Starting phenix.real_space_refine on Thu Jul 2 01:37:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8p6v_17508/07_2026/8p6v_17508.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p6v_17508/07_2026/8p6v_17508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p6v_17508/07_2026/8p6v_17508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p6v_17508/07_2026/8p6v_17508.map" model { file = "/net/cci-nas-00/data/ceres_data/8p6v_17508/07_2026/8p6v_17508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p6v_17508/07_2026/8p6v_17508.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8p6v_17508/07_2026/8p6v_17508.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8p6v_17508/07_2026/8p6v_17508.cif" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 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 31 5.16 5 C 3291 2.51 5 N 870 2.21 5 O 1051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5243 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'I74': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Time building chain proxies: 1.17, per 1000 atoms: 0.22 Number of scatterers: 5243 At special positions: 0 Unit cell: (84.7875, 94.05, 69.1125, 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 31 16.00 O 1051 8.00 N 870 7.00 C 3291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 149.0 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 3 sheets defined 63.0% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'H' and resid 262 through 266 Processing helix chain 'H' and resid 270 through 275 removed outlier: 3.520A pdb=" N VAL H 275 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 285 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.860A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 38 Processing helix chain 'I' and resid 49 through 71 Processing helix chain 'I' and resid 76 through 93 removed outlier: 4.008A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.827A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.570A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 183 through 186 Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.516A pdb=" N THR I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 228 through 235 removed outlier: 3.913A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 240 Processing helix chain 'I' and resid 241 through 262 Processing helix chain 'I' and resid 266 through 284 Processing helix chain 'J' and resid 56 through 69 removed outlier: 4.136A pdb=" N GLU J 68 " --> pdb=" O LYS J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.573A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 230 Processing helix chain 'J' and resid 239 through 243 removed outlier: 3.556A pdb=" N LEU J 243 " --> pdb=" O MET J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 292 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.655A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'J' and resid 17 through 21 removed outlier: 5.582A pdb=" N PHE J 17 " --> pdb=" O LYS J 28 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LYS J 28 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR J 25 " --> pdb=" O LYS J 42 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 279 hydrogen bonds defined for protein. 780 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.67 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1637 1.34 - 1.46: 969 1.46 - 1.58: 2572 1.58 - 1.69: 2 1.69 - 1.81: 49 Bond restraints: 5229 Sorted by residual: bond pdb=" C3 I74 J 401 " pdb=" N10 I74 J 401 " ideal model delta sigma weight residual 1.335 1.489 -0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" C26 I74 J 401 " pdb=" C8 I74 J 401 " ideal model delta sigma weight residual 1.497 1.602 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C5 I74 J 401 " pdb=" N18 I74 J 401 " ideal model delta sigma weight residual 1.350 1.453 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C41 I74 J 401 " pdb=" C46 I74 J 401 " ideal model delta sigma weight residual 1.532 1.456 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C40 I74 J 401 " pdb=" C41 I74 J 401 " ideal model delta sigma weight residual 1.524 1.592 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 5224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 6921 1.72 - 3.43: 124 3.43 - 5.15: 23 5.15 - 6.87: 8 6.87 - 8.59: 1 Bond angle restraints: 7077 Sorted by residual: angle pdb=" CA LYS I 260 " pdb=" CB LYS I 260 " pdb=" CG LYS I 260 " ideal model delta sigma weight residual 114.10 120.32 -6.22 2.00e+00 2.50e-01 9.68e+00 angle pdb=" CB LYS J 293 " pdb=" CG LYS J 293 " pdb=" CD LYS J 293 " ideal model delta sigma weight residual 111.30 118.04 -6.74 2.30e+00 1.89e-01 8.59e+00 angle pdb=" CA GLU I 268 " pdb=" CB GLU I 268 " pdb=" CG GLU I 268 " ideal model delta sigma weight residual 114.10 119.75 -5.65 2.00e+00 2.50e-01 7.97e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.45 4.45 1.80e+00 3.09e-01 6.10e+00 angle pdb=" CB LYS I 260 " pdb=" CG LYS I 260 " pdb=" CD LYS I 260 " ideal model delta sigma weight residual 111.30 116.85 -5.55 2.30e+00 1.89e-01 5.82e+00 ... (remaining 7072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 2783 17.41 - 34.83: 270 34.83 - 52.24: 73 52.24 - 69.65: 15 69.65 - 87.06: 13 Dihedral angle restraints: 3154 sinusoidal: 1307 harmonic: 1847 Sorted by residual: dihedral pdb=" CA THR J 175 " pdb=" C THR J 175 " pdb=" N ARG J 176 " pdb=" CA ARG J 176 " ideal model delta harmonic sigma weight residual 180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CG ARG J 176 " pdb=" CD ARG J 176 " pdb=" NE ARG J 176 " pdb=" CZ ARG J 176 " ideal model delta sinusoidal sigma weight residual 180.00 136.01 43.99 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 164.41 15.59 0 5.00e+00 4.00e-02 9.72e+00 ... (remaining 3151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 445 0.028 - 0.057: 210 0.057 - 0.085: 75 0.085 - 0.114: 39 0.114 - 0.142: 8 Chirality restraints: 777 Sorted by residual: chirality pdb=" CA TYR I 91 " pdb=" N TYR I 91 " pdb=" C TYR I 91 " pdb=" CB TYR I 91 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA VAL J 210 " pdb=" N VAL J 210 " pdb=" C VAL J 210 " pdb=" CB VAL J 210 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA VAL H 260 " pdb=" N VAL H 260 " pdb=" C VAL H 260 " pdb=" CB VAL H 260 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 774 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS J 14 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C LYS J 14 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS J 14 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU J 15 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 162 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO I 163 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO I 163 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO I 163 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS J 201 " 0.006 2.00e-02 2.50e+03 1.21e-02 1.47e+00 pdb=" C CYS J 201 " -0.021 2.00e-02 2.50e+03 pdb=" O CYS J 201 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE J 202 " 0.007 2.00e-02 2.50e+03 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 836 2.76 - 3.29: 5304 3.29 - 3.83: 9756 3.83 - 4.36: 11745 4.36 - 4.90: 18996 Nonbonded interactions: 46637 Sorted by model distance: nonbonded pdb=" O GLY H 285 " pdb=" O HOH H 401 " model vdw 2.221 3.040 nonbonded pdb=" O LEU I 236 " pdb=" O HOH I 401 " model vdw 2.225 3.040 nonbonded pdb=" O MET J 189 " pdb=" O HOH J 501 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR I 178 " pdb=" OG SER I 230 " model vdw 2.238 3.040 nonbonded pdb=" O HOH J 567 " pdb=" O HOH J 571 " model vdw 2.243 3.040 ... (remaining 46632 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: 3.540 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.710 Find NCS groups from input model: 0.020 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:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 : 0.005 0.154 5229 Z= 0.240 Angle : 0.616 8.587 7077 Z= 0.309 Chirality : 0.041 0.142 777 Planarity : 0.004 0.031 903 Dihedral : 16.214 87.063 1958 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.26 % Allowed : 13.90 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.34), residues: 618 helix: 1.80 (0.28), residues: 337 sheet: 0.43 (1.28), residues: 20 loop : 0.10 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 268 TYR 0.015 0.002 TYR I 91 PHE 0.015 0.002 PHE I 110 TRP 0.012 0.001 TRP J 132 HIS 0.007 0.001 HIS H 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.24 ( 5229) covalent geometry : angle 0.61558 / 0.31 ( 7077) hydrogen bonds : bond 0.14389 / 9.13 ( 279) hydrogen bonds : angle 6.06668 / 4.42 ( 780) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.163 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 92 average time/residue: 0.6571 time to fit residues: 62.6811 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 249 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.174854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.152418 restraints weight = 4837.764| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 0.97 r_work: 0.3743 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5229 Z= 0.183 Angle : 0.629 7.622 7077 Z= 0.327 Chirality : 0.044 0.138 777 Planarity : 0.005 0.036 903 Dihedral : 7.781 88.095 707 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 3.25 % Allowed : 12.82 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.34), residues: 618 helix: 1.73 (0.28), residues: 340 sheet: 0.17 (1.14), residues: 20 loop : 0.09 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 268 TYR 0.020 0.002 TYR I 2 PHE 0.014 0.002 PHE I 110 TRP 0.015 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 ( 5229) covalent geometry : angle 0.62865 / 0.33 ( 7077) hydrogen bonds : bond 0.05740 / 3.86 ( 279) hydrogen bonds : angle 5.08252 / 3.64 ( 780) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.235 Fit side-chains REVERT: I 141 GLU cc_start: 0.7077 (tp30) cc_final: 0.6676 (tp30) REVERT: J 169 TYR cc_start: 0.6083 (OUTLIER) cc_final: 0.5861 (m-80) outliers start: 18 outliers final: 7 residues processed: 98 average time/residue: 0.6012 time to fit residues: 61.1607 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 253 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 169 TYR Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 249 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 0.1980 chunk 9 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.174564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.152010 restraints weight = 4807.924| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 0.97 r_work: 0.3739 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5229 Z= 0.201 Angle : 0.653 7.831 7077 Z= 0.338 Chirality : 0.045 0.146 777 Planarity : 0.005 0.034 903 Dihedral : 7.421 88.210 700 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 4.33 % Allowed : 12.45 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.33), residues: 618 helix: 1.52 (0.27), residues: 341 sheet: 0.59 (1.15), residues: 15 loop : -0.14 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 268 TYR 0.021 0.002 TYR I 2 PHE 0.014 0.002 PHE I 110 TRP 0.017 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 ( 5229) covalent geometry : angle 0.65251 / 0.34 ( 7077) hydrogen bonds : bond 0.05915 / 3.97 ( 279) hydrogen bonds : angle 5.08440 / 3.63 ( 780) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.258 Fit side-chains REVERT: I 141 GLU cc_start: 0.7092 (tp30) cc_final: 0.6678 (tp30) REVERT: I 242 ARG cc_start: 0.6099 (OUTLIER) cc_final: 0.5885 (ptm-80) REVERT: I 261 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7125 (pttt) REVERT: J 62 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6765 (tt0) outliers start: 24 outliers final: 10 residues processed: 102 average time/residue: 0.6543 time to fit residues: 69.2073 Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 75 MET Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 242 ARG Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 253 LYS Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 249 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 46 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.175577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.152931 restraints weight = 4788.823| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 0.98 r_work: 0.3750 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5229 Z= 0.171 Angle : 0.617 7.045 7077 Z= 0.320 Chirality : 0.043 0.145 777 Planarity : 0.005 0.034 903 Dihedral : 7.354 88.647 700 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 3.79 % Allowed : 13.00 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.33), residues: 618 helix: 1.63 (0.27), residues: 341 sheet: 0.56 (1.17), residues: 15 loop : -0.18 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 268 TYR 0.019 0.002 TYR I 2 PHE 0.014 0.002 PHE I 110 TRP 0.015 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 5229) covalent geometry : angle 0.61703 / 0.32 ( 7077) hydrogen bonds : bond 0.05423 / 3.64 ( 279) hydrogen bonds : angle 4.92709 / 3.51 ( 780) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.203 Fit side-chains REVERT: I 141 GLU cc_start: 0.7091 (tp30) cc_final: 0.6676 (tp30) REVERT: J 62 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6721 (tt0) outliers start: 21 outliers final: 12 residues processed: 101 average time/residue: 0.6612 time to fit residues: 69.1902 Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 75 MET Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 253 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 247 VAL Chi-restraints excluded: chain J residue 249 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.176350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.153674 restraints weight = 4860.809| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 0.98 r_work: 0.3758 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5229 Z= 0.150 Angle : 0.589 6.605 7077 Z= 0.304 Chirality : 0.043 0.143 777 Planarity : 0.005 0.033 903 Dihedral : 7.327 89.622 700 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 3.43 % Allowed : 13.90 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.33), residues: 618 helix: 1.76 (0.27), residues: 341 sheet: 0.81 (1.22), residues: 15 loop : -0.13 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 279 TYR 0.018 0.002 TYR I 91 PHE 0.014 0.002 PHE I 110 TRP 0.013 0.002 TRP J 132 HIS 0.006 0.002 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 5229) covalent geometry : angle 0.58917 / 0.30 ( 7077) hydrogen bonds : bond 0.05105 / 3.43 ( 279) hydrogen bonds : angle 4.86076 / 3.49 ( 780) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.216 Fit side-chains REVERT: J 62 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6732 (tt0) outliers start: 19 outliers final: 10 residues processed: 100 average time/residue: 0.6371 time to fit residues: 66.0730 Evaluate side-chains 94 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 253 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 53 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.175626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.152966 restraints weight = 4846.332| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 0.98 r_work: 0.3751 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5229 Z= 0.170 Angle : 0.612 7.055 7077 Z= 0.317 Chirality : 0.043 0.144 777 Planarity : 0.005 0.033 903 Dihedral : 7.057 89.633 698 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 3.43 % Allowed : 13.54 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.33), residues: 618 helix: 1.68 (0.27), residues: 341 sheet: 0.64 (1.22), residues: 15 loop : -0.17 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 268 TYR 0.019 0.002 TYR I 91 PHE 0.014 0.002 PHE I 110 TRP 0.014 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 5229) covalent geometry : angle 0.61222 / 0.32 ( 7077) hydrogen bonds : bond 0.05372 / 3.61 ( 279) hydrogen bonds : angle 4.89368 / 3.48 ( 780) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.219 Fit side-chains REVERT: I 141 GLU cc_start: 0.7147 (tp30) cc_final: 0.6696 (tp30) REVERT: J 62 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6748 (tt0) outliers start: 19 outliers final: 11 residues processed: 95 average time/residue: 0.6677 time to fit residues: 65.7226 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 75 MET Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 253 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 52 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 259 HIS I 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.177853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.155220 restraints weight = 4869.764| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 0.99 r_work: 0.3775 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5229 Z= 0.121 Angle : 0.538 5.969 7077 Z= 0.278 Chirality : 0.041 0.140 777 Planarity : 0.004 0.032 903 Dihedral : 6.916 88.669 698 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.53 % Allowed : 14.62 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.34), residues: 618 helix: 2.05 (0.28), residues: 338 sheet: 1.22 (1.32), residues: 15 loop : -0.12 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 279 TYR 0.016 0.002 TYR I 91 PHE 0.013 0.001 PHE I 30 TRP 0.011 0.001 TRP J 132 HIS 0.007 0.001 HIS H 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 5229) covalent geometry : angle 0.53768 / 0.28 ( 7077) hydrogen bonds : bond 0.04563 / 3.08 ( 279) hydrogen bonds : angle 4.69670 / 3.37 ( 780) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.155 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 96 average time/residue: 0.6692 time to fit residues: 66.4057 Evaluate side-chains 89 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 253 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 259 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.177387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.154638 restraints weight = 4848.162| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 0.98 r_work: 0.3772 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5229 Z= 0.130 Angle : 0.569 7.005 7077 Z= 0.293 Chirality : 0.041 0.139 777 Planarity : 0.004 0.032 903 Dihedral : 6.568 88.237 697 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.53 % Allowed : 14.62 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.34), residues: 618 helix: 2.03 (0.28), residues: 338 sheet: 1.34 (1.37), residues: 15 loop : -0.11 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 279 TYR 0.016 0.002 TYR I 91 PHE 0.013 0.002 PHE I 110 TRP 0.011 0.001 TRP J 132 HIS 0.006 0.001 HIS H 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 5229) covalent geometry : angle 0.56897 / 0.29 ( 7077) hydrogen bonds : bond 0.04643 / 3.12 ( 279) hydrogen bonds : angle 4.65973 / 3.32 ( 780) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.213 Fit side-chains REVERT: I 141 GLU cc_start: 0.7175 (tp30) cc_final: 0.6778 (tp30) outliers start: 14 outliers final: 7 residues processed: 94 average time/residue: 0.6747 time to fit residues: 65.6385 Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 253 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 10 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 0.0010 chunk 0 optimal weight: 5.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 259 HIS I 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.179399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.156732 restraints weight = 4787.461| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 0.98 r_work: 0.3796 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5229 Z= 0.110 Angle : 0.534 6.559 7077 Z= 0.273 Chirality : 0.041 0.136 777 Planarity : 0.004 0.031 903 Dihedral : 6.437 87.277 697 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.17 % Allowed : 14.44 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.34), residues: 618 helix: 2.20 (0.28), residues: 338 sheet: 0.45 (1.39), residues: 20 loop : 0.11 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 279 TYR 0.015 0.001 TYR I 60 PHE 0.012 0.001 PHE I 30 TRP 0.009 0.001 TRP J 132 HIS 0.007 0.001 HIS H 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 5229) covalent geometry : angle 0.53383 / 0.27 ( 7077) hydrogen bonds : bond 0.04199 / 2.84 ( 279) hydrogen bonds : angle 4.55830 / 3.26 ( 780) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.208 Fit side-chains REVERT: I 260 LYS cc_start: 0.6914 (pptt) cc_final: 0.6667 (ttmt) outliers start: 12 outliers final: 7 residues processed: 95 average time/residue: 0.6495 time to fit residues: 63.7746 Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 253 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 259 HIS I 142 GLN I 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.174517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.151594 restraints weight = 4804.226| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 0.98 r_work: 0.3736 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5229 Z= 0.235 Angle : 0.714 8.945 7077 Z= 0.368 Chirality : 0.047 0.142 777 Planarity : 0.006 0.073 903 Dihedral : 6.912 89.463 697 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.99 % Allowed : 15.16 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.33), residues: 618 helix: 1.46 (0.27), residues: 340 sheet: 0.72 (1.22), residues: 15 loop : -0.13 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 279 TYR 0.023 0.003 TYR J 27 PHE 0.014 0.003 PHE J 156 TRP 0.017 0.002 TRP J 132 HIS 0.009 0.002 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 ( 5229) covalent geometry : angle 0.71360 / 0.37 ( 7077) hydrogen bonds : bond 0.05994 / 4.02 ( 279) hydrogen bonds : angle 5.00019 / 3.52 ( 780) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.208 Fit side-chains REVERT: I 141 GLU cc_start: 0.7151 (tp30) cc_final: 0.6698 (tp30) REVERT: J 14 LYS cc_start: 0.6237 (tppt) cc_final: 0.5579 (tptt) REVERT: J 169 TYR cc_start: 0.6099 (m-80) cc_final: 0.5878 (m-80) outliers start: 11 outliers final: 9 residues processed: 94 average time/residue: 0.6598 time to fit residues: 64.2476 Evaluate side-chains 95 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 75 MET Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 253 LYS Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 259 HIS I 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.174440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.151505 restraints weight = 4839.742| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 0.98 r_work: 0.3735 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5229 Z= 0.248 Angle : 0.741 9.892 7077 Z= 0.382 Chirality : 0.048 0.143 777 Planarity : 0.006 0.065 903 Dihedral : 7.009 89.641 697 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.53 % Allowed : 14.80 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.32), residues: 618 helix: 1.13 (0.27), residues: 341 sheet: 0.38 (1.20), residues: 15 loop : -0.34 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 279 TYR 0.023 0.003 TYR I 91 PHE 0.014 0.003 PHE J 156 TRP 0.018 0.002 TRP J 132 HIS 0.009 0.002 HIS J 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.25 ( 5229) covalent geometry : angle 0.74103 / 0.38 ( 7077) hydrogen bonds : bond 0.06145 / 4.12 ( 279) hydrogen bonds : angle 5.11729 / 3.60 ( 780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2744.46 seconds wall clock time: 47 minutes 24.83 seconds (2844.83 seconds total)