Starting phenix.real_space_refine on Thu Jul 24 04:50:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p6z_17512/07_2025/8p6z_17512.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p6z_17512/07_2025/8p6z_17512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p6z_17512/07_2025/8p6z_17512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p6z_17512/07_2025/8p6z_17512.map" model { file = "/net/cci-nas-00/data/ceres_data/8p6z_17512/07_2025/8p6z_17512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p6z_17512/07_2025/8p6z_17512.cif" } resolution = 2.1 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= 0.001 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 3289 2.51 5 N 869 2.21 5 O 1039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5228 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 511 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 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: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'X4L': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "I" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "J" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Time building chain proxies: 4.78, per 1000 atoms: 0.91 Number of scatterers: 5228 At special positions: 0 Unit cell: (82.65, 91.9125, 68.4, 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 1039 8.00 N 869 7.00 C 3289 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: 1.45 Conformation dependent library (CDL) restraints added in 636.1 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: 1194 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 3 sheets defined 61.9% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'H' and resid 262 through 264 No H-bonds generated for 'chain 'H' and resid 262 through 264' Processing helix chain 'H' and resid 265 through 270 Processing helix chain 'H' and resid 271 through 275 Processing helix chain 'H' and resid 279 through 286 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.843A 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 70 Processing helix chain 'I' and resid 76 through 93 removed outlier: 3.927A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.654A 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: 4.694A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.654A 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 removed outlier: 3.507A pdb=" N ILE I 186 " --> pdb=" O ASN I 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 183 through 186' Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.598A 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 225 Processing helix chain 'I' and resid 229 through 234 Processing helix chain 'I' and resid 237 through 240 Processing helix chain 'I' and resid 241 through 261 Processing helix chain 'I' and resid 266 through 281 Processing helix chain 'J' and resid 56 through 68 removed outlier: 3.984A 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 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.509A 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 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 291 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.773A 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 14 through 20 removed outlier: 6.272A pdb=" N VAL J 26 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.774A 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 134 274 hydrogen bonds defined for protein. 771 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: 1.38 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1639 1.34 - 1.46: 1103 1.46 - 1.58: 2432 1.58 - 1.70: 2 1.70 - 1.81: 49 Bond restraints: 5225 Sorted by residual: bond pdb=" C15 X4L J 401 " pdb=" N16 X4L J 401 " ideal model delta sigma weight residual 1.337 1.491 -0.154 2.00e-02 2.50e+03 5.89e+01 bond pdb=" C02 X4L J 401 " pdb=" C04 X4L J 401 " ideal model delta sigma weight residual 1.499 1.601 -0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C07 X4L J 401 " pdb=" N08 X4L J 401 " ideal model delta sigma weight residual 1.353 1.452 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" N24 X4L J 401 " pdb=" N25 X4L J 401 " ideal model delta sigma weight residual 1.344 1.414 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C17 X4L J 401 " pdb=" N16 X4L J 401 " ideal model delta sigma weight residual 1.441 1.507 -0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 5220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 6883 1.60 - 3.19: 133 3.19 - 4.79: 44 4.79 - 6.38: 7 6.38 - 7.98: 4 Bond angle restraints: 7071 Sorted by residual: angle pdb=" C07 X4L J 401 " pdb=" N08 X4L J 401 " pdb=" C09 X4L J 401 " ideal model delta sigma weight residual 124.82 132.80 -7.98 3.00e+00 1.11e-01 7.07e+00 angle pdb=" CB LYS J 293 " pdb=" CG LYS J 293 " pdb=" CD LYS J 293 " ideal model delta sigma weight residual 111.30 117.21 -5.91 2.30e+00 1.89e-01 6.59e+00 angle pdb=" C14 X4L J 401 " pdb=" C15 X4L J 401 " pdb=" N16 X4L J 401 " ideal model delta sigma weight residual 126.65 119.61 7.04 3.00e+00 1.11e-01 5.51e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.69 4.21 1.80e+00 3.09e-01 5.47e+00 angle pdb=" CB MET J 189 " pdb=" CG MET J 189 " pdb=" SD MET J 189 " ideal model delta sigma weight residual 112.70 119.68 -6.98 3.00e+00 1.11e-01 5.41e+00 ... (remaining 7066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 2735 17.70 - 35.40: 307 35.40 - 53.10: 87 53.10 - 70.80: 24 70.80 - 88.50: 8 Dihedral angle restraints: 3161 sinusoidal: 1316 harmonic: 1845 Sorted by residual: dihedral pdb=" CG ARG J 57 " pdb=" CD ARG J 57 " pdb=" NE ARG J 57 " pdb=" CZ ARG J 57 " ideal model delta sinusoidal sigma weight residual 90.00 39.62 50.38 2 1.50e+01 4.44e-03 1.27e+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 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CB GLU I 131 " pdb=" CG GLU I 131 " pdb=" CD GLU I 131 " pdb=" OE1 GLU I 131 " ideal model delta sinusoidal sigma weight residual 0.00 88.50 -88.50 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 3158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 639 0.054 - 0.109: 121 0.109 - 0.163: 13 0.163 - 0.217: 1 0.217 - 0.271: 1 Chirality restraints: 775 Sorted by residual: chirality pdb=" C09 X4L J 401 " pdb=" C10 X4L J 401 " pdb=" C13 X4L J 401 " pdb=" N08 X4L J 401 " both_signs ideal model delta sigma weight residual False 2.69 2.42 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CG LEU I 218 " pdb=" CB LEU I 218 " pdb=" CD1 LEU I 218 " pdb=" CD2 LEU I 218 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.67e-01 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 5.23e-01 ... (remaining 772 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN I 183 " -0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO I 184 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO I 184 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO I 184 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 279 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO H 280 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO H 280 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 280 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN I 162 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO I 163 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO I 163 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO I 163 " -0.017 5.00e-02 4.00e+02 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1034 2.77 - 3.30: 5277 3.30 - 3.84: 9974 3.84 - 4.37: 11550 4.37 - 4.90: 18899 Nonbonded interactions: 46734 Sorted by model distance: nonbonded pdb=" O TRP J 177 " pdb=" O HOH J 501 " model vdw 2.241 3.040 nonbonded pdb=" O HOH J 564 " pdb=" O HOH J 565 " model vdw 2.262 3.040 nonbonded pdb=" O PRO J 280 " pdb=" O HOH J 502 " model vdw 2.262 3.040 nonbonded pdb=" O HOH J 549 " pdb=" O HOH J 564 " model vdw 2.273 3.040 nonbonded pdb=" O GLY H 286 " pdb=" O HOH H 401 " model vdw 2.290 3.040 ... (remaining 46729 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: 2.450 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.760 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 5225 Z= 0.221 Angle : 0.622 7.975 7071 Z= 0.299 Chirality : 0.042 0.271 775 Planarity : 0.004 0.032 903 Dihedral : 17.164 88.499 1967 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 0.72 % Allowed : 20.04 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.30 (0.33), residues: 618 helix: 1.55 (0.28), residues: 346 sheet: None (None), residues: 0 loop : 0.05 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 11 HIS 0.004 0.001 HIS J 83 PHE 0.020 0.001 PHE I 110 TYR 0.018 0.002 TYR I 60 ARG 0.008 0.000 ARG J 57 Details of bonding type rmsd hydrogen bonds : bond 0.12994 ( 274) hydrogen bonds : angle 6.05220 ( 771) covalent geometry : bond 0.00455 ( 5225) covalent geometry : angle 0.62172 ( 7071) *********************** 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 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.666 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 98 average time/residue: 1.5593 time to fit residues: 158.0257 Evaluate side-chains 93 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain J residue 25 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 0.0870 chunk 18 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN J 236 GLN J 259 HIS J 306 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.165033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.143837 restraints weight = 4678.169| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 0.98 r_work: 0.3579 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5225 Z= 0.146 Angle : 0.578 6.163 7071 Z= 0.297 Chirality : 0.043 0.193 775 Planarity : 0.005 0.035 903 Dihedral : 5.191 59.107 708 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 3.43 % Allowed : 16.61 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.56 (0.34), residues: 618 helix: 1.80 (0.28), residues: 345 sheet: None (None), residues: 0 loop : 0.12 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 PHE 0.015 0.002 PHE I 110 TYR 0.020 0.002 TYR I 91 ARG 0.007 0.000 ARG J 57 Details of bonding type rmsd hydrogen bonds : bond 0.04977 ( 274) hydrogen bonds : angle 4.98332 ( 771) covalent geometry : bond 0.00320 ( 5225) covalent geometry : angle 0.57778 ( 7071) *********************** 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 120 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.621 Fit side-chains REVERT: H 262 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6551 (tp30) REVERT: H 264 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7471 (pp20) REVERT: I 21 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.7017 (ttp-110) outliers start: 19 outliers final: 7 residues processed: 110 average time/residue: 1.5240 time to fit residues: 173.4886 Evaluate side-chains 108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain H residue 264 GLU Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 248 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN H 298 GLN ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN J 236 GLN J 259 HIS J 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.164266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.142977 restraints weight = 4678.549| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 0.98 r_work: 0.3566 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5225 Z= 0.169 Angle : 0.599 5.479 7071 Z= 0.310 Chirality : 0.044 0.153 775 Planarity : 0.005 0.036 903 Dihedral : 5.268 58.652 708 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 3.43 % Allowed : 16.61 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.39 (0.33), residues: 618 helix: 1.65 (0.28), residues: 345 sheet: None (None), residues: 0 loop : 0.06 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.016 0.002 PHE J 295 TYR 0.021 0.002 TYR I 91 ARG 0.006 0.000 ARG J 57 Details of bonding type rmsd hydrogen bonds : bond 0.05064 ( 274) hydrogen bonds : angle 4.93779 ( 771) covalent geometry : bond 0.00375 ( 5225) covalent geometry : angle 0.59883 ( 7071) *********************** 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 123 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.606 Fit side-chains REVERT: H 262 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6557 (tp30) REVERT: H 264 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7466 (pp20) REVERT: I 21 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.7056 (ttp-110) REVERT: I 63 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6850 (mmt180) outliers start: 19 outliers final: 7 residues processed: 112 average time/residue: 1.5788 time to fit residues: 182.6404 Evaluate side-chains 108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain H residue 264 GLU Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 248 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 0.0970 chunk 47 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN J 236 GLN J 259 HIS J 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.166993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145802 restraints weight = 4818.784| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.01 r_work: 0.3617 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5225 Z= 0.115 Angle : 0.533 5.099 7071 Z= 0.274 Chirality : 0.041 0.159 775 Planarity : 0.004 0.035 903 Dihedral : 5.059 59.669 708 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 3.07 % Allowed : 16.79 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.63 (0.34), residues: 618 helix: 1.90 (0.28), residues: 345 sheet: None (None), residues: 0 loop : 0.09 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 132 HIS 0.004 0.001 HIS J 131 PHE 0.018 0.001 PHE I 110 TYR 0.018 0.001 TYR I 60 ARG 0.008 0.000 ARG J 57 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 274) hydrogen bonds : angle 4.67083 ( 771) covalent geometry : bond 0.00251 ( 5225) covalent geometry : angle 0.53252 ( 7071) *********************** 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 116 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.587 Fit side-chains REVERT: H 264 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7458 (pp20) REVERT: I 54 MET cc_start: 0.8084 (mmm) cc_final: 0.7852 (tpt) REVERT: J 40 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8263 (mp) outliers start: 17 outliers final: 6 residues processed: 107 average time/residue: 1.5366 time to fit residues: 170.0021 Evaluate side-chains 105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 264 GLU Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 248 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 47 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN H 298 GLN H 307 GLN I 124 GLN I 136 GLN J 236 GLN J 259 HIS J 306 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.163646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.142176 restraints weight = 4701.467| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 0.99 r_work: 0.3553 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5225 Z= 0.201 Angle : 0.632 5.984 7071 Z= 0.328 Chirality : 0.046 0.190 775 Planarity : 0.005 0.037 903 Dihedral : 5.153 59.071 706 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 3.61 % Allowed : 16.61 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.28 (0.33), residues: 618 helix: 1.55 (0.28), residues: 345 sheet: None (None), residues: 0 loop : 0.03 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.007 0.001 HIS J 131 PHE 0.017 0.002 PHE J 295 TYR 0.025 0.002 TYR I 60 ARG 0.008 0.001 ARG J 57 Details of bonding type rmsd hydrogen bonds : bond 0.05277 ( 274) hydrogen bonds : angle 4.95498 ( 771) covalent geometry : bond 0.00450 ( 5225) covalent geometry : angle 0.63233 ( 7071) *********************** 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 114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.657 Fit side-chains REVERT: H 264 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7502 (pp20) REVERT: I 21 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7114 (ttp-110) REVERT: I 63 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6871 (mmm160) outliers start: 20 outliers final: 6 residues processed: 103 average time/residue: 1.5545 time to fit residues: 165.4257 Evaluate side-chains 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 264 GLU Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 248 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 18 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 7 optimal weight: 0.0970 chunk 1 optimal weight: 0.0020 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN J 83 HIS J 236 GLN J 259 HIS J 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.167909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146864 restraints weight = 4743.873| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.00 r_work: 0.3618 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5225 Z= 0.109 Angle : 0.538 5.562 7071 Z= 0.275 Chirality : 0.041 0.181 775 Planarity : 0.004 0.037 903 Dihedral : 4.899 59.605 706 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.17 % Allowed : 18.05 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.63 (0.34), residues: 618 helix: 1.90 (0.28), residues: 345 sheet: -1.52 (1.87), residues: 6 loop : 0.14 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 11 HIS 0.003 0.001 HIS J 258 PHE 0.018 0.001 PHE I 110 TYR 0.021 0.001 TYR I 60 ARG 0.007 0.000 ARG J 57 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 274) hydrogen bonds : angle 4.60144 ( 771) covalent geometry : bond 0.00240 ( 5225) covalent geometry : angle 0.53779 ( 7071) *********************** 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 114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.741 Fit side-chains REVERT: H 264 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7426 (pp20) REVERT: I 21 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.7096 (ttp-110) REVERT: I 54 MET cc_start: 0.8059 (mmm) cc_final: 0.7850 (tpt) outliers start: 12 outliers final: 5 residues processed: 105 average time/residue: 1.6275 time to fit residues: 176.4722 Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 264 GLU Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 83 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN H 298 GLN H 307 GLN I 124 GLN I 136 GLN J 236 GLN J 259 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.162765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.141194 restraints weight = 4675.878| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 0.99 r_work: 0.3525 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 5225 Z= 0.261 Angle : 0.713 6.587 7071 Z= 0.369 Chirality : 0.050 0.212 775 Planarity : 0.006 0.039 903 Dihedral : 5.294 58.428 706 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % Rotamer: Outliers : 3.07 % Allowed : 17.69 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.04 (0.33), residues: 618 helix: 1.32 (0.27), residues: 345 sheet: None (None), residues: 0 loop : -0.02 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP J 237 HIS 0.009 0.002 HIS J 83 PHE 0.020 0.003 PHE I 13 TYR 0.026 0.003 TYR I 91 ARG 0.008 0.001 ARG I 23 Details of bonding type rmsd hydrogen bonds : bond 0.05779 ( 274) hydrogen bonds : angle 5.08938 ( 771) covalent geometry : bond 0.00585 ( 5225) covalent geometry : angle 0.71275 ( 7071) *********************** 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 113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.610 Fit side-chains REVERT: I 21 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7122 (ttp-110) REVERT: I 54 MET cc_start: 0.8117 (mmm) cc_final: 0.7872 (tpt) REVERT: I 63 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6868 (mmm160) outliers start: 17 outliers final: 8 residues processed: 102 average time/residue: 1.5125 time to fit residues: 159.7529 Evaluate side-chains 105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 264 GLU Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 83 HIS Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 240 MET Chi-restraints excluded: chain J residue 248 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 3 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN H 298 GLN ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN J 236 GLN J 259 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.164641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.143156 restraints weight = 4714.907| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.00 r_work: 0.3559 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5225 Z= 0.168 Angle : 0.628 7.114 7071 Z= 0.322 Chirality : 0.045 0.215 775 Planarity : 0.005 0.037 903 Dihedral : 5.175 59.564 706 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.53 % Allowed : 18.23 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.18 (0.33), residues: 618 helix: 1.46 (0.28), residues: 345 sheet: None (None), residues: 0 loop : 0.00 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 11 HIS 0.006 0.001 HIS J 131 PHE 0.015 0.002 PHE J 295 TYR 0.022 0.002 TYR I 91 ARG 0.008 0.001 ARG J 57 Details of bonding type rmsd hydrogen bonds : bond 0.04966 ( 274) hydrogen bonds : angle 4.89270 ( 771) covalent geometry : bond 0.00375 ( 5225) covalent geometry : angle 0.62826 ( 7071) *********************** 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 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.655 Fit side-chains REVERT: H 264 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7463 (pp20) REVERT: I 21 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7074 (ttp-110) REVERT: I 54 MET cc_start: 0.8097 (mmm) cc_final: 0.7883 (tpt) REVERT: I 63 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6859 (mmm160) outliers start: 14 outliers final: 6 residues processed: 99 average time/residue: 1.7161 time to fit residues: 175.7448 Evaluate side-chains 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 264 GLU Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 83 HIS Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 248 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 124 GLN I 136 GLN J 236 GLN J 259 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.165067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144294 restraints weight = 4749.688| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 0.98 r_work: 0.3583 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5225 Z= 0.159 Angle : 0.632 6.541 7071 Z= 0.321 Chirality : 0.045 0.231 775 Planarity : 0.005 0.036 903 Dihedral : 5.149 59.843 706 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.35 % Allowed : 18.41 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.26 (0.34), residues: 618 helix: 1.52 (0.28), residues: 345 sheet: None (None), residues: 0 loop : 0.03 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.015 0.002 PHE J 295 TYR 0.021 0.002 TYR I 91 ARG 0.009 0.001 ARG J 57 Details of bonding type rmsd hydrogen bonds : bond 0.04838 ( 274) hydrogen bonds : angle 4.83835 ( 771) covalent geometry : bond 0.00356 ( 5225) covalent geometry : angle 0.63199 ( 7071) *********************** 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 113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.604 Fit side-chains REVERT: H 264 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7466 (pp20) REVERT: I 21 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7076 (ttp-110) REVERT: I 54 MET cc_start: 0.8091 (mmm) cc_final: 0.7881 (tpt) REVERT: I 137 GLU cc_start: 0.6988 (mp0) cc_final: 0.6620 (tm-30) REVERT: J 40 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8249 (mp) outliers start: 13 outliers final: 5 residues processed: 103 average time/residue: 1.6682 time to fit residues: 177.6907 Evaluate side-chains 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 264 GLU Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 83 HIS Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 39 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN H 298 GLN ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 124 GLN I 136 GLN J 236 GLN J 259 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.164597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143123 restraints weight = 4698.733| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 0.99 r_work: 0.3577 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5225 Z= 0.173 Angle : 0.654 8.605 7071 Z= 0.331 Chirality : 0.046 0.246 775 Planarity : 0.005 0.037 903 Dihedral : 5.183 59.427 706 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.17 % Allowed : 18.77 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.37 (0.34), residues: 618 helix: 1.58 (0.28), residues: 339 sheet: None (None), residues: 0 loop : 0.17 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 11 HIS 0.006 0.001 HIS J 131 PHE 0.016 0.002 PHE J 295 TYR 0.022 0.002 TYR I 91 ARG 0.009 0.001 ARG J 57 Details of bonding type rmsd hydrogen bonds : bond 0.04994 ( 274) hydrogen bonds : angle 4.90252 ( 771) covalent geometry : bond 0.00390 ( 5225) covalent geometry : angle 0.65415 ( 7071) ********************** 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 109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.582 Fit side-chains REVERT: H 264 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7483 (pp20) REVERT: I 21 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7072 (ttp-110) REVERT: I 54 MET cc_start: 0.8111 (mmm) cc_final: 0.7872 (tpt) REVERT: J 40 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8257 (mp) outliers start: 12 outliers final: 7 residues processed: 101 average time/residue: 1.5276 time to fit residues: 159.6414 Evaluate side-chains 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 264 GLU Chi-restraints excluded: chain I residue 21 ARG Chi-restraints excluded: chain I residue 105 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 83 HIS Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 248 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.4980 chunk 8 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 249 GLN ** H 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 124 GLN I 136 GLN J 236 GLN J 259 HIS J 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.167724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.147431 restraints weight = 4819.026| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 0.98 r_work: 0.3587 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5225 Z= 0.123 Angle : 0.606 9.002 7071 Z= 0.302 Chirality : 0.043 0.217 775 Planarity : 0.004 0.039 903 Dihedral : 4.987 59.217 706 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 1.81 % Allowed : 19.13 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.68 (0.34), residues: 618 helix: 1.89 (0.29), residues: 339 sheet: -1.48 (1.86), residues: 6 loop : 0.28 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.004 0.001 HIS J 258 PHE 0.019 0.002 PHE I 110 TYR 0.019 0.002 TYR I 60 ARG 0.009 0.000 ARG J 57 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 274) hydrogen bonds : angle 4.66572 ( 771) covalent geometry : bond 0.00276 ( 5225) covalent geometry : angle 0.60644 ( 7071) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5880.91 seconds wall clock time: 100 minutes 40.14 seconds (6040.14 seconds total)