Starting phenix.real_space_refine on Sun Mar 10 15:55:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd5_29002/03_2024/8fd5_29002.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd5_29002/03_2024/8fd5_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_29002/03_2024/8fd5_29002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd5_29002/03_2024/8fd5_29002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd5_29002/03_2024/8fd5_29002.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd5_29002/03_2024/8fd5_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-dev-5265/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: 2.25, per 1000 atoms: 0.70 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: 1.11 Conformation dependent library (CDL) restraints added in 573.1 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: 0.26 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: 0.58 Time building geometry restraints manager: 1.23 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: 0.070 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: 0.460 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.090 Find NCS groups from input model: 0.080 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.630 ------------------------------------------------------------------------------- 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 : 0.353 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.2030 time to fit residues: 8.8268 Evaluate side-chains 21 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 : 0.374 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.1086 (ppp) cc_final: 0.0636 (pmm) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1864 time to fit residues: 5.4099 Evaluate side-chains 20 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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: 6.9990 chunk 11 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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: 0.0599 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3279 Z= 0.143 Angle : 0.585 7.712 4424 Z= 0.314 Chirality : 0.042 0.173 457 Planarity : 0.005 0.052 602 Dihedral : 5.311 19.161 459 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.40), residues: 417 helix: -1.22 (0.59), residues: 63 sheet: 0.21 (1.17), residues: 20 loop : -0.73 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 301 HIS 0.006 0.001 HIS A 59 PHE 0.017 0.002 PHE A 363 TYR 0.013 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 : 0.354 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.1228 (ppp) cc_final: 0.0870 (pmm) REVERT: A 20 PRO cc_start: 0.2692 (Cg_endo) cc_final: 0.2462 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1724 time to fit residues: 5.3942 Evaluate side-chains 21 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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: 0.4980 chunk 28 optimal weight: 8.9990 chunk 19 optimal weight: 0.0370 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 0.2980 chunk 39 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 overall best weight: 2.3662 ------------------------------------------------------------------------------- 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: 0.0782 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3279 Z= 0.165 Angle : 0.604 8.450 4424 Z= 0.321 Chirality : 0.043 0.181 457 Planarity : 0.006 0.060 602 Dihedral : 5.022 16.964 459 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.78 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: -1.26 (0.40), residues: 417 helix: -1.91 (0.55), residues: 66 sheet: 0.42 (1.28), residues: 20 loop : -0.72 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 301 HIS 0.007 0.002 HIS A 59 PHE 0.016 0.002 PHE A 363 TYR 0.017 0.002 TYR A 298 ARG 0.005 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 25 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.382 Fit side-chains REVERT: A 20 PRO cc_start: 0.3414 (Cg_endo) cc_final: 0.3128 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2062 time to fit residues: 6.4178 Evaluate side-chains 22 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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: 10.0000 chunk 0 optimal weight: 30.0000 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.0728 moved from start: 0.4148 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= 0.135 Angle : 0.550 8.942 4424 Z= 0.288 Chirality : 0.041 0.147 457 Planarity : 0.006 0.055 602 Dihedral : 4.710 16.670 459 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: -1.68 (0.55), residues: 67 sheet: 0.15 (1.15), residues: 22 loop : -0.71 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 301 HIS 0.005 0.001 HIS A 59 PHE 0.019 0.002 PHE A 171 TYR 0.008 0.001 TYR A 298 ARG 0.004 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 26 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.351 Fit side-chains REVERT: A 20 PRO cc_start: 0.3659 (Cg_endo) cc_final: 0.3374 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.2022 time to fit residues: 6.6081 Evaluate side-chains 23 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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: 2.9990 chunk 39 optimal weight: 30.0000 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 30.0000 chunk 4 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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: 0.1003 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3279 Z= 0.184 Angle : 0.627 8.953 4424 Z= 0.330 Chirality : 0.044 0.176 457 Planarity : 0.006 0.056 602 Dihedral : 4.886 16.592 459 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: -1.43 (0.39), residues: 417 helix: -1.91 (0.57), residues: 64 sheet: 0.13 (1.18), residues: 22 loop : -0.87 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 301 HIS 0.005 0.002 HIS A 59 PHE 0.014 0.003 PHE A 171 TYR 0.013 0.002 TYR A 298 ARG 0.009 0.001 ARG A 226 *********************** 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 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 REVERT: A 20 PRO cc_start: 0.4222 (Cg_endo) cc_final: 0.3812 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.2238 time to fit residues: 6.5822 Evaluate side-chains 21 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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: 20.0000 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 50.0000 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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: 0.1130 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3279 Z= 0.188 Angle : 0.613 9.642 4424 Z= 0.324 Chirality : 0.043 0.169 457 Planarity : 0.006 0.056 602 Dihedral : 5.199 32.783 459 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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 (0.39), residues: 417 helix: -1.44 (0.63), residues: 58 sheet: 0.18 (1.25), residues: 20 loop : -1.03 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 301 HIS 0.005 0.002 HIS A 356 PHE 0.022 0.003 PHE A 274 TYR 0.013 0.002 TYR A 298 ARG 0.010 0.001 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 28 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.357 Fit side-chains REVERT: A 20 PRO cc_start: 0.4956 (Cg_endo) cc_final: 0.4552 (Cg_exo) REVERT: A 401 ASP cc_start: 0.2500 (m-30) cc_final: 0.2084 (m-30) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1677 time to fit residues: 6.0602 Evaluate side-chains 23 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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: 9.9990 chunk 19 optimal weight: 0.0050 chunk 3 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 0.0030 chunk 28 optimal weight: 3.9990 overall best weight: 1.2010 ------------------------------------------------------------------------------- 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 ** 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: 0.1093 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3279 Z= 0.145 Angle : 0.567 10.155 4424 Z= 0.294 Chirality : 0.041 0.165 457 Planarity : 0.005 0.054 602 Dihedral : 4.919 35.473 459 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % 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: -1.42 (0.39), residues: 417 helix: -1.17 (0.64), residues: 58 sheet: 0.12 (1.25), residues: 20 loop : -1.04 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 301 HIS 0.003 0.001 HIS A 59 PHE 0.010 0.002 PHE A 363 TYR 0.016 0.001 TYR A 87 ARG 0.005 0.000 ARG A 226 *********************** 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 23 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.362 Fit side-chains REVERT: A 20 PRO cc_start: 0.4958 (Cg_endo) cc_final: 0.4541 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1457 time to fit residues: 4.6300 Evaluate side-chains 22 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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: 20.0000 chunk 33 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 0.0030 chunk 38 optimal weight: 0.0000 chunk 23 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- 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 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1137 moved from start: 0.6343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3279 Z= 0.143 Angle : 0.572 10.031 4424 Z= 0.297 Chirality : 0.042 0.187 457 Planarity : 0.006 0.054 602 Dihedral : 4.818 38.214 459 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.37 (0.40), residues: 417 helix: -0.94 (0.66), residues: 58 sheet: 0.21 (1.27), residues: 20 loop : -1.05 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 301 HIS 0.004 0.001 HIS A 59 PHE 0.010 0.002 PHE A 171 TYR 0.014 0.001 TYR A 87 ARG 0.005 0.001 ARG A 177 *********************** 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 26 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.365 Fit side-chains REVERT: A 401 ASP cc_start: 0.2602 (m-30) cc_final: 0.2196 (m-30) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1466 time to fit residues: 5.2245 Evaluate side-chains 22 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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: 8.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.0040 chunk 13 optimal weight: 30.0000 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.6972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1052 moved from start: 0.6408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3279 Z= 0.117 Angle : 0.531 9.761 4424 Z= 0.275 Chirality : 0.040 0.152 457 Planarity : 0.005 0.053 602 Dihedral : 4.474 37.568 459 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.23 (0.40), residues: 417 helix: -0.57 (0.67), residues: 61 sheet: -0.05 (1.18), residues: 22 loop : -0.98 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 301 HIS 0.003 0.001 HIS A 59 PHE 0.012 0.001 PHE A 363 TYR 0.008 0.001 TYR A 87 ARG 0.003 0.000 ARG A 262 ********************** 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 26 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.460 Fit side-chains REVERT: A 20 PRO cc_start: 0.5078 (Cg_endo) cc_final: 0.4646 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1338 time to fit residues: 4.7796 Evaluate side-chains 21 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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: 10.0000 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.0770 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5459 r_free = 0.5459 target = 0.305430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5369 r_free = 0.5369 target = 0.296483 restraints weight = 7631.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.5381 r_free = 0.5381 target = 0.297890 restraints weight = 6455.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5390 r_free = 0.5390 target = 0.298785 restraints weight = 5300.476| |-----------------------------------------------------------------------------| r_work (final): 0.5381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1203 moved from start: 0.6521 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= 0.123 Angle : 0.536 9.674 4424 Z= 0.278 Chirality : 0.040 0.152 457 Planarity : 0.005 0.053 602 Dihedral : 4.468 37.646 459 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: -1.15 (0.40), residues: 417 helix: -0.56 (0.67), residues: 61 sheet: 0.42 (1.27), residues: 20 loop : -0.94 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 301 HIS 0.003 0.001 HIS A 59 PHE 0.010 0.001 PHE A 363 TYR 0.012 0.001 TYR A 87 ARG 0.003 0.000 ARG A 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1017.24 seconds wall clock time: 19 minutes 20.74 seconds (1160.74 seconds total)