Starting phenix.real_space_refine on Thu Dec 7 17:23:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd5_29002/12_2023/8fd5_29002.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd5_29002/12_2023/8fd5_29002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd5_29002/12_2023/8fd5_29002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd5_29002/12_2023/8fd5_29002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd5_29002/12_2023/8fd5_29002.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd5_29002/12_2023/8fd5_29002.pdb" } resolution = 4.57 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 7 5.16 5 C 1971 2.51 5 N 607 2.21 5 O 629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 32": "NH1" <-> "NH2" Residue "A ARG 36": "NH1" <-> "NH2" Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 68": "NH1" <-> "NH2" Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 92": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3214 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3214 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 390} Time building chain proxies: 2.12, per 1000 atoms: 0.66 Number of scatterers: 3214 At special positions: 0 Unit cell: (78.4, 76, 88.8, 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 7 16.00 O 629 8.00 N 607 7.00 C 1971 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=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 575.2 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 2 sheets defined 22.9% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.567A pdb=" N LEU A 104 " --> pdb=" O MET A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 234 removed outlier: 4.518A pdb=" N LYS A 233 " --> pdb=" O GLN A 229 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.924A pdb=" N SER A 255 " --> pdb=" O ALA A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 310 through 315 removed outlier: 4.543A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 357 removed outlier: 4.721A pdb=" N ILE A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASN A 354 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.664A pdb=" N THR A 362 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 416 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 323 60 hydrogen bonds defined for protein. 147 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.62 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 550 1.31 - 1.44: 859 1.44 - 1.57: 1852 1.57 - 1.70: 4 1.70 - 1.82: 14 Bond restraints: 3279 Sorted by residual: bond pdb=" N THR A 49 " pdb=" CA THR A 49 " ideal model delta sigma weight residual 1.457 1.531 -0.074 6.40e-03 2.44e+04 1.35e+02 bond pdb=" CA THR A 49 " pdb=" C THR A 49 " ideal model delta sigma weight residual 1.533 1.579 -0.045 5.60e-03 3.19e+04 6.58e+01 bond pdb=" C ASN A 48 " pdb=" N THR A 49 " ideal model delta sigma weight residual 1.326 1.367 -0.041 8.30e-03 1.45e+04 2.43e+01 bond pdb=" CA ASN A 48 " pdb=" C ASN A 48 " ideal model delta sigma weight residual 1.522 1.581 -0.059 1.20e-02 6.94e+03 2.41e+01 bond pdb=" C THR A 49 " pdb=" O THR A 49 " ideal model delta sigma weight residual 1.235 1.186 0.050 1.26e-02 6.30e+03 1.55e+01 ... (remaining 3274 not shown) Histogram of bond angle deviations from ideal: 94.61 - 102.22: 11 102.22 - 109.82: 598 109.82 - 117.43: 1641 117.43 - 125.03: 2024 125.03 - 132.64: 150 Bond angle restraints: 4424 Sorted by residual: angle pdb=" O THR A 49 " pdb=" C THR A 49 " pdb=" N ALA A 50 " ideal model delta sigma weight residual 121.47 115.26 6.21 7.50e-01 1.78e+00 6.85e+01 angle pdb=" CA PHE A 363 " pdb=" C PHE A 363 " pdb=" N PRO A 364 " ideal model delta sigma weight residual 117.67 125.19 -7.52 1.01e+00 9.80e-01 5.55e+01 angle pdb=" CA ASN A 354 " pdb=" CB ASN A 354 " pdb=" CG ASN A 354 " ideal model delta sigma weight residual 112.60 105.60 7.00 1.00e+00 1.00e+00 4.90e+01 angle pdb=" N GLN A 58 " pdb=" CA GLN A 58 " pdb=" C GLN A 58 " ideal model delta sigma weight residual 111.69 120.16 -8.47 1.23e+00 6.61e-01 4.74e+01 angle pdb=" C SER A 188 " pdb=" N ARG A 189 " pdb=" CA ARG A 189 " ideal model delta sigma weight residual 120.28 129.50 -9.22 1.34e+00 5.57e-01 4.73e+01 ... (remaining 4419 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.97: 1848 16.97 - 33.93: 136 33.93 - 50.89: 16 50.89 - 67.85: 11 67.85 - 84.81: 3 Dihedral angle restraints: 2014 sinusoidal: 833 harmonic: 1181 Sorted by residual: dihedral pdb=" CA ASN A 27 " pdb=" C ASN A 27 " pdb=" N GLN A 28 " pdb=" CA GLN A 28 " ideal model delta harmonic sigma weight residual -180.00 -151.80 -28.20 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" C SER A 187 " pdb=" N SER A 187 " pdb=" CA SER A 187 " pdb=" CB SER A 187 " ideal model delta harmonic sigma weight residual -122.60 -135.24 12.64 0 2.50e+00 1.60e-01 2.56e+01 dihedral pdb=" CA ASN A 285 " pdb=" C ASN A 285 " pdb=" N PHE A 286 " pdb=" CA PHE A 286 " ideal model delta harmonic sigma weight residual 180.00 -155.79 -24.21 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 2011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 284 0.095 - 0.191: 111 0.191 - 0.286: 46 0.286 - 0.381: 12 0.381 - 0.477: 4 Chirality restraints: 457 Sorted by residual: chirality pdb=" CA THR A 245 " pdb=" N THR A 245 " pdb=" C THR A 245 " pdb=" CB THR A 245 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA THR A 198 " pdb=" N THR A 198 " pdb=" C THR A 198 " pdb=" CB THR A 198 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.47 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" CA THR A 393 " pdb=" N THR A 393 " pdb=" C THR A 393 " pdb=" CB THR A 393 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.44 2.00e-01 2.50e+01 4.87e+00 ... (remaining 454 not shown) Planarity restraints: 602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 330 " -0.109 2.00e-02 2.50e+03 5.52e-02 7.61e+01 pdb=" CG TRP A 330 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 330 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP A 330 " 0.071 2.00e-02 2.50e+03 pdb=" NE1 TRP A 330 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 330 " 0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP A 330 " 0.066 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 330 " -0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 330 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 330 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 52 " 0.056 2.00e-02 2.50e+03 4.85e-02 5.88e+01 pdb=" CG TRP A 52 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP A 52 " -0.107 2.00e-02 2.50e+03 pdb=" CD2 TRP A 52 " 0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP A 52 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 52 " 0.040 2.00e-02 2.50e+03 pdb=" CE3 TRP A 52 " -0.022 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 52 " 0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 52 " -0.055 2.00e-02 2.50e+03 pdb=" CH2 TRP A 52 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 87 " -0.098 2.00e-02 2.50e+03 5.02e-02 5.05e+01 pdb=" CG TYR A 87 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 87 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR A 87 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR A 87 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 87 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 87 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 87 " -0.067 2.00e-02 2.50e+03 ... (remaining 599 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1517 3.01 - 3.48: 3142 3.48 - 3.96: 4768 3.96 - 4.43: 5173 4.43 - 4.90: 8304 Nonbonded interactions: 22904 Sorted by model distance: nonbonded pdb=" N ASN A 150 " pdb=" O ASN A 150 " model vdw 2.541 2.496 nonbonded pdb=" OD2 ASP A 63 " pdb=" NZ LYS A 65 " model vdw 2.545 2.520 nonbonded pdb=" N VAL A 392 " pdb=" O VAL A 392 " model vdw 2.551 2.496 nonbonded pdb=" NZ LYS A 347 " pdb=" OD1 ASP A 348 " model vdw 2.559 2.520 nonbonded pdb=" OE2 GLU A 253 " pdb=" NZ LYS A 256 " model vdw 2.564 2.520 ... (remaining 22899 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 group one per residue 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: 0.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.880 Find NCS groups from input model: 0.090 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0222 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 : 0.016 0.074 3279 Z= 1.065 Angle : 2.155 9.218 4424 Z= 1.492 Chirality : 0.128 0.477 457 Planarity : 0.016 0.132 602 Dihedral : 13.136 84.806 1262 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 0.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.29 % Allowed : 2.65 % Favored : 97.05 % Cbeta Deviations : 1.06 % 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: -1.38 (0.37), residues: 417 helix: -0.87 (0.61), residues: 64 sheet: 0.60 (1.57), residues: 10 loop : -1.06 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.029 TRP A 330 HIS 0.005 0.002 HIS A 145 PHE 0.055 0.013 PHE A 171 TYR 0.098 0.026 TYR A 87 ARG 0.013 0.002 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.328 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.1992 time to fit residues: 8.6185 Evaluate side-chains 21 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.345 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 0.3980 chunk 16 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 0.0010 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.8968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0522 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3279 Z= 0.190 Angle : 0.667 7.611 4424 Z= 0.371 Chirality : 0.044 0.151 457 Planarity : 0.006 0.048 602 Dihedral : 6.165 18.985 459 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: -1.25 (0.40), residues: 417 helix: -1.28 (0.60), residues: 62 sheet: -0.13 (1.12), residues: 20 loop : -0.83 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 330 HIS 0.008 0.002 HIS A 59 PHE 0.013 0.002 PHE A 403 TYR 0.013 0.002 TYR A 112 ARG 0.004 0.001 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.357 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1875 time to fit residues: 5.3084 Evaluate side-chains 20 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 30.0000 chunk 29 optimal weight: 8.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0567 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3279 Z= 0.149 Angle : 0.577 7.826 4424 Z= 0.311 Chirality : 0.042 0.178 457 Planarity : 0.005 0.051 602 Dihedral : 5.312 18.615 459 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: -1.08 (0.40), residues: 417 helix: -1.17 (0.59), residues: 63 sheet: 0.20 (1.16), residues: 20 loop : -0.72 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 301 HIS 0.005 0.001 HIS A 59 PHE 0.020 0.002 PHE A 363 TYR 0.012 0.001 TYR A 298 ARG 0.003 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.358 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1750 time to fit residues: 5.4613 Evaluate side-chains 21 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.340 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.0020 chunk 39 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 overall best weight: 2.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0710 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3279 Z= 0.151 Angle : 0.597 8.400 4424 Z= 0.317 Chirality : 0.042 0.175 457 Planarity : 0.006 0.059 602 Dihedral : 5.000 17.215 459 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: -1.21 (0.40), residues: 417 helix: -1.72 (0.56), residues: 66 sheet: 0.28 (1.26), residues: 20 loop : -0.71 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 301 HIS 0.006 0.002 HIS A 59 PHE 0.016 0.002 PHE A 363 TYR 0.015 0.002 TYR A 298 ARG 0.004 0.001 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.329 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.2131 time to fit residues: 6.0740 Evaluate side-chains 20 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.326 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 0.4980 chunk 35 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 30.0000 chunk 7 optimal weight: 20.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0781 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3279 Z= 0.147 Angle : 0.573 8.959 4424 Z= 0.299 Chirality : 0.041 0.154 457 Planarity : 0.006 0.056 602 Dihedral : 4.832 17.227 459 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: -1.22 (0.40), residues: 417 helix: -1.75 (0.55), residues: 66 sheet: 0.40 (1.27), residues: 20 loop : -0.72 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 301 HIS 0.006 0.002 HIS A 59 PHE 0.021 0.002 PHE A 171 TYR 0.012 0.001 TYR A 298 ARG 0.005 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.342 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.2114 time to fit residues: 6.2984 Evaluate side-chains 21 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 30.0000 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 0.3980 chunk 38 optimal weight: 20.0000 chunk 4 optimal weight: 0.0570 chunk 22 optimal weight: 0.9980 overall best weight: 2.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0870 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3279 Z= 0.180 Angle : 0.580 8.927 4424 Z= 0.306 Chirality : 0.043 0.170 457 Planarity : 0.007 0.087 602 Dihedral : 4.781 15.866 459 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: -1.46 (0.40), residues: 417 helix: -1.93 (0.53), residues: 73 sheet: 0.13 (1.18), residues: 22 loop : -0.85 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 301 HIS 0.004 0.001 HIS A 59 PHE 0.017 0.002 PHE A 171 TYR 0.010 0.002 TYR A 87 ARG 0.008 0.001 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.352 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1758 time to fit residues: 6.2870 Evaluate side-chains 22 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.399 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 18 optimal weight: 50.0000 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN A 283 GLN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1557 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 3279 Z= 0.396 Angle : 1.013 12.023 4424 Z= 0.527 Chirality : 0.055 0.297 457 Planarity : 0.011 0.128 602 Dihedral : 7.447 37.545 459 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 22.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.28 (0.37), residues: 417 helix: -2.64 (0.59), residues: 56 sheet: -0.63 (1.09), residues: 20 loop : -1.49 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 52 HIS 0.017 0.005 HIS A 356 PHE 0.024 0.004 PHE A 171 TYR 0.033 0.005 TYR A 87 ARG 0.025 0.002 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.318 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1506 time to fit residues: 5.1812 Evaluate side-chains 17 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.318 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 0.0980 chunk 3 optimal weight: 0.0370 chunk 31 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.0570 chunk 34 optimal weight: 0.0170 chunk 36 optimal weight: 0.0770 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 overall best weight: 0.0510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS A 160 GLN A 229 GLN A 354 ASN ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1161 moved from start: 0.6795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3279 Z= 0.160 Angle : 0.626 10.213 4424 Z= 0.330 Chirality : 0.042 0.158 457 Planarity : 0.006 0.054 602 Dihedral : 5.534 32.038 459 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.85 (0.39), residues: 417 helix: -2.15 (0.56), residues: 58 sheet: -0.59 (1.05), residues: 20 loop : -1.19 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 301 HIS 0.003 0.001 HIS A 145 PHE 0.014 0.002 PHE A 403 TYR 0.008 0.001 TYR A 268 ARG 0.004 0.000 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.353 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1679 time to fit residues: 5.4320 Evaluate side-chains 20 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.304 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 30.0000 chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1331 moved from start: 0.7222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3279 Z= 0.183 Angle : 0.641 10.763 4424 Z= 0.331 Chirality : 0.043 0.149 457 Planarity : 0.006 0.056 602 Dihedral : 5.375 35.318 459 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -1.69 (0.39), residues: 417 helix: -1.81 (0.66), residues: 52 sheet: -0.40 (1.10), residues: 20 loop : -1.15 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 52 HIS 0.004 0.002 HIS A 356 PHE 0.017 0.002 PHE A 110 TYR 0.013 0.002 TYR A 87 ARG 0.006 0.001 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.358 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1489 time to fit residues: 4.1299 Evaluate side-chains 19 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.346 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.0870 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 6 optimal weight: 0.0470 overall best weight: 1.1658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 160 GLN A 283 GLN ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1226 moved from start: 0.7290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3279 Z= 0.133 Angle : 0.572 9.874 4424 Z= 0.298 Chirality : 0.041 0.153 457 Planarity : 0.005 0.054 602 Dihedral : 4.958 35.815 459 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -1.57 (0.39), residues: 417 helix: -1.45 (0.63), residues: 58 sheet: -0.22 (1.07), residues: 20 loop : -1.10 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 301 HIS 0.004 0.001 HIS A 59 PHE 0.010 0.001 PHE A 363 TYR 0.007 0.001 TYR A 87 ARG 0.003 0.000 ARG A 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.324 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1707 time to fit residues: 5.0406 Evaluate side-chains 21 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5393 r_free = 0.5393 target = 0.296823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.5230 r_free = 0.5230 target = 0.283543 restraints weight = 78974.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5250 r_free = 0.5250 target = 0.285373 restraints weight = 59437.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5255 r_free = 0.5255 target = 0.285359 restraints weight = 51021.226| |-----------------------------------------------------------------------------| r_work (final): 0.5211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1750 moved from start: 0.7988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3279 Z= 0.209 Angle : 0.688 10.448 4424 Z= 0.353 Chirality : 0.044 0.145 457 Planarity : 0.006 0.055 602 Dihedral : 5.804 46.501 459 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -1.75 (0.39), residues: 417 helix: -1.63 (0.62), residues: 58 sheet: -0.19 (1.06), residues: 20 loop : -1.24 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 52 HIS 0.007 0.002 HIS A 356 PHE 0.020 0.003 PHE A 110 TYR 0.018 0.003 TYR A 87 ARG 0.009 0.001 ARG A 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 972.41 seconds wall clock time: 18 minutes 26.64 seconds (1106.64 seconds total)