Starting phenix.real_space_refine on Tue Feb 11 10:14:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qbi_13887/02_2025/7qbi_13887.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qbi_13887/02_2025/7qbi_13887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qbi_13887/02_2025/7qbi_13887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qbi_13887/02_2025/7qbi_13887.map" model { file = "/net/cci-nas-00/data/ceres_data/7qbi_13887/02_2025/7qbi_13887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qbi_13887/02_2025/7qbi_13887.cif" } resolution = 3.46 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= 0.002 sd= 0.093 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3360 2.51 5 N 718 2.21 5 O 898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4996 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2140 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 289} Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 98 Chain: "I" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 120 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Chain: "K" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 120 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Chain: "B" Number of atoms: 2140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2140 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 289} Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 98 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'NAG': 2, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'NAG': 2, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.61, per 1000 atoms: 0.72 Number of scatterers: 4996 At special positions: 0 Unit cell: (75.9, 73.7, 94.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 898 8.00 N 718 7.00 C 3360 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 - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 25 " " NAG A 502 " - " ASN A 32 " " NAG B 501 " - " ASN B 32 " " NAG B 502 " - " ASN B 25 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 550.2 milliseconds 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1180 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 78.8% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 Processing helix chain 'A' and resid 18 through 21 removed outlier: 3.827A pdb=" N GLN A 21 " --> pdb=" O ASN A 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 18 through 21' Processing helix chain 'A' and resid 38 through 73 Processing helix chain 'A' and resid 78 through 102 Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 121 through 154 removed outlier: 3.522A pdb=" N VAL A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 195 removed outlier: 3.921A pdb=" N VAL A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 236 removed outlier: 3.678A pdb=" N ASN A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 268 removed outlier: 3.581A pdb=" N ILE A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 276 through 301 removed outlier: 3.801A pdb=" N VAL A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Proline residue: A 290 - end of helix Processing helix chain 'B' and resid 9 through 13 Processing helix chain 'B' and resid 18 through 21 removed outlier: 3.827A pdb=" N GLN B 21 " --> pdb=" O ASN B 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 18 through 21' Processing helix chain 'B' and resid 38 through 73 Processing helix chain 'B' and resid 78 through 102 Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 121 through 154 removed outlier: 3.522A pdb=" N VAL B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 195 removed outlier: 3.921A pdb=" N VAL B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 236 removed outlier: 3.678A pdb=" N ASN B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 268 removed outlier: 3.600A pdb=" N ILE B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 276 through 301 removed outlier: 3.801A pdb=" N VAL B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Proline residue: B 290 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 24 372 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.30 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: 1.18 - 1.31: 734 1.31 - 1.44: 1298 1.44 - 1.57: 3052 1.57 - 1.69: 6 1.69 - 1.82: 36 Bond restraints: 5126 Sorted by residual: bond pdb=" C7 NAG B 502 " pdb=" N2 NAG B 502 " ideal model delta sigma weight residual 1.346 1.455 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C7 NAG A 502 " pdb=" N2 NAG A 502 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C7 NAG A 501 " pdb=" N2 NAG A 501 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C7 NAG B 501 " pdb=" N2 NAG B 501 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.42e+01 ... (remaining 5121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 6640 2.08 - 4.16: 367 4.16 - 6.23: 75 6.23 - 8.31: 6 8.31 - 10.39: 4 Bond angle restraints: 7092 Sorted by residual: angle pdb=" N PHE B 244 " pdb=" CA PHE B 244 " pdb=" C PHE B 244 " ideal model delta sigma weight residual 111.33 104.11 7.22 1.21e+00 6.83e-01 3.56e+01 angle pdb=" N PHE A 244 " pdb=" CA PHE A 244 " pdb=" C PHE A 244 " ideal model delta sigma weight residual 111.33 104.51 6.82 1.21e+00 6.83e-01 3.18e+01 angle pdb=" C SER A 104 " pdb=" CA SER A 104 " pdb=" CB SER A 104 " ideal model delta sigma weight residual 114.40 108.58 5.82 1.25e+00 6.40e-01 2.17e+01 angle pdb=" C SER B 104 " pdb=" CA SER B 104 " pdb=" CB SER B 104 " ideal model delta sigma weight residual 114.40 108.63 5.77 1.25e+00 6.40e-01 2.13e+01 angle pdb=" N TRP A 70 " pdb=" CA TRP A 70 " pdb=" C TRP A 70 " ideal model delta sigma weight residual 111.03 106.31 4.72 1.11e+00 8.12e-01 1.81e+01 ... (remaining 7087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.62: 3413 23.62 - 47.23: 160 47.23 - 70.85: 29 70.85 - 94.47: 12 94.47 - 118.08: 4 Dihedral angle restraints: 3618 sinusoidal: 1792 harmonic: 1826 Sorted by residual: dihedral pdb=" CAR Y01 I 102 " pdb=" CAV Y01 I 102 " pdb=" CBC Y01 I 102 " pdb=" CAZ Y01 I 102 " ideal model delta sinusoidal sigma weight residual 55.40 -62.68 118.08 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" CAR Y01 K 102 " pdb=" CAV Y01 K 102 " pdb=" CBC Y01 K 102 " pdb=" CAZ Y01 K 102 " ideal model delta sinusoidal sigma weight residual 55.40 -60.15 115.55 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" CAZ Y01 I 102 " pdb=" CAV Y01 I 102 " pdb=" CBC Y01 I 102 " pdb=" OAW Y01 I 102 " ideal model delta sinusoidal sigma weight residual -174.31 -59.08 -115.23 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 3615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 738 0.061 - 0.122: 156 0.122 - 0.183: 20 0.183 - 0.244: 8 0.244 - 0.305: 2 Chirality restraints: 924 Sorted by residual: chirality pdb=" CA LEU B 236 " pdb=" N LEU B 236 " pdb=" C LEU B 236 " pdb=" CB LEU B 236 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA LEU A 236 " pdb=" N LEU A 236 " pdb=" C LEU A 236 " pdb=" CB LEU A 236 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA PHE B 244 " pdb=" N PHE B 244 " pdb=" C PHE B 244 " pdb=" CB PHE B 244 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 921 not shown) Planarity restraints: 804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 219 " 0.021 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" C SER A 219 " -0.072 2.00e-02 2.50e+03 pdb=" O SER A 219 " 0.027 2.00e-02 2.50e+03 pdb=" N PHE A 220 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 219 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.60e+01 pdb=" C SER B 219 " 0.069 2.00e-02 2.50e+03 pdb=" O SER B 219 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE B 220 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 74 " -0.275 9.50e-02 1.11e+02 1.23e-01 9.48e+00 pdb=" NE ARG A 74 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 74 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 74 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 74 " -0.008 2.00e-02 2.50e+03 ... (remaining 801 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 903 2.77 - 3.30: 5100 3.30 - 3.83: 8016 3.83 - 4.37: 9430 4.37 - 4.90: 16177 Nonbonded interactions: 39626 Sorted by model distance: nonbonded pdb=" OE1 GLN B 51 " pdb=" OH TYR B 98 " model vdw 2.231 3.040 nonbonded pdb=" OE1 GLN A 51 " pdb=" OH TYR A 98 " model vdw 2.232 3.040 nonbonded pdb=" O ARG B 122 " pdb=" ND1 HIS B 126 " model vdw 2.296 3.120 nonbonded pdb=" O ARG A 122 " pdb=" ND1 HIS A 126 " model vdw 2.297 3.120 nonbonded pdb=" NH2 ARG A 74 " pdb=" O ALA B 298 " model vdw 2.330 3.120 ... (remaining 39621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.200 Find NCS groups from input model: 0.080 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 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 : 0.008 0.109 5126 Z= 0.532 Angle : 1.064 10.390 7092 Z= 0.600 Chirality : 0.053 0.305 924 Planarity : 0.009 0.123 800 Dihedral : 14.753 118.083 2438 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: -1.45 (0.31), residues: 614 helix: -0.82 (0.22), residues: 444 sheet: None (None), residues: 0 loop : -0.86 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 70 HIS 0.003 0.001 HIS A 94 PHE 0.025 0.003 PHE B 171 TYR 0.026 0.003 TYR A 266 ARG 0.007 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.481 Fit side-chains REVERT: A 120 ILE cc_start: 0.8098 (mm) cc_final: 0.7731 (mm) REVERT: B 120 ILE cc_start: 0.8135 (mm) cc_final: 0.7768 (mm) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1552 time to fit residues: 23.1832 Evaluate side-chains 104 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 2 HIS K 2 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.193386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.154692 restraints weight = 6308.482| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.29 r_work: 0.3596 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5126 Z= 0.330 Angle : 0.696 7.274 7092 Z= 0.328 Chirality : 0.040 0.139 924 Planarity : 0.004 0.028 800 Dihedral : 10.803 90.862 1592 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % 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: 1.24 (0.33), residues: 614 helix: 1.31 (0.23), residues: 448 sheet: None (None), residues: 0 loop : -0.36 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 1 HIS 0.003 0.001 HIS B 94 PHE 0.017 0.002 PHE A 171 TYR 0.010 0.002 TYR B 106 ARG 0.002 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.510 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1506 time to fit residues: 22.9133 Evaluate side-chains 94 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 59 optimal weight: 0.3980 chunk 18 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.181806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.143256 restraints weight = 6488.762| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.42 r_work: 0.3504 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5126 Z= 0.195 Angle : 0.586 7.661 7092 Z= 0.277 Chirality : 0.037 0.134 924 Planarity : 0.003 0.025 800 Dihedral : 9.538 78.842 1592 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.87 % Allowed : 14.41 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.33), residues: 614 helix: 2.51 (0.24), residues: 434 sheet: None (None), residues: 0 loop : -0.60 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 3 HIS 0.002 0.001 HIS A 94 PHE 0.014 0.001 PHE B 171 TYR 0.008 0.001 TYR B 128 ARG 0.001 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.565 Fit side-chains REVERT: A 64 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8169 (tt) REVERT: A 149 GLN cc_start: 0.8347 (tt0) cc_final: 0.8073 (tt0) REVERT: B 64 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8093 (tt) REVERT: B 70 TRP cc_start: 0.7834 (OUTLIER) cc_final: 0.7409 (m100) outliers start: 4 outliers final: 1 residues processed: 105 average time/residue: 0.1627 time to fit residues: 22.1502 Evaluate side-chains 103 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 38 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.178993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.138819 restraints weight = 6672.097| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.48 r_work: 0.3439 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5126 Z= 0.286 Angle : 0.670 7.872 7092 Z= 0.306 Chirality : 0.039 0.137 924 Planarity : 0.003 0.027 800 Dihedral : 9.024 59.635 1592 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.28 % Allowed : 16.59 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.33), residues: 614 helix: 2.50 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.50 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 70 HIS 0.003 0.001 HIS B 94 PHE 0.018 0.002 PHE B 55 TYR 0.007 0.001 TYR A 128 ARG 0.002 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.501 Fit side-chains REVERT: A 64 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8180 (tp) REVERT: A 106 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.8392 (m-80) REVERT: A 149 GLN cc_start: 0.8390 (tt0) cc_final: 0.8126 (tt0) REVERT: B 64 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8196 (tp) REVERT: B 106 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.8399 (m-80) outliers start: 15 outliers final: 6 residues processed: 107 average time/residue: 0.1507 time to fit residues: 21.1205 Evaluate side-chains 105 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.178649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139234 restraints weight = 6503.903| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.42 r_work: 0.3460 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5126 Z= 0.220 Angle : 0.596 6.788 7092 Z= 0.278 Chirality : 0.037 0.135 924 Planarity : 0.003 0.027 800 Dihedral : 8.467 57.859 1592 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.97 % Allowed : 20.31 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.33), residues: 614 helix: 2.83 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.36 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 3 HIS 0.002 0.001 HIS A 94 PHE 0.011 0.001 PHE A 55 TYR 0.008 0.001 TYR B 128 ARG 0.001 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.486 Fit side-chains REVERT: A 64 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8292 (tp) REVERT: A 106 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.8472 (m-80) REVERT: A 149 GLN cc_start: 0.8360 (tt0) cc_final: 0.8123 (tt0) REVERT: B 64 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8268 (tp) REVERT: B 106 TYR cc_start: 0.8921 (OUTLIER) cc_final: 0.8520 (m-80) REVERT: B 225 LYS cc_start: 0.6910 (ttmt) cc_final: 0.6700 (ttmt) outliers start: 9 outliers final: 5 residues processed: 103 average time/residue: 0.1576 time to fit residues: 21.1234 Evaluate side-chains 105 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.176795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136954 restraints weight = 6530.093| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.44 r_work: 0.3448 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5126 Z= 0.237 Angle : 0.608 6.788 7092 Z= 0.285 Chirality : 0.038 0.135 924 Planarity : 0.003 0.027 800 Dihedral : 8.428 58.452 1592 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.18 % Allowed : 20.74 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.33), residues: 614 helix: 2.81 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.28 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 3 HIS 0.002 0.001 HIS B 94 PHE 0.014 0.001 PHE B 55 TYR 0.007 0.001 TYR A 128 ARG 0.001 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.528 Fit side-chains REVERT: A 64 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8179 (tp) REVERT: A 106 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: B 64 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8215 (tp) REVERT: B 106 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.8155 (m-80) outliers start: 10 outliers final: 5 residues processed: 105 average time/residue: 0.1525 time to fit residues: 21.0696 Evaluate side-chains 106 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 0.0010 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.179306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.140320 restraints weight = 6471.843| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.41 r_work: 0.3486 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5126 Z= 0.186 Angle : 0.560 6.634 7092 Z= 0.267 Chirality : 0.037 0.132 924 Planarity : 0.003 0.027 800 Dihedral : 8.089 59.351 1592 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.75 % Allowed : 20.74 % Favored : 77.51 % 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: 3.25 (0.33), residues: 614 helix: 3.05 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.18 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 70 HIS 0.002 0.001 HIS K 2 PHE 0.011 0.001 PHE B 55 TYR 0.008 0.001 TYR B 128 ARG 0.001 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.552 Fit side-chains REVERT: A 64 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8266 (tp) REVERT: B 64 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8302 (tp) outliers start: 8 outliers final: 5 residues processed: 103 average time/residue: 0.1602 time to fit residues: 21.5450 Evaluate side-chains 101 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 0.0470 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.177536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.138443 restraints weight = 6546.826| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.42 r_work: 0.3455 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5126 Z= 0.216 Angle : 0.590 6.783 7092 Z= 0.280 Chirality : 0.037 0.136 924 Planarity : 0.003 0.028 800 Dihedral : 8.217 59.556 1592 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.06 % Allowed : 21.40 % Favored : 75.55 % 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: 3.32 (0.32), residues: 614 helix: 3.11 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.17 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 3 HIS 0.002 0.001 HIS I 2 PHE 0.016 0.001 PHE B 55 TYR 0.007 0.001 TYR B 128 ARG 0.000 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.516 Fit side-chains REVERT: A 64 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8274 (tp) REVERT: A 106 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: B 64 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8320 (tp) REVERT: B 106 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.7992 (m-80) outliers start: 14 outliers final: 10 residues processed: 98 average time/residue: 0.1622 time to fit residues: 20.6571 Evaluate side-chains 108 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.177216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.137927 restraints weight = 6469.006| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.40 r_work: 0.3442 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5126 Z= 0.230 Angle : 0.595 6.696 7092 Z= 0.283 Chirality : 0.038 0.136 924 Planarity : 0.003 0.030 800 Dihedral : 8.369 58.855 1592 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.49 % Allowed : 21.18 % Favored : 75.33 % 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: 3.27 (0.32), residues: 614 helix: 3.10 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.28 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 3 HIS 0.002 0.001 HIS A 94 PHE 0.014 0.001 PHE A 55 TYR 0.007 0.001 TYR A 128 ARG 0.001 0.000 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8249 (tp) REVERT: A 106 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: B 64 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8326 (tp) REVERT: B 106 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8047 (m-80) outliers start: 16 outliers final: 12 residues processed: 102 average time/residue: 0.1509 time to fit residues: 20.1269 Evaluate side-chains 112 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.178550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.139605 restraints weight = 6526.033| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.42 r_work: 0.3466 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5126 Z= 0.195 Angle : 0.568 6.559 7092 Z= 0.274 Chirality : 0.037 0.131 924 Planarity : 0.003 0.030 800 Dihedral : 8.204 59.614 1592 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.18 % Allowed : 23.14 % Favored : 74.67 % 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: 3.37 (0.32), residues: 614 helix: 3.18 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.25 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 3 HIS 0.002 0.001 HIS I 2 PHE 0.010 0.001 PHE B 55 TYR 0.007 0.001 TYR B 128 ARG 0.001 0.000 ARG B 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.503 Fit side-chains REVERT: A 64 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8223 (tp) REVERT: B 64 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8296 (tp) outliers start: 10 outliers final: 8 residues processed: 100 average time/residue: 0.1358 time to fit residues: 18.3666 Evaluate side-chains 104 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 3 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.177654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138482 restraints weight = 6508.676| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.40 r_work: 0.3459 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5126 Z= 0.207 Angle : 0.581 6.606 7092 Z= 0.280 Chirality : 0.037 0.138 924 Planarity : 0.003 0.030 800 Dihedral : 8.258 59.552 1592 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.84 % Allowed : 22.49 % Favored : 74.67 % 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: 3.29 (0.32), residues: 614 helix: 3.12 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.30 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 3 HIS 0.002 0.001 HIS I 2 PHE 0.012 0.001 PHE A 55 TYR 0.007 0.001 TYR B 128 ARG 0.001 0.000 ARG A 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2373.59 seconds wall clock time: 42 minutes 55.52 seconds (2575.52 seconds total)