Starting phenix.real_space_refine on Mon Jun 24 16:16:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd0_38261/06_2024/8xd0_38261_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd0_38261/06_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_38261/06_2024/8xd0_38261.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd0_38261/06_2024/8xd0_38261.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd0_38261/06_2024/8xd0_38261_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd0_38261/06_2024/8xd0_38261_neut_updated.pdb" } 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-5370/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: 4.28, per 1000 atoms: 1.27 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: 1.47 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... running ksdssp... Secondary structure from input PDB file: 17 helices and 4 sheets defined 49.4% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 3.904A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.519A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 134 removed outlier: 5.716A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 222 through 234 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 281 through 286 removed outlier: 4.239A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 removed outlier: 4.707A pdb=" N ASP A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASN A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 308' Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 340 through 343 No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 366 through 391 Processing helix chain 'A' and resid 395 through 414 Processing sheet with id= A, 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) Processing sheet with id= B, first strand: chain 'A' and resid 68 through 71 removed outlier: 3.503A pdb=" N GLY A 70 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.267A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 242 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.697A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 163 hydrogen bonds defined for protein. 472 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: 0.93 Time building geometry restraints manager: 1.51 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: 1414 2.94 - 3.43: 3446 3.43 - 3.92: 5887 3.92 - 4.41: 6724 4.41 - 4.90: 11030 Nonbonded interactions: 28501 Sorted by model distance: nonbonded pdb=" OD2 ASP A 244 " pdb=" N VAL A 270 " model vdw 2.449 2.520 nonbonded pdb=" NZ LYS A 229 " pdb=" OE2 GLU A 233 " model vdw 2.456 2.520 nonbonded pdb=" O VAL A 317 " pdb=" ND2 ASN A 344 " model vdw 2.469 2.520 nonbonded pdb=" O ILE A 174 " pdb=" NZ LYS A 177 " model vdw 2.499 2.520 nonbonded pdb=" OE1 GLU A 383 " pdb=" NH2 ARG A 406 " model vdw 2.511 2.520 ... (remaining 28496 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: 3.470 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.340 Find NCS groups from input model: 0.100 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.320 ------------------------------------------------------------------------------- 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= 0.636 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 : 0.437 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 74 average time/residue: 1.2522 time to fit residues: 95.4039 Evaluate side-chains 61 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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: 0.9980 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.8489 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3422 Z= 0.172 Angle : 0.490 6.535 4653 Z= 0.253 Chirality : 0.042 0.151 505 Planarity : 0.005 0.056 596 Dihedral : 8.438 121.804 479 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.64 % Allowed : 12.02 % Favored : 85.34 % 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: 2.29 (0.36), residues: 211 sheet: 0.13 (0.67), residues: 66 loop : 0.14 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 PHE 0.006 0.001 PHE A 381 TYR 0.007 0.001 TYR A 363 ARG 0.006 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 69 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.348 Fit side-chains REVERT: A 218 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8116 (tm-30) outliers start: 8 outliers final: 3 residues processed: 64 average time/residue: 1.1024 time to fit residues: 72.9311 Evaluate side-chains 63 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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: 0.0030 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- 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: 0.8501 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3422 Z= 0.192 Angle : 0.521 8.460 4653 Z= 0.270 Chirality : 0.043 0.177 505 Planarity : 0.005 0.049 596 Dihedral : 8.164 123.022 479 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.05 % Allowed : 14.66 % 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: 1.94 (0.43), residues: 418 helix: 2.44 (0.36), residues: 211 sheet: 0.24 (0.67), residues: 66 loop : 0.09 (0.57), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.010 0.002 HIS A 388 PHE 0.007 0.001 PHE A 381 TYR 0.012 0.001 TYR A 250 ARG 0.005 0.000 ARG A 16 *********************** 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 69 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.351 Fit side-chains REVERT: A 218 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8208 (tm-30) REVERT: A 312 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8073 (mttm) outliers start: 6 outliers final: 2 residues processed: 67 average time/residue: 1.1169 time to fit residues: 77.2728 Evaluate side-chains 65 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 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 312 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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: 0.8518 moved from start: 0.1419 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= 0.218 Angle : 0.515 6.687 4653 Z= 0.267 Chirality : 0.043 0.137 505 Planarity : 0.005 0.047 596 Dihedral : 8.040 124.136 477 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.35 % Allowed : 16.13 % Favored : 81.52 % 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: 1.90 (0.43), residues: 418 helix: 2.47 (0.35), residues: 210 sheet: 0.33 (0.67), residues: 66 loop : -0.10 (0.56), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.009 0.002 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.006 0.000 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 66 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.399 Fit side-chains REVERT: A 218 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8084 (tm-30) REVERT: A 312 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8066 (mttm) outliers start: 7 outliers final: 3 residues processed: 64 average time/residue: 1.0978 time to fit residues: 72.6069 Evaluate side-chains 63 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 270 VAL Chi-restraints excluded: chain A residue 312 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.8487 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3422 Z= 0.151 Angle : 0.482 7.678 4653 Z= 0.249 Chirality : 0.042 0.143 505 Planarity : 0.004 0.046 596 Dihedral : 7.827 123.661 477 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.47 % Allowed : 16.42 % Favored : 82.11 % 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: 1.93 (0.43), residues: 418 helix: 2.53 (0.35), residues: 210 sheet: 0.28 (0.67), residues: 66 loop : -0.11 (0.56), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.008 0.002 HIS A 388 PHE 0.007 0.001 PHE A 341 TYR 0.010 0.001 TYR A 250 ARG 0.004 0.000 ARG A 16 *********************** 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 63 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.403 Fit side-chains REVERT: A 4 ILE cc_start: 0.7581 (pp) cc_final: 0.7339 (pp) REVERT: A 218 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8113 (tm-30) outliers start: 4 outliers final: 2 residues processed: 62 average time/residue: 1.1243 time to fit residues: 72.0026 Evaluate side-chains 62 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 270 VAL 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: 0.9990 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.0020 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.0870 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 overall best weight: 0.4966 ------------------------------------------------------------------------------- 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: 0.8451 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3422 Z= 0.130 Angle : 0.473 7.126 4653 Z= 0.243 Chirality : 0.041 0.125 505 Planarity : 0.004 0.046 596 Dihedral : 7.482 122.610 475 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % Rotamer: Outliers : 1.17 % Allowed : 17.60 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.43), residues: 418 helix: 2.54 (0.35), residues: 211 sheet: 0.22 (0.66), residues: 66 loop : -0.10 (0.57), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.008 0.001 HIS A 388 PHE 0.006 0.001 PHE A 341 TYR 0.006 0.001 TYR A 408 ARG 0.006 0.000 ARG A 265 *********************** 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 66 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.409 Fit side-chains REVERT: A 4 ILE cc_start: 0.7477 (pp) cc_final: 0.7049 (pp) REVERT: A 218 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8012 (tm-30) outliers start: 3 outliers final: 2 residues processed: 64 average time/residue: 1.0176 time to fit residues: 67.4631 Evaluate side-chains 62 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 270 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3422 Z= 0.262 Angle : 0.512 6.531 4653 Z= 0.266 Chirality : 0.044 0.123 505 Planarity : 0.005 0.046 596 Dihedral : 7.799 127.310 475 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.01 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: 1.87 (0.43), residues: 418 helix: 2.43 (0.35), residues: 211 sheet: 0.25 (0.67), residues: 66 loop : -0.05 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.008 0.002 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.006 0.000 ARG A 265 *********************** 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 60 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.409 Fit side-chains REVERT: A 4 ILE cc_start: 0.7521 (pp) cc_final: 0.7070 (pp) REVERT: A 218 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8098 (tm-30) REVERT: A 312 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8068 (mttm) outliers start: 4 outliers final: 2 residues processed: 58 average time/residue: 1.0759 time to fit residues: 64.7172 Evaluate side-chains 60 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3422 Z= 0.229 Angle : 0.510 6.275 4653 Z= 0.266 Chirality : 0.043 0.129 505 Planarity : 0.005 0.046 596 Dihedral : 7.749 129.240 473 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % Rotamer: Outliers : 1.47 % Allowed : 19.35 % 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: 1.81 (0.43), residues: 418 helix: 2.40 (0.35), residues: 211 sheet: 0.22 (0.67), residues: 66 loop : -0.12 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 382 HIS 0.009 0.002 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.006 0.000 ARG A 265 *********************** 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 61 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.400 Fit side-chains REVERT: A 4 ILE cc_start: 0.7488 (pp) cc_final: 0.7047 (pp) REVERT: A 218 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8114 (tm-30) REVERT: A 267 HIS cc_start: 0.7866 (m90) cc_final: 0.7638 (m-70) REVERT: A 312 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8067 (mttm) outliers start: 4 outliers final: 2 residues processed: 57 average time/residue: 1.0754 time to fit residues: 63.5012 Evaluate side-chains 59 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL 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: 3.9990 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3422 Z= 0.164 Angle : 0.476 5.509 4653 Z= 0.246 Chirality : 0.042 0.136 505 Planarity : 0.004 0.046 596 Dihedral : 7.673 129.455 473 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.13 % Favored : 96.63 % Rotamer: Outliers : 1.76 % Allowed : 18.77 % 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: 1.91 (0.43), residues: 418 helix: 2.49 (0.35), residues: 211 sheet: 0.20 (0.66), residues: 66 loop : -0.05 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.009 0.002 HIS A 388 PHE 0.007 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.006 0.000 ARG A 265 *********************** 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 60 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.392 Fit side-chains REVERT: A 4 ILE cc_start: 0.7450 (pp) cc_final: 0.7017 (pp) REVERT: A 218 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8124 (tm-30) REVERT: A 312 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8048 (mttm) outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 1.0995 time to fit residues: 63.6862 Evaluate side-chains 59 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 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 32 optimal weight: 0.0470 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3422 Z= 0.160 Angle : 0.488 5.498 4653 Z= 0.253 Chirality : 0.042 0.141 505 Planarity : 0.004 0.045 596 Dihedral : 7.631 129.717 473 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % Rotamer: Outliers : 1.76 % Allowed : 19.06 % 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: 1.94 (0.43), residues: 418 helix: 2.53 (0.35), residues: 211 sheet: 0.20 (0.66), residues: 66 loop : -0.05 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.009 0.002 HIS A 388 PHE 0.007 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.007 0.000 ARG A 265 ********************** 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 58 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.412 Fit side-chains REVERT: A 218 GLN cc_start: 0.8770 (tm-30) cc_final: 0.7974 (tm-30) REVERT: A 312 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8045 (mttm) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 1.0797 time to fit residues: 60.4063 Evaluate side-chains 58 residues out of total 337 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 270 VAL 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: 6.9990 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 0.0870 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.109298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.087152 restraints weight = 17751.138| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.52 r_work: 0.2699 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3422 Z= 0.235 Angle : 0.505 6.436 4653 Z= 0.262 Chirality : 0.043 0.151 505 Planarity : 0.004 0.045 596 Dihedral : 7.862 132.470 473 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.89 % Favored : 96.87 % Rotamer: Outliers : 2.05 % Allowed : 18.18 % 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: 1.84 (0.43), residues: 418 helix: 2.45 (0.35), residues: 211 sheet: 0.18 (0.66), residues: 66 loop : -0.11 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 263 HIS 0.008 0.002 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.006 0.000 ARG A 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1810.75 seconds wall clock time: 32 minutes 48.94 seconds (1968.94 seconds total)