Starting phenix.real_space_refine on Sun Apr 27 00:07:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c45_45175/04_2025/9c45_45175.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c45_45175/04_2025/9c45_45175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c45_45175/04_2025/9c45_45175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c45_45175/04_2025/9c45_45175.map" model { file = "/net/cci-nas-00/data/ceres_data/9c45_45175/04_2025/9c45_45175.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c45_45175/04_2025/9c45_45175.cif" } resolution = 3.2 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= 0.085 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 14 5.16 5 C 2530 2.51 5 N 642 2.21 5 O 714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3900 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 806 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 923 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2048 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 14, 'TRANS': 253} Chain breaks: 4 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.19, per 1000 atoms: 1.33 Number of scatterers: 3900 At special positions: 0 Unit cell: (91.044, 69.126, 80.928, 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 14 16.00 O 714 8.00 N 642 7.00 C 2530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 17 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 165 " " NAG B 1 " - " ASN A 122 " " NAG C 1 " - " ASN A 234 " Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 487.9 milliseconds 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 922 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 11 sheets defined 5.4% alpha, 50.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 294 through 304 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.042A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.760A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.760A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.652A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.766A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.766A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.425A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.276A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 153 through 155 167 hydrogen bonds defined for protein. 402 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: 1.18 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 847 1.33 - 1.45: 978 1.45 - 1.57: 2159 1.57 - 1.70: 1 1.70 - 1.82: 18 Bond restraints: 4003 Sorted by residual: bond pdb=" CB LEU A 176 " pdb=" CG LEU A 176 " ideal model delta sigma weight residual 1.530 1.587 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.66e+00 bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.466 -0.053 2.00e-02 2.50e+03 7.14e+00 bond pdb=" C5 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.413 1.466 -0.053 2.00e-02 2.50e+03 7.09e+00 ... (remaining 3998 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4637 1.56 - 3.12: 677 3.12 - 4.68: 79 4.68 - 6.25: 48 6.25 - 7.81: 18 Bond angle restraints: 5459 Sorted by residual: angle pdb=" C LEU A 24 " pdb=" N PRO A 25 " pdb=" CA PRO A 25 " ideal model delta sigma weight residual 119.66 126.00 -6.34 7.20e-01 1.93e+00 7.76e+01 angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.63 -7.60 9.90e-01 1.02e+00 5.89e+01 angle pdb=" C ASP A 138 " pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta sigma weight residual 119.85 127.30 -7.45 1.01e+00 9.80e-01 5.45e+01 angle pdb=" C PRO A 25 " pdb=" N PRO A 26 " pdb=" CA PRO A 26 " ideal model delta sigma weight residual 119.85 127.07 -7.22 1.01e+00 9.80e-01 5.11e+01 angle pdb=" C GLY L 99 " pdb=" N PRO L 100 " pdb=" CA PRO L 100 " ideal model delta sigma weight residual 119.32 127.13 -7.81 1.14e+00 7.69e-01 4.69e+01 ... (remaining 5454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.34: 2351 21.34 - 42.68: 53 42.68 - 64.02: 9 64.02 - 85.36: 7 85.36 - 106.70: 4 Dihedral angle restraints: 2424 sinusoidal: 984 harmonic: 1440 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 47.61 45.39 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CA ASP A 138 " pdb=" C ASP A 138 " pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta harmonic sigma weight residual -180.00 -161.30 -18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.99 106.70 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 2421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 456 0.071 - 0.143: 122 0.143 - 0.214: 35 0.214 - 0.285: 3 0.285 - 0.356: 8 Chirality restraints: 624 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 3.17e+01 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.89e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 1.86e+01 ... (remaining 621 not shown) Planarity restraints: 697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE L 31 " 0.019 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C PHE L 31 " -0.068 2.00e-02 2.50e+03 pdb=" O PHE L 31 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR L 32 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 122 " -0.028 2.00e-02 2.50e+03 2.88e-02 1.04e+01 pdb=" CG ASN A 122 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 122 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 122 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " 0.024 2.00e-02 2.50e+03 1.20e-02 3.63e+00 pdb=" CG TRP H 47 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " 0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " 0.010 2.00e-02 2.50e+03 ... (remaining 694 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1953 2.99 - 3.46: 3208 3.46 - 3.94: 6396 3.94 - 4.42: 7253 4.42 - 4.90: 12349 Nonbonded interactions: 31159 Sorted by model distance: nonbonded pdb=" O THR H 28 " pdb=" CG2 THR H 28 " model vdw 2.507 3.460 nonbonded pdb=" N ASP A 138 " pdb=" OD1 ASP A 138 " model vdw 2.573 3.120 nonbonded pdb=" N ARG A 158 " pdb=" N VAL A 159 " model vdw 2.574 2.560 nonbonded pdb=" N PHE H 27 " pdb=" O PHE H 27 " model vdw 2.602 2.496 nonbonded pdb=" OG1 THR A 108 " pdb=" N THR A 109 " model vdw 2.607 3.120 ... (remaining 31154 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.770 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.990 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.011 0.060 4017 Z= 0.597 Angle : 1.272 7.808 5496 Z= 0.838 Chirality : 0.078 0.356 624 Planarity : 0.005 0.040 691 Dihedral : 11.880 106.704 1487 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.38), residues: 482 helix: 0.89 (1.63), residues: 11 sheet: 1.24 (0.35), residues: 215 loop : 0.87 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP H 47 HIS 0.002 0.001 HIS A 66 PHE 0.016 0.003 PHE A 55 TYR 0.025 0.004 TYR A 269 ARG 0.003 0.000 ARG H 103 Details of bonding type rmsd link_NAG-ASN : bond 0.05533 ( 6) link_NAG-ASN : angle 2.07045 ( 18) link_BETA1-4 : bond 0.05693 ( 3) link_BETA1-4 : angle 2.69629 ( 9) hydrogen bonds : bond 0.14217 ( 155) hydrogen bonds : angle 8.54372 ( 402) SS BOND : bond 0.00737 ( 5) SS BOND : angle 3.65067 ( 10) covalent geometry : bond 0.01092 ( 4003) covalent geometry : angle 1.25623 ( 5459) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8751 (m-80) cc_final: 0.8448 (m-80) REVERT: A 202 LYS cc_start: 0.8586 (mttm) cc_final: 0.8355 (mttp) REVERT: A 280 ASN cc_start: 0.8658 (p0) cc_final: 0.8088 (p0) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2137 time to fit residues: 13.4285 Evaluate side-chains 40 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.108974 restraints weight = 4211.975| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.34 r_work: 0.3036 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4017 Z= 0.171 Angle : 0.642 13.771 5496 Z= 0.316 Chirality : 0.046 0.172 624 Planarity : 0.004 0.031 691 Dihedral : 8.746 68.882 723 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.84 % Allowed : 3.65 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.54 (0.39), residues: 482 helix: 2.66 (1.69), residues: 11 sheet: 1.27 (0.35), residues: 218 loop : 0.86 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS A 66 PHE 0.014 0.002 PHE H 50 TYR 0.017 0.002 TYR A 170 ARG 0.002 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 6) link_NAG-ASN : angle 4.79033 ( 18) link_BETA1-4 : bond 0.00540 ( 3) link_BETA1-4 : angle 2.21970 ( 9) hydrogen bonds : bond 0.03493 ( 155) hydrogen bonds : angle 6.33180 ( 402) SS BOND : bond 0.00362 ( 5) SS BOND : angle 0.99427 ( 10) covalent geometry : bond 0.00409 ( 4003) covalent geometry : angle 0.57437 ( 5459) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.9055 (t) cc_final: 0.8836 (m) REVERT: A 202 LYS cc_start: 0.8655 (mttm) cc_final: 0.8333 (mttp) outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 0.1969 time to fit residues: 11.2513 Evaluate side-chains 42 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain A residue 165 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.0060 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.137396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.105084 restraints weight = 4201.094| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.33 r_work: 0.2943 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4017 Z= 0.142 Angle : 0.568 10.502 5496 Z= 0.282 Chirality : 0.045 0.148 624 Planarity : 0.004 0.031 691 Dihedral : 6.098 41.155 723 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.56 % Allowed : 5.06 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.39), residues: 482 helix: 2.76 (1.63), residues: 11 sheet: 1.15 (0.36), residues: 206 loop : 0.58 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS A 49 PHE 0.012 0.001 PHE H 50 TYR 0.016 0.001 TYR A 170 ARG 0.007 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 6) link_NAG-ASN : angle 3.86072 ( 18) link_BETA1-4 : bond 0.00447 ( 3) link_BETA1-4 : angle 2.00423 ( 9) hydrogen bonds : bond 0.03069 ( 155) hydrogen bonds : angle 5.76465 ( 402) SS BOND : bond 0.00210 ( 5) SS BOND : angle 0.60649 ( 10) covalent geometry : bond 0.00336 ( 4003) covalent geometry : angle 0.51844 ( 5459) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 165 ASN cc_start: 0.6698 (OUTLIER) cc_final: 0.6405 (t160) REVERT: A 273 ARG cc_start: 0.8770 (mmt180) cc_final: 0.8525 (mmt180) outliers start: 2 outliers final: 0 residues processed: 44 average time/residue: 0.2028 time to fit residues: 10.9410 Evaluate side-chains 40 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 11 optimal weight: 0.0030 chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.129718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.097385 restraints weight = 4274.842| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.31 r_work: 0.2974 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4017 Z= 0.170 Angle : 0.564 9.318 5496 Z= 0.281 Chirality : 0.044 0.140 624 Planarity : 0.004 0.030 691 Dihedral : 4.916 36.017 723 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.97 % Allowed : 4.78 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.00 (0.39), residues: 482 helix: 2.55 (1.58), residues: 11 sheet: 1.15 (0.37), residues: 201 loop : 0.29 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.014 0.002 PHE H 50 TYR 0.016 0.002 TYR A 170 ARG 0.005 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 6) link_NAG-ASN : angle 3.37057 ( 18) link_BETA1-4 : bond 0.00397 ( 3) link_BETA1-4 : angle 1.76766 ( 9) hydrogen bonds : bond 0.03046 ( 155) hydrogen bonds : angle 5.59558 ( 402) SS BOND : bond 0.00287 ( 5) SS BOND : angle 0.72580 ( 10) covalent geometry : bond 0.00411 ( 4003) covalent geometry : angle 0.52594 ( 5459) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.410 Fit side-chains REVERT: A 215 ASP cc_start: 0.8008 (p0) cc_final: 0.7795 (p0) REVERT: A 273 ARG cc_start: 0.8771 (mmt180) cc_final: 0.8545 (mmt180) outliers start: 7 outliers final: 3 residues processed: 46 average time/residue: 0.1874 time to fit residues: 10.7080 Evaluate side-chains 42 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 0.0470 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 6 optimal weight: 0.0050 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 overall best weight: 0.5092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.129426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.097052 restraints weight = 4389.726| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.33 r_work: 0.2889 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4017 Z= 0.152 Angle : 0.511 7.995 5496 Z= 0.261 Chirality : 0.045 0.181 624 Planarity : 0.004 0.030 691 Dihedral : 4.701 33.367 723 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.69 % Allowed : 5.90 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.90 (0.38), residues: 482 helix: 2.64 (1.60), residues: 11 sheet: 1.05 (0.36), residues: 201 loop : 0.23 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.013 0.001 PHE A 133 TYR 0.017 0.001 TYR A 170 ARG 0.003 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 6) link_NAG-ASN : angle 1.60464 ( 18) link_BETA1-4 : bond 0.00415 ( 3) link_BETA1-4 : angle 1.60398 ( 9) hydrogen bonds : bond 0.02864 ( 155) hydrogen bonds : angle 5.50691 ( 402) SS BOND : bond 0.00227 ( 5) SS BOND : angle 0.45375 ( 10) covalent geometry : bond 0.00368 ( 4003) covalent geometry : angle 0.50010 ( 5459) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.411 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 45 average time/residue: 0.2037 time to fit residues: 11.2291 Evaluate side-chains 44 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 210 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 0.0670 chunk 26 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.140448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.108595 restraints weight = 4159.612| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.26 r_work: 0.2974 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4017 Z= 0.153 Angle : 0.508 8.327 5496 Z= 0.260 Chirality : 0.044 0.154 624 Planarity : 0.004 0.030 691 Dihedral : 4.439 25.771 723 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.53 % Allowed : 5.62 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.81 (0.38), residues: 482 helix: 2.66 (1.60), residues: 11 sheet: 0.85 (0.36), residues: 204 loop : 0.30 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.012 0.001 PHE H 50 TYR 0.015 0.001 TYR A 170 ARG 0.003 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 6) link_NAG-ASN : angle 1.35679 ( 18) link_BETA1-4 : bond 0.00385 ( 3) link_BETA1-4 : angle 1.57195 ( 9) hydrogen bonds : bond 0.02832 ( 155) hydrogen bonds : angle 5.48418 ( 402) SS BOND : bond 0.00232 ( 5) SS BOND : angle 0.43374 ( 10) covalent geometry : bond 0.00369 ( 4003) covalent geometry : angle 0.49888 ( 5459) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.472 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 46 average time/residue: 0.2029 time to fit residues: 11.6303 Evaluate side-chains 44 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 210 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.139477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.107393 restraints weight = 4151.920| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.27 r_work: 0.2879 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4017 Z= 0.183 Angle : 0.542 8.356 5496 Z= 0.278 Chirality : 0.047 0.338 624 Planarity : 0.004 0.030 691 Dihedral : 4.394 20.420 723 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.97 % Allowed : 5.90 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.71 (0.38), residues: 482 helix: 2.79 (1.62), residues: 11 sheet: 0.70 (0.35), residues: 204 loop : 0.30 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.002 0.001 HIS A 49 PHE 0.015 0.002 PHE H 29 TYR 0.018 0.002 TYR A 170 ARG 0.003 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 6) link_NAG-ASN : angle 1.39602 ( 18) link_BETA1-4 : bond 0.00369 ( 3) link_BETA1-4 : angle 1.58252 ( 9) hydrogen bonds : bond 0.02965 ( 155) hydrogen bonds : angle 5.52017 ( 402) SS BOND : bond 0.00276 ( 5) SS BOND : angle 0.53836 ( 10) covalent geometry : bond 0.00448 ( 4003) covalent geometry : angle 0.53339 ( 5459) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.403 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 43 average time/residue: 0.2256 time to fit residues: 11.9309 Evaluate side-chains 43 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 210 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 41 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.139874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107806 restraints weight = 4145.170| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.26 r_work: 0.2915 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4017 Z= 0.158 Angle : 0.526 8.383 5496 Z= 0.269 Chirality : 0.046 0.298 624 Planarity : 0.004 0.030 691 Dihedral : 4.275 17.481 723 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.69 % Allowed : 6.18 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.68 (0.38), residues: 482 helix: 2.72 (1.60), residues: 11 sheet: 0.63 (0.35), residues: 204 loop : 0.33 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.013 0.001 PHE A 133 TYR 0.018 0.001 TYR A 170 ARG 0.003 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 6) link_NAG-ASN : angle 1.44627 ( 18) link_BETA1-4 : bond 0.00373 ( 3) link_BETA1-4 : angle 1.52797 ( 9) hydrogen bonds : bond 0.02795 ( 155) hydrogen bonds : angle 5.45904 ( 402) SS BOND : bond 0.00239 ( 5) SS BOND : angle 0.51256 ( 10) covalent geometry : bond 0.00382 ( 4003) covalent geometry : angle 0.51741 ( 5459) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.537 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 42 average time/residue: 0.3181 time to fit residues: 16.8907 Evaluate side-chains 44 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 210 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.128349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.096211 restraints weight = 4327.282| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.30 r_work: 0.2991 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4017 Z= 0.156 Angle : 0.536 7.879 5496 Z= 0.273 Chirality : 0.046 0.279 624 Planarity : 0.004 0.030 691 Dihedral : 4.244 18.481 723 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.97 % Allowed : 6.18 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.64 (0.38), residues: 482 helix: 2.73 (1.60), residues: 11 sheet: 0.57 (0.35), residues: 204 loop : 0.34 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.014 0.001 PHE A 133 TYR 0.019 0.001 TYR A 170 ARG 0.003 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 6) link_NAG-ASN : angle 1.75248 ( 18) link_BETA1-4 : bond 0.00368 ( 3) link_BETA1-4 : angle 1.50651 ( 9) hydrogen bonds : bond 0.02760 ( 155) hydrogen bonds : angle 5.42892 ( 402) SS BOND : bond 0.00231 ( 5) SS BOND : angle 0.44023 ( 10) covalent geometry : bond 0.00378 ( 4003) covalent geometry : angle 0.52421 ( 5459) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.501 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 42 average time/residue: 0.2778 time to fit residues: 14.9192 Evaluate side-chains 43 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 210 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.0270 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 47 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.146596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.114941 restraints weight = 4129.264| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.20 r_work: 0.3028 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4017 Z= 0.170 Angle : 0.540 7.734 5496 Z= 0.275 Chirality : 0.046 0.273 624 Planarity : 0.004 0.030 691 Dihedral : 4.254 17.119 723 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.97 % Allowed : 6.18 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.59 (0.38), residues: 482 helix: 2.73 (1.60), residues: 11 sheet: 0.52 (0.35), residues: 204 loop : 0.31 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.012 0.002 PHE H 50 TYR 0.019 0.002 TYR A 170 ARG 0.003 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 6) link_NAG-ASN : angle 1.55260 ( 18) link_BETA1-4 : bond 0.00380 ( 3) link_BETA1-4 : angle 1.53455 ( 9) hydrogen bonds : bond 0.02829 ( 155) hydrogen bonds : angle 5.46948 ( 402) SS BOND : bond 0.00260 ( 5) SS BOND : angle 0.45429 ( 10) covalent geometry : bond 0.00416 ( 4003) covalent geometry : angle 0.53067 ( 5459) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.562 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 39 average time/residue: 0.2117 time to fit residues: 10.2704 Evaluate side-chains 42 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 210 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.146542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.115036 restraints weight = 4043.223| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.18 r_work: 0.3034 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4017 Z= 0.173 Angle : 0.542 7.930 5496 Z= 0.275 Chirality : 0.046 0.266 624 Planarity : 0.004 0.030 691 Dihedral : 4.265 16.492 723 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.97 % Allowed : 6.18 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.58 (0.38), residues: 482 helix: 2.70 (1.60), residues: 11 sheet: 0.51 (0.35), residues: 204 loop : 0.30 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.012 0.002 PHE A 133 TYR 0.019 0.002 TYR A 170 ARG 0.003 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 6) link_NAG-ASN : angle 1.50772 ( 18) link_BETA1-4 : bond 0.00359 ( 3) link_BETA1-4 : angle 1.54290 ( 9) hydrogen bonds : bond 0.02804 ( 155) hydrogen bonds : angle 5.48329 ( 402) SS BOND : bond 0.00258 ( 5) SS BOND : angle 0.43384 ( 10) covalent geometry : bond 0.00422 ( 4003) covalent geometry : angle 0.53289 ( 5459) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3504.76 seconds wall clock time: 62 minutes 56.47 seconds (3776.47 seconds total)