Starting phenix.real_space_refine on Fri Aug 2 16:31:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd0_38261/08_2024/8xd0_38261_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd0_38261/08_2024/8xd0_38261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd0_38261/08_2024/8xd0_38261.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd0_38261/08_2024/8xd0_38261.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd0_38261/08_2024/8xd0_38261_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd0_38261/08_2024/8xd0_38261_neut.cif" } resolution = 2.83 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= 0.002 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2124 2.51 5 N 565 2.21 5 O 651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 3": "OE1" <-> "OE2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A ASP 307": "OD1" <-> "OD2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A GLU 383": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3357 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3285 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 417, 3267 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 396} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 417, 3267 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 396} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 3319 Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 72 Unusual residues: {'AKG': 1, 'NDP': 1} Classifications: {'undetermined': 2, 'water': 14} Link IDs: {None: 15} Time building chain proxies: 3.99, per 1000 atoms: 1.19 Number of scatterers: 3357 At special positions: 0 Unit cell: (66.176, 74.448, 72.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 651 8.00 N 565 7.00 C 2124 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: 1.37 Conformation dependent library (CDL) restraints added in 1.2 seconds 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 55.6% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.519A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.809A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 302 through 307 removed outlier: 4.707A pdb=" N ASP A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.617A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ALA A 143 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY A 70 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279 removed outlier: 3.617A pdb=" N VAL A 242 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE A 215 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 242 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL A 217 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 180 hydrogen bonds defined for protein. 517 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: 0.92 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1074 1.34 - 1.45: 425 1.45 - 1.57: 1893 1.57 - 1.69: 3 1.69 - 1.81: 27 Bond restraints: 3422 Sorted by residual: bond pdb=" O1N NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.477 1.548 -0.071 1.00e-02 1.00e+04 5.04e+01 bond pdb=" O2B NDP A 500 " pdb=" P2B NDP A 500 " ideal model delta sigma weight residual 1.833 1.569 0.264 3.80e-02 6.93e+02 4.84e+01 bond pdb=" C GLU A 114 " pdb=" CA BGLU A 114 " ideal model delta sigma weight residual 1.523 1.611 -0.089 1.48e-02 4.57e+03 3.58e+01 bond pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.757 1.559 0.198 3.50e-02 8.16e+02 3.20e+01 bond pdb=" N GLN A 19 " pdb=" CA BGLN A 19 " ideal model delta sigma weight residual 1.459 1.528 -0.069 1.28e-02 6.10e+03 2.93e+01 ... (remaining 3417 not shown) Histogram of bond angle deviations from ideal: 95.91 - 103.53: 52 103.53 - 111.16: 1343 111.16 - 118.78: 1430 118.78 - 126.41: 1751 126.41 - 134.03: 77 Bond angle restraints: 4653 Sorted by residual: angle pdb=" C1D NDP A 500 " pdb=" O4D NDP A 500 " pdb=" C4D NDP A 500 " ideal model delta sigma weight residual 105.41 127.56 -22.15 2.71e+00 1.37e-01 6.70e+01 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 119.06 -15.22 1.91e+00 2.73e-01 6.32e+01 angle pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 107.74 122.49 -14.75 1.95e+00 2.62e-01 5.70e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 109.51 7.95 1.17e+00 7.36e-01 4.65e+01 angle pdb=" N ARG A 16 " pdb=" CA ARG A 16 " pdb=" C ARG A 16 " ideal model delta sigma weight residual 112.23 104.47 7.76 1.26e+00 6.30e-01 3.79e+01 ... (remaining 4648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.47: 1872 22.47 - 44.94: 122 44.94 - 67.42: 29 67.42 - 89.89: 10 89.89 - 112.36: 1 Dihedral angle restraints: 2034 sinusoidal: 830 harmonic: 1204 Sorted by residual: dihedral pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " ideal model delta sinusoidal sigma weight residual 175.04 62.68 112.36 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C GLU A 15 " pdb=" N GLU A 15 " pdb=" CA BGLU A 15 " pdb=" CB BGLU A 15 " ideal model delta harmonic sigma weight residual -122.60 -131.06 8.46 0 2.50e+00 1.60e-01 1.15e+01 dihedral pdb=" CB GLU A 288 " pdb=" CG GLU A 288 " pdb=" CD GLU A 288 " pdb=" OE1 GLU A 288 " ideal model delta sinusoidal sigma weight residual 0.00 88.69 -88.69 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 2031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 497 0.144 - 0.289: 2 0.289 - 0.433: 5 0.433 - 0.577: 0 0.577 - 0.721: 1 Chirality restraints: 505 Sorted by residual: chirality pdb=" C4B NDP A 500 " pdb=" C3B NDP A 500 " pdb=" C5B NDP A 500 " pdb=" O4B NDP A 500 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" C4D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" C5D NDP A 500 " pdb=" O4D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.32 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" C2D NDP A 500 " pdb=" C1D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" O2D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.34 -0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 502 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 500 " -0.104 2.00e-02 2.50e+03 1.98e-01 3.91e+02 pdb=" C5N NDP A 500 " 0.255 2.00e-02 2.50e+03 pdb=" C6N NDP A 500 " -0.262 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 500 " 0.059 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" C3N NDP A 500 " 0.166 2.00e-02 2.50e+03 pdb=" C4N NDP A 500 " -0.038 2.00e-02 2.50e+03 pdb=" C7N NDP A 500 " -0.106 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 143 " -0.044 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO A 144 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " -0.037 5.00e-02 4.00e+02 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 1404 2.94 - 3.43: 3437 3.43 - 3.92: 5864 3.92 - 4.41: 6694 4.41 - 4.90: 11033 Nonbonded interactions: 28432 Sorted by model distance: nonbonded pdb=" OD2 ASP A 244 " pdb=" N VAL A 270 " model vdw 2.449 3.120 nonbonded pdb=" NZ LYS A 229 " pdb=" OE2 GLU A 233 " model vdw 2.456 3.120 nonbonded pdb=" O VAL A 317 " pdb=" ND2 ASN A 344 " model vdw 2.469 3.120 nonbonded pdb=" O ILE A 174 " pdb=" NZ LYS A 177 " model vdw 2.499 3.120 nonbonded pdb=" OE1 GLU A 383 " pdb=" NH2 ARG A 406 " model vdw 2.511 3.120 ... (remaining 28427 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 16.740 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 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 : 0.009 0.264 3422 Z= 0.579 Angle : 1.133 22.149 4653 Z= 0.583 Chirality : 0.066 0.721 505 Planarity : 0.010 0.198 596 Dihedral : 16.465 112.360 1268 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.35 % Allowed : 3.23 % Favored : 94.43 % 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: 1.32 (0.43), residues: 418 helix: 1.92 (0.37), residues: 211 sheet: -0.42 (0.67), residues: 66 loop : 0.05 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.002 0.001 HIS A 388 PHE 0.007 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.394 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 74 average time/residue: 1.2405 time to fit residues: 94.3272 Evaluate side-chains 61 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 297 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.0770 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3422 Z= 0.156 Angle : 0.489 6.574 4653 Z= 0.253 Chirality : 0.042 0.134 505 Planarity : 0.005 0.056 596 Dihedral : 8.639 124.793 479 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.93 % Allowed : 12.02 % Favored : 85.04 % 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: 1.74 (0.44), residues: 418 helix: 2.29 (0.36), residues: 214 sheet: -0.10 (0.68), residues: 68 loop : 0.06 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.005 0.001 PHE A 381 TYR 0.007 0.001 TYR A 408 ARG 0.007 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.383 Fit side-chains REVERT: A 218 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8320 (tm-30) outliers start: 9 outliers final: 3 residues processed: 68 average time/residue: 1.1340 time to fit residues: 79.5351 Evaluate side-chains 64 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 297 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3422 Z= 0.214 Angle : 0.528 8.252 4653 Z= 0.277 Chirality : 0.044 0.191 505 Planarity : 0.005 0.050 596 Dihedral : 8.213 128.511 479 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.76 % Allowed : 14.96 % Favored : 83.28 % 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: 1.88 (0.44), residues: 418 helix: 2.42 (0.35), residues: 213 sheet: -0.02 (0.69), residues: 68 loop : 0.12 (0.59), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.009 0.002 HIS A 388 PHE 0.007 0.001 PHE A 7 TYR 0.010 0.001 TYR A 250 ARG 0.006 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.356 Fit side-chains REVERT: A 218 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8244 (tm-30) REVERT: A 267 HIS cc_start: 0.7788 (m90) cc_final: 0.7474 (m-70) REVERT: A 312 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8035 (mttm) REVERT: A 389 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8053 (mptt) outliers start: 5 outliers final: 1 residues processed: 65 average time/residue: 1.0988 time to fit residues: 73.7443 Evaluate side-chains 63 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 389 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3422 Z= 0.317 Angle : 0.561 6.881 4653 Z= 0.296 Chirality : 0.046 0.141 505 Planarity : 0.005 0.045 596 Dihedral : 8.153 131.404 475 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.23 % Allowed : 14.37 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.43), residues: 418 helix: 2.29 (0.35), residues: 212 sheet: -0.03 (0.69), residues: 68 loop : -0.10 (0.58), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 382 HIS 0.008 0.002 HIS A 388 PHE 0.010 0.002 PHE A 7 TYR 0.011 0.001 TYR A 363 ARG 0.006 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.351 Fit side-chains REVERT: A 211 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6867 (tmtm) REVERT: A 218 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8155 (tm-30) REVERT: A 267 HIS cc_start: 0.7755 (m90) cc_final: 0.7378 (m-70) REVERT: A 312 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8091 (mttt) REVERT: A 351 SER cc_start: 0.9124 (t) cc_final: 0.8875 (m) REVERT: A 389 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8016 (mptt) outliers start: 10 outliers final: 2 residues processed: 68 average time/residue: 1.0985 time to fit residues: 77.0753 Evaluate side-chains 67 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 389 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3422 Z= 0.168 Angle : 0.498 7.469 4653 Z= 0.261 Chirality : 0.043 0.131 505 Planarity : 0.005 0.045 596 Dihedral : 7.832 131.042 473 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.13 % Favored : 96.63 % Rotamer: Outliers : 1.47 % Allowed : 16.13 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.43), residues: 418 helix: 2.40 (0.35), residues: 212 sheet: -0.07 (0.68), residues: 68 loop : -0.14 (0.58), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.007 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.006 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.345 Fit side-chains REVERT: A 4 ILE cc_start: 0.7627 (pp) cc_final: 0.7226 (pp) REVERT: A 218 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8031 (tm-30) REVERT: A 312 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8057 (mttm) REVERT: A 389 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.7933 (mptt) outliers start: 4 outliers final: 2 residues processed: 63 average time/residue: 1.1420 time to fit residues: 74.2129 Evaluate side-chains 64 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 389 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 0.1980 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 3 optimal weight: 0.0870 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3422 Z= 0.138 Angle : 0.495 6.180 4653 Z= 0.258 Chirality : 0.042 0.128 505 Planarity : 0.005 0.046 596 Dihedral : 7.717 130.556 473 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % Rotamer: Outliers : 1.47 % Allowed : 18.77 % Favored : 79.77 % 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: 1.81 (0.43), residues: 418 helix: 2.47 (0.35), residues: 211 sheet: 0.08 (0.69), residues: 68 loop : -0.18 (0.58), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.007 0.002 HIS A 388 PHE 0.007 0.001 PHE A 341 TYR 0.007 0.001 TYR A 408 ARG 0.010 0.001 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.394 Fit side-chains REVERT: A 218 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8034 (tm-30) outliers start: 4 outliers final: 0 residues processed: 64 average time/residue: 1.2603 time to fit residues: 82.9976 Evaluate side-chains 56 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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: 2.9990 chunk 22 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 0.1980 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3422 Z= 0.215 Angle : 0.508 7.000 4653 Z= 0.264 Chirality : 0.044 0.126 505 Planarity : 0.005 0.045 596 Dihedral : 7.839 132.717 473 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.65 % Favored : 97.11 % Rotamer: Outliers : 1.47 % Allowed : 18.48 % Favored : 80.06 % 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: 1.66 (0.43), residues: 418 helix: 2.34 (0.35), residues: 212 sheet: -0.10 (0.68), residues: 68 loop : -0.17 (0.57), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 382 HIS 0.007 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.010 0.001 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.412 Fit side-chains REVERT: A 218 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8144 (tm-30) outliers start: 4 outliers final: 2 residues processed: 58 average time/residue: 1.1703 time to fit residues: 69.9861 Evaluate side-chains 58 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 277 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 0.0050 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3422 Z= 0.191 Angle : 0.515 6.766 4653 Z= 0.268 Chirality : 0.043 0.127 505 Planarity : 0.005 0.046 596 Dihedral : 7.846 133.576 473 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % Rotamer: Outliers : 2.05 % Allowed : 18.77 % Favored : 79.18 % 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: 1.63 (0.43), residues: 418 helix: 2.38 (0.35), residues: 211 sheet: -0.03 (0.68), residues: 68 loop : -0.33 (0.57), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 263 HIS 0.007 0.002 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.010 0.001 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.371 Fit side-chains REVERT: A 218 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8268 (tm-30) REVERT: A 312 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8066 (mttm) outliers start: 6 outliers final: 1 residues processed: 61 average time/residue: 1.2137 time to fit residues: 76.2854 Evaluate side-chains 58 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 312 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3422 Z= 0.153 Angle : 0.484 6.790 4653 Z= 0.250 Chirality : 0.043 0.133 505 Planarity : 0.005 0.047 596 Dihedral : 7.797 133.149 473 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % Rotamer: Outliers : 1.47 % Allowed : 19.06 % Favored : 79.47 % 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: 1.64 (0.43), residues: 418 helix: 2.42 (0.35), residues: 211 sheet: 0.07 (0.72), residues: 63 loop : -0.44 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 263 HIS 0.007 0.002 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.009 0.001 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.381 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 58 average time/residue: 1.2462 time to fit residues: 74.5139 Evaluate side-chains 53 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3422 Z= 0.231 Angle : 0.534 7.509 4653 Z= 0.278 Chirality : 0.044 0.148 505 Planarity : 0.005 0.046 596 Dihedral : 7.934 134.852 473 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % Rotamer: Outliers : 1.17 % Allowed : 20.23 % Favored : 78.59 % 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: 1.58 (0.43), residues: 418 helix: 2.31 (0.35), residues: 212 sheet: 0.02 (0.72), residues: 63 loop : -0.38 (0.56), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 263 HIS 0.007 0.002 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.008 0.001 ARG A 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.358 Fit side-chains REVERT: A 211 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6635 (tmtm) REVERT: A 218 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8263 (tm-30) REVERT: A 312 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8059 (mttm) outliers start: 3 outliers final: 1 residues processed: 55 average time/residue: 1.2288 time to fit residues: 69.7163 Evaluate side-chains 57 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 312 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.108704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.086541 restraints weight = 17060.538| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.45 r_work: 0.2666 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3422 Z= 0.294 Angle : 0.540 8.584 4653 Z= 0.279 Chirality : 0.045 0.164 505 Planarity : 0.005 0.046 596 Dihedral : 8.162 138.678 473 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.13 % Favored : 96.63 % Rotamer: Outliers : 1.47 % Allowed : 19.06 % Favored : 79.47 % 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: 1.47 (0.43), residues: 418 helix: 2.26 (0.35), residues: 211 sheet: -0.09 (0.71), residues: 63 loop : -0.45 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 263 HIS 0.007 0.002 HIS A 388 PHE 0.011 0.002 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.009 0.001 ARG A 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1801.59 seconds wall clock time: 32 minutes 7.54 seconds (1927.54 seconds total)