Starting phenix.real_space_refine on Mon Jan 13 20:15:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c45_45175/01_2025/9c45_45175.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c45_45175/01_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_45175/01_2025/9c45_45175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c45_45175/01_2025/9c45_45175.map" model { file = "/net/cci-nas-00/data/ceres_data/9c45_45175/01_2025/9c45_45175.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c45_45175/01_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 6.05, per 1000 atoms: 1.55 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: 1.14 Conformation dependent library (CDL) restraints added in 493.3 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: 0.62 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: 1.30 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: 7.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.650 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.390 ------------------------------------------------------------------------------- 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 4003 Z= 0.709 Angle : 1.256 7.808 5459 Z= 0.836 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 *********************** 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 : 0.420 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: 0.2186 time to fit residues: 13.7435 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 : 0.386 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.108972 restraints weight = 4211.976| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.34 r_work: 0.3038 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 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 4003 Z= 0.266 Angle : 0.574 7.558 5459 Z= 0.301 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 *********************** 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 : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.9052 (t) cc_final: 0.8833 (m) REVERT: A 202 LYS cc_start: 0.8649 (mttm) cc_final: 0.8326 (mttp) outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 0.1984 time to fit residues: 11.3826 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 : 0.432 ------------------------------------------------------------------------------- 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: 0.0770 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 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: 0.0030 overall best weight: 0.4148 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.134870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.102784 restraints weight = 4221.927| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.28 r_work: 0.3023 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4003 Z= 0.213 Angle : 0.513 7.012 5459 Z= 0.268 Chirality : 0.045 0.146 624 Planarity : 0.004 0.032 691 Dihedral : 5.668 40.441 723 Min Nonbonded Distance : 2.556 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: 1.24 (0.39), residues: 482 helix: 2.63 (1.61), residues: 11 sheet: 1.25 (0.36), residues: 203 loop : 0.51 (0.39), residues: 268 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 0.017 0.001 TYR A 170 ARG 0.006 0.000 ARG A 190 *********************** 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 46 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 165 ASN cc_start: 0.6587 (OUTLIER) cc_final: 0.6316 (t160) REVERT: A 273 ARG cc_start: 0.8766 (mmt180) cc_final: 0.8535 (mmt180) REVERT: A 304 LYS cc_start: 0.8576 (mmtm) cc_final: 0.7481 (mttt) outliers start: 2 outliers final: 0 residues processed: 46 average time/residue: 0.2143 time to fit residues: 12.0820 Evaluate side-chains 42 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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: 0.9990 chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 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 = 0.3470 r_free = 0.3470 target = 0.131870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.099839 restraints weight = 4255.182| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.29 r_work: 0.2961 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4003 Z= 0.283 Angle : 0.533 7.929 5459 Z= 0.276 Chirality : 0.045 0.148 624 Planarity : 0.004 0.030 691 Dihedral : 4.910 33.864 723 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.25 % Allowed : 4.49 % 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: 0.99 (0.38), residues: 482 helix: 2.70 (1.61), residues: 11 sheet: 1.13 (0.37), residues: 201 loop : 0.28 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.015 0.002 PHE H 50 TYR 0.016 0.002 TYR A 170 ARG 0.003 0.000 ARG A 190 *********************** 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 51 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.444 Fit side-chains REVERT: A 215 ASP cc_start: 0.7987 (p0) cc_final: 0.7775 (p0) outliers start: 8 outliers final: 3 residues processed: 49 average time/residue: 0.2061 time to fit residues: 12.2923 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 : 0.398 ------------------------------------------------------------------------------- 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: 0.7980 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 25 optimal weight: 0.0980 chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.129170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.096971 restraints weight = 4391.683| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.31 r_work: 0.2914 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4003 Z= 0.234 Angle : 0.500 7.899 5459 Z= 0.259 Chirality : 0.045 0.205 624 Planarity : 0.004 0.030 691 Dihedral : 4.699 34.707 723 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.15 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: 0.86 (0.38), residues: 482 helix: 2.61 (1.60), residues: 11 sheet: 1.01 (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 *********************** 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 46 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.436 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 43 average time/residue: 0.2039 time to fit residues: 10.8219 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 : 0.408 ------------------------------------------------------------------------------- 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: 0.9990 chunk 26 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 9 optimal weight: 0.0870 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.0030 chunk 42 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 overall best weight: 0.4768 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.129083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.096948 restraints weight = 4307.146| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.31 r_work: 0.2842 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4003 Z= 0.227 Angle : 0.504 7.844 5459 Z= 0.262 Chirality : 0.046 0.323 624 Planarity : 0.004 0.030 691 Dihedral : 4.352 23.764 723 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.53 % Allowed : 5.90 % Favored : 91.57 % 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: 0.84 (0.38), residues: 482 helix: 2.60 (1.60), residues: 11 sheet: 0.93 (0.36), residues: 201 loop : 0.27 (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 0.012 0.001 PHE A 133 TYR 0.017 0.001 TYR A 170 ARG 0.004 0.000 ARG A 190 *********************** 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 : 0.429 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 45 average time/residue: 0.1821 time to fit residues: 10.2784 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 : 0.434 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.0010 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.139911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.108096 restraints weight = 4150.854| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.25 r_work: 0.2941 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4003 Z= 0.253 Angle : 0.513 7.869 5459 Z= 0.267 Chirality : 0.046 0.268 624 Planarity : 0.004 0.030 691 Dihedral : 4.266 17.567 723 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.69 % Allowed : 7.02 % Favored : 91.29 % 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: 0.76 (0.38), residues: 482 helix: 2.70 (1.61), residues: 11 sheet: 0.71 (0.35), residues: 204 loop : 0.36 (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 0.017 0.001 TYR A 170 ARG 0.004 0.000 ARG A 190 *********************** 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 45 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.444 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 42 average time/residue: 0.2055 time to fit residues: 10.7188 Evaluate side-chains 43 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 198 ASP 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: 0.9980 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 41 optimal weight: 0.0670 chunk 30 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.140266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.108235 restraints weight = 4145.404| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.28 r_work: 0.2876 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 4003 Z= 0.234 Angle : 0.509 8.107 5459 Z= 0.263 Chirality : 0.045 0.247 624 Planarity : 0.003 0.030 691 Dihedral : 4.195 17.030 723 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.97 % Allowed : 6.46 % Favored : 91.57 % 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: 0.72 (0.38), residues: 482 helix: 2.64 (1.60), residues: 11 sheet: 0.64 (0.35), residues: 204 loop : 0.38 (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 0.022 0.001 TYR A 170 ARG 0.003 0.000 ARG A 190 *********************** 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 48 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.388 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 0.1988 time to fit residues: 10.8965 Evaluate side-chains 45 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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: 0.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 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 = 0.3580 r_free = 0.3580 target = 0.140007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.108131 restraints weight = 4177.214| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.26 r_work: 0.2922 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4003 Z= 0.253 Angle : 0.525 7.985 5459 Z= 0.271 Chirality : 0.045 0.234 624 Planarity : 0.004 0.030 691 Dihedral : 4.211 18.461 723 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.25 % Allowed : 6.46 % Favored : 91.29 % 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: 2.68 (1.60), residues: 11 sheet: 0.59 (0.35), residues: 204 loop : 0.36 (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 0.014 0.001 PHE A 133 TYR 0.022 0.002 TYR A 170 ARG 0.003 0.000 ARG A 190 *********************** 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: 8 poor density : 37 time to evaluate : 0.407 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 41 average time/residue: 0.2117 time to fit residues: 10.6572 Evaluate side-chains 42 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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: 0.0770 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 47 optimal weight: 0.0670 overall best weight: 0.5476 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.139990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.108077 restraints weight = 4173.223| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.25 r_work: 0.2888 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4003 Z= 0.256 Angle : 0.523 7.664 5459 Z= 0.269 Chirality : 0.045 0.224 624 Planarity : 0.004 0.030 691 Dihedral : 4.210 16.817 723 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.25 % Allowed : 6.46 % Favored : 91.29 % 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: 2.67 (1.60), residues: 11 sheet: 0.55 (0.35), residues: 204 loop : 0.36 (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 0.001 PHE H 50 TYR 0.022 0.002 TYR A 170 ARG 0.003 0.000 ARG A 190 ********************** 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 45 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.478 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 41 average time/residue: 0.2019 time to fit residues: 10.3307 Evaluate side-chains 44 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 63 THR 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: 0.9980 chunk 11 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.145720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.114221 restraints weight = 4052.590| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.17 r_work: 0.3026 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 4003 Z= 0.323 Angle : 0.555 8.218 5459 Z= 0.284 Chirality : 0.046 0.225 624 Planarity : 0.004 0.030 691 Dihedral : 4.348 16.405 723 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.53 % Allowed : 6.18 % Favored : 91.29 % 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: 0.54 (0.38), residues: 482 helix: 2.82 (1.63), residues: 11 sheet: 0.47 (0.35), residues: 204 loop : 0.28 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.014 0.002 PHE H 50 TYR 0.023 0.002 TYR A 170 ARG 0.003 0.000 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2640.87 seconds wall clock time: 48 minutes 12.71 seconds (2892.71 seconds total)