Starting phenix.real_space_refine on Fri Oct 10 12:40:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p6z_17512/10_2025/8p6z_17512.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p6z_17512/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8p6z_17512/10_2025/8p6z_17512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p6z_17512/10_2025/8p6z_17512.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p6z_17512/10_2025/8p6z_17512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p6z_17512/10_2025/8p6z_17512.map" } resolution = 2.1 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 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.58, per 1000 atoms: 0.30 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: 0.44 Conformation dependent library (CDL) restraints added in 159.7 milliseconds Enol-peptide restraints added in 0.0 nanoseconds 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: 0.18 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: 0.80 Time building geometry restraints manager: 0.55 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: 4.820 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.450 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.000 ARG J 57 TYR 0.018 0.002 TYR I 60 PHE 0.020 0.001 PHE I 110 TRP 0.012 0.001 TRP I 11 HIS 0.004 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 5225) covalent geometry : angle 0.62172 ( 7071) hydrogen bonds : bond 0.12994 ( 274) hydrogen bonds : angle 6.05220 ( 771) *********************** 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 : 0.217 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 98 average time/residue: 0.7582 time to fit residues: 76.6767 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 : 0.232 ------------------------------------------------------------------------------- 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 54 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 0.0870 chunk 56 optimal weight: 0.0040 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.1974 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.164670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.143361 restraints weight = 4744.133| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 0.99 r_work: 0.3566 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5225 Z= 0.154 Angle : 0.587 6.305 7071 Z= 0.303 Chirality : 0.043 0.191 775 Planarity : 0.005 0.035 903 Dihedral : 5.230 59.160 708 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 3.61 % Allowed : 16.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.34), residues: 618 helix: 1.75 (0.28), residues: 345 sheet: None (None), residues: 0 loop : 0.11 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 57 TYR 0.021 0.002 TYR I 91 PHE 0.016 0.002 PHE J 295 TRP 0.012 0.002 TRP J 132 HIS 0.005 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 5225) covalent geometry : angle 0.58749 ( 7071) hydrogen bonds : bond 0.05049 ( 274) hydrogen bonds : angle 4.99019 ( 771) *********************** 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 123 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.163 Fit side-chains REVERT: H 262 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6546 (tp30) REVERT: H 264 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7470 (pp20) REVERT: I 21 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.7049 (ttp-110) outliers start: 20 outliers final: 7 residues processed: 113 average time/residue: 0.7373 time to fit residues: 86.0911 Evaluate side-chains 111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 26 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 136 GLN J 236 GLN J 259 HIS J 306 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.165300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.144060 restraints weight = 4716.973| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 0.99 r_work: 0.3596 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.0832 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= 0.137 Angle : 0.559 5.230 7071 Z= 0.288 Chirality : 0.042 0.145 775 Planarity : 0.004 0.036 903 Dihedral : 5.156 59.534 708 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 3.61 % Allowed : 16.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.34), residues: 618 helix: 1.81 (0.28), residues: 345 sheet: None (None), residues: 0 loop : 0.08 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 57 TYR 0.019 0.002 TYR I 91 PHE 0.015 0.002 PHE I 110 TRP 0.009 0.001 TRP J 132 HIS 0.005 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5225) covalent geometry : angle 0.55933 ( 7071) hydrogen bonds : bond 0.04650 ( 274) hydrogen bonds : angle 4.81697 ( 771) *********************** 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 124 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.207 Fit side-chains REVERT: H 264 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7480 (pp20) REVERT: I 21 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.7053 (ttp-110) REVERT: J 40 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8254 (mp) outliers start: 20 outliers final: 7 residues processed: 112 average time/residue: 0.7558 time to fit residues: 87.3818 Evaluate side-chains 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 106 SER 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 2 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 0.0070 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 0.0370 chunk 4 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 0.1980 chunk 49 optimal weight: 0.7980 overall best weight: 0.3076 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.169083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.148119 restraints weight = 4763.904| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.00 r_work: 0.3635 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5225 Z= 0.102 Angle : 0.507 4.927 7071 Z= 0.260 Chirality : 0.040 0.142 775 Planarity : 0.004 0.038 903 Dihedral : 4.800 59.211 706 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.53 % Allowed : 17.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.34), residues: 618 helix: 2.03 (0.29), residues: 346 sheet: -0.99 (2.04), residues: 6 loop : 0.22 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 57 TYR 0.020 0.001 TYR I 60 PHE 0.017 0.001 PHE I 110 TRP 0.006 0.001 TRP J 132 HIS 0.003 0.001 HIS J 258 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 5225) covalent geometry : angle 0.50700 ( 7071) hydrogen bonds : bond 0.03821 ( 274) hydrogen bonds : angle 4.52277 ( 771) *********************** 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: 14 poor density : 102 time to evaluate : 0.163 Fit side-chains REVERT: H 264 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7391 (pp20) REVERT: I 263 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6799 (pt0) outliers start: 14 outliers final: 5 residues processed: 108 average time/residue: 0.7299 time to fit residues: 81.4124 Evaluate side-chains 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 264 GLU 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 169 TYR Chi-restraints excluded: chain J residue 233 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 0.0170 chunk 23 optimal weight: 3.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- 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 136 GLN J 236 GLN J 259 HIS J 306 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.164515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143010 restraints weight = 4793.302| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.00 r_work: 0.3551 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5225 Z= 0.177 Angle : 0.609 5.930 7071 Z= 0.314 Chirality : 0.044 0.185 775 Planarity : 0.005 0.038 903 Dihedral : 5.041 57.824 706 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 3.43 % Allowed : 16.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.34), residues: 618 helix: 1.88 (0.28), residues: 339 sheet: None (None), residues: 0 loop : 0.25 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 57 TYR 0.023 0.002 TYR I 91 PHE 0.015 0.002 PHE J 295 TRP 0.010 0.002 TRP I 11 HIS 0.007 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 5225) covalent geometry : angle 0.60934 ( 7071) hydrogen bonds : bond 0.05014 ( 274) hydrogen bonds : angle 4.85490 ( 771) *********************** 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 116 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.232 Fit side-chains REVERT: H 264 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7500 (pp20) REVERT: I 21 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.7173 (ttp-110) REVERT: I 63 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6874 (mmm160) REVERT: I 137 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6473 (tm-30) outliers start: 19 outliers final: 6 residues processed: 104 average time/residue: 0.7716 time to fit residues: 82.9144 Evaluate side-chains 105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 42 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.166589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145301 restraints weight = 4816.810| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.01 r_work: 0.3605 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5225 Z= 0.126 Angle : 0.563 5.624 7071 Z= 0.287 Chirality : 0.042 0.143 775 Planarity : 0.004 0.038 903 Dihedral : 4.949 59.165 706 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 2.53 % Allowed : 17.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.34), residues: 618 helix: 1.99 (0.28), residues: 339 sheet: None (None), residues: 0 loop : 0.26 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 57 TYR 0.020 0.002 TYR I 60 PHE 0.015 0.002 PHE I 110 TRP 0.009 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5225) covalent geometry : angle 0.56341 ( 7071) hydrogen bonds : bond 0.04352 ( 274) hydrogen bonds : angle 4.65790 ( 771) *********************** 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 119 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.225 Fit side-chains REVERT: H 264 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7443 (pp20) REVERT: I 21 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.7098 (ttp-110) REVERT: I 63 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6865 (mmm160) REVERT: I 137 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6478 (tm-30) REVERT: J 40 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8273 (mp) outliers start: 14 outliers final: 5 residues processed: 109 average time/residue: 0.7817 time to fit residues: 87.9510 Evaluate side-chains 108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 10 optimal weight: 0.0040 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8192 ------------------------------------------------------------------------------- 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 J 306 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.166520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145267 restraints weight = 4791.985| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.01 r_work: 0.3587 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.0947 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= 0.130 Angle : 0.576 6.039 7071 Z= 0.291 Chirality : 0.042 0.184 775 Planarity : 0.004 0.038 903 Dihedral : 4.949 59.326 706 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.53 % Allowed : 17.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.34), residues: 618 helix: 2.00 (0.28), residues: 339 sheet: None (None), residues: 0 loop : 0.29 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 57 TYR 0.021 0.002 TYR I 60 PHE 0.014 0.002 PHE I 110 TRP 0.009 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 5225) covalent geometry : angle 0.57572 ( 7071) hydrogen bonds : bond 0.04377 ( 274) hydrogen bonds : angle 4.64834 ( 771) *********************** 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 116 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.246 Fit side-chains REVERT: H 264 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7411 (pp20) REVERT: I 21 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.7082 (ttp-110) REVERT: I 63 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6867 (mmm160) REVERT: I 137 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6456 (tm-30) REVERT: J 40 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8267 (mp) outliers start: 14 outliers final: 6 residues processed: 106 average time/residue: 0.7651 time to fit residues: 83.9371 Evaluate side-chains 111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 39 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 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 = 0.3944 r_free = 0.3944 target = 0.162639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.141071 restraints weight = 4737.174| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 0.99 r_work: 0.3531 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 5225 Z= 0.277 Angle : 0.733 6.650 7071 Z= 0.379 Chirality : 0.051 0.213 775 Planarity : 0.006 0.039 903 Dihedral : 5.322 58.277 706 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 2.71 % Allowed : 17.69 % Favored : 79.60 % 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 aren not related in a simple way. whole: 1.00 (0.33), residues: 618 helix: 1.27 (0.27), residues: 345 sheet: None (None), residues: 0 loop : -0.01 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 23 TYR 0.028 0.003 TYR I 60 PHE 0.021 0.003 PHE I 13 TRP 0.015 0.003 TRP J 237 HIS 0.008 0.002 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00622 ( 5225) covalent geometry : angle 0.73303 ( 7071) hydrogen bonds : bond 0.05856 ( 274) hydrogen bonds : angle 5.11228 ( 771) *********************** 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 109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: I 21 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.7158 (ttp-110) REVERT: I 63 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6883 (mmm160) outliers start: 15 outliers final: 6 residues processed: 100 average time/residue: 0.7734 time to fit residues: 79.7805 Evaluate side-chains 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 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 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 83 HIS 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 = 0.3988 r_free = 0.3988 target = 0.166662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.145403 restraints weight = 4791.544| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.00 r_work: 0.3622 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5225 Z= 0.124 Angle : 0.587 6.100 7071 Z= 0.298 Chirality : 0.043 0.206 775 Planarity : 0.004 0.036 903 Dihedral : 5.045 59.941 706 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.17 % Allowed : 18.41 % Favored : 79.42 % 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 aren not related in a simple way. whole: 1.48 (0.34), residues: 618 helix: 1.76 (0.28), residues: 345 sheet: None (None), residues: 0 loop : 0.06 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 57 TYR 0.022 0.002 TYR I 60 PHE 0.017 0.001 PHE I 110 TRP 0.011 0.001 TRP I 11 HIS 0.005 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5225) covalent geometry : angle 0.58739 ( 7071) hydrogen bonds : bond 0.04344 ( 274) hydrogen bonds : angle 4.67652 ( 771) *********************** 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 111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.367 Fit side-chains REVERT: H 264 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7400 (pp20) REVERT: I 21 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.7087 (ttp-110) REVERT: I 137 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6550 (pp20) outliers start: 12 outliers final: 5 residues processed: 102 average time/residue: 0.7552 time to fit residues: 79.7135 Evaluate side-chains 105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 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 13 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.164883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.144366 restraints weight = 4796.599| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 0.97 r_work: 0.3546 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.0934 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= 0.177 Angle : 0.659 7.893 7071 Z= 0.332 Chirality : 0.046 0.239 775 Planarity : 0.005 0.036 903 Dihedral : 5.147 59.104 706 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 1.62 % Allowed : 18.95 % Favored : 79.42 % 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 aren not related in a simple way. whole: 1.50 (0.34), residues: 618 helix: 1.71 (0.28), residues: 339 sheet: None (None), residues: 0 loop : 0.20 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 57 TYR 0.023 0.002 TYR I 60 PHE 0.015 0.002 PHE J 295 TRP 0.012 0.002 TRP J 132 HIS 0.006 0.002 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 5225) covalent geometry : angle 0.65883 ( 7071) hydrogen bonds : bond 0.05003 ( 274) hydrogen bonds : angle 4.86850 ( 771) ********************** 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 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.234 Fit side-chains REVERT: H 264 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7434 (pp20) REVERT: I 21 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.7054 (ttp-110) REVERT: I 97 MET cc_start: 0.7929 (mtm) cc_final: 0.7692 (mtm) outliers start: 9 outliers final: 4 residues processed: 103 average time/residue: 0.8247 time to fit residues: 87.5515 Evaluate side-chains 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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 53 ASP 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 56 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 83 HIS J 236 GLN J 259 HIS J 306 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.166728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.146258 restraints weight = 4879.076| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 0.98 r_work: 0.3568 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.0896 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= 0.135 Angle : 0.625 10.901 7071 Z= 0.311 Chirality : 0.044 0.219 775 Planarity : 0.004 0.036 903 Dihedral : 5.041 59.641 706 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 1.99 % Allowed : 18.59 % Favored : 79.42 % 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 aren not related in a simple way. whole: 1.66 (0.34), residues: 618 helix: 1.88 (0.28), residues: 339 sheet: None (None), residues: 0 loop : 0.20 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 57 TYR 0.021 0.002 TYR I 60 PHE 0.016 0.002 PHE I 110 TRP 0.010 0.001 TRP I 11 HIS 0.005 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 5225) covalent geometry : angle 0.62488 ( 7071) hydrogen bonds : bond 0.04432 ( 274) hydrogen bonds : angle 4.70200 ( 771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2929.16 seconds wall clock time: 50 minutes 38.24 seconds (3038.24 seconds total)