 2 residues processed: 39 average time/residue: 0.6328 time to fit residues: 26.6642 Evaluate side-chains 38 residues out of total 425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 40 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 0.0050 chunk 2 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.133028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.120239 restraints weight = 4815.474| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.35 r_work: 0.3277 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1952 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= 0.175 Angle : 0.527 6.099 5623 Z= 0.259 Chirality : 0.044 0.282 635 Planarity : 0.004 0.037 703 Dihedral : 10.641 109.887 614 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.73 % Allowed : 12.17 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.65 (0.39), residues: 506 helix: 1.34 (0.34), residues: 262 sheet: -0.13 (0.65), residues: 56 loop : -0.61 (0.47), residues: 188 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 174 TYR 0.005 0.001 TYR A 313 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: 1583.00 seconds wall clock time: 28 minutes 46.12 seconds (1726.12 seconds total)