Starting phenix.real_space_refine on Thu Jul 2 01:20:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qbi_13887/07_2026/7qbi_13887.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qbi_13887/07_2026/7qbi_13887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qbi_13887/07_2026/7qbi_13887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qbi_13887/07_2026/7qbi_13887.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7qbi_13887/07_2026/7qbi_13887.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qbi_13887/07_2026/7qbi_13887.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qbi_13887/07_2026/7qbi_13887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qbi_13887/07_2026/7qbi_13887.map" } resolution = 3.46 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= 0.002 sd= 0.093 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 20 5.16 5 C 3360 2.51 5 N 718 2.21 5 O 898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4996 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2140 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 289} Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 4, 'PHE:plan': 6, 'ASN:plan1': 4, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "I" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 120 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Chain: "K" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 120 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Chain: "B" Number of atoms: 2140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2140 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 289} Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 4, 'PHE:plan': 6, 'ASN:plan1': 4, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'NAG': 2, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'NAG': 2, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.24, per 1000 atoms: 0.25 Number of scatterers: 4996 At special positions: 0 Unit cell: (75.9, 73.7, 94.6, 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 20 16.00 O 898 8.00 N 718 7.00 C 3360 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 25 " " NAG A 502 " - " ASN A 32 " " NAG B 501 " - " ASN B 32 " " NAG B 502 " - " ASN B 25 " Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 184.6 milliseconds 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1180 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 78.8% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 Processing helix chain 'A' and resid 18 through 21 removed outlier: 3.827A pdb=" N GLN A 21 " --> pdb=" O ASN A 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 18 through 21' Processing helix chain 'A' and resid 38 through 73 Processing helix chain 'A' and resid 78 through 102 Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 121 through 154 removed outlier: 3.522A pdb=" N VAL A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 195 removed outlier: 3.921A pdb=" N VAL A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 236 removed outlier: 3.678A pdb=" N ASN A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 268 removed outlier: 3.581A pdb=" N ILE A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 276 through 301 removed outlier: 3.801A pdb=" N VAL A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Proline residue: A 290 - end of helix Processing helix chain 'B' and resid 9 through 13 Processing helix chain 'B' and resid 18 through 21 removed outlier: 3.827A pdb=" N GLN B 21 " --> pdb=" O ASN B 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 18 through 21' Processing helix chain 'B' and resid 38 through 73 Processing helix chain 'B' and resid 78 through 102 Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 121 through 154 removed outlier: 3.522A pdb=" N VAL B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 195 removed outlier: 3.921A pdb=" N VAL B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 236 removed outlier: 3.678A pdb=" N ASN B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 268 removed outlier: 3.600A pdb=" N ILE B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 276 through 301 removed outlier: 3.801A pdb=" N VAL B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Proline residue: B 290 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 24 372 hydrogen bonds defined for protein. 1086 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: 0.75 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 734 1.31 - 1.44: 1298 1.44 - 1.57: 3052 1.57 - 1.69: 6 1.69 - 1.82: 36 Bond restraints: 5126 Sorted by residual: bond pdb=" C7 NAG B 502 " pdb=" N2 NAG B 502 " ideal model delta sigma weight residual 1.346 1.455 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C7 NAG A 502 " pdb=" N2 NAG A 502 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C7 NAG A 501 " pdb=" N2 NAG A 501 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C7 NAG B 501 " pdb=" N2 NAG B 501 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.42e+01 ... (remaining 5121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 6640 2.08 - 4.16: 367 4.16 - 6.23: 75 6.23 - 8.31: 6 8.31 - 10.39: 4 Bond angle restraints: 7092 Sorted by residual: angle pdb=" N PHE B 244 " pdb=" CA PHE B 244 " pdb=" C PHE B 244 " ideal model delta sigma weight residual 111.33 104.11 7.22 1.21e+00 6.83e-01 3.56e+01 angle pdb=" N PHE A 244 " pdb=" CA PHE A 244 " pdb=" C PHE A 244 " ideal model delta sigma weight residual 111.33 104.51 6.82 1.21e+00 6.83e-01 3.18e+01 angle pdb=" C SER A 104 " pdb=" CA SER A 104 " pdb=" CB SER A 104 " ideal model delta sigma weight residual 114.40 108.58 5.82 1.25e+00 6.40e-01 2.17e+01 angle pdb=" C SER B 104 " pdb=" CA SER B 104 " pdb=" CB SER B 104 " ideal model delta sigma weight residual 114.40 108.63 5.77 1.25e+00 6.40e-01 2.13e+01 angle pdb=" N TRP A 70 " pdb=" CA TRP A 70 " pdb=" C TRP A 70 " ideal model delta sigma weight residual 111.03 106.31 4.72 1.11e+00 8.12e-01 1.81e+01 ... (remaining 7087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 2567 17.33 - 34.65: 194 34.65 - 51.98: 58 51.98 - 69.31: 11 69.31 - 86.64: 8 Dihedral angle restraints: 2838 sinusoidal: 1012 harmonic: 1826 Sorted by residual: dihedral pdb=" CG ARG A 74 " pdb=" CD ARG A 74 " pdb=" NE ARG A 74 " pdb=" CZ ARG A 74 " ideal model delta sinusoidal sigma weight residual -180.00 -135.05 -44.95 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG B 74 " pdb=" CD ARG B 74 " pdb=" NE ARG B 74 " pdb=" CZ ARG B 74 " ideal model delta sinusoidal sigma weight residual -180.00 -135.06 -44.94 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB MET A 54 " pdb=" CG MET A 54 " pdb=" SD MET A 54 " pdb=" CE MET A 54 " ideal model delta sinusoidal sigma weight residual -180.00 -120.11 -59.89 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 738 0.061 - 0.122: 156 0.122 - 0.183: 20 0.183 - 0.244: 8 0.244 - 0.305: 2 Chirality restraints: 924 Sorted by residual: chirality pdb=" CA LEU B 236 " pdb=" N LEU B 236 " pdb=" C LEU B 236 " pdb=" CB LEU B 236 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA LEU A 236 " pdb=" N LEU A 236 " pdb=" C LEU A 236 " pdb=" CB LEU A 236 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA PHE B 244 " pdb=" N PHE B 244 " pdb=" C PHE B 244 " pdb=" CB PHE B 244 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 921 not shown) Planarity restraints: 804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 219 " 0.021 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" C SER A 219 " -0.072 2.00e-02 2.50e+03 pdb=" O SER A 219 " 0.027 2.00e-02 2.50e+03 pdb=" N PHE A 220 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 219 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.60e+01 pdb=" C SER B 219 " 0.069 2.00e-02 2.50e+03 pdb=" O SER B 219 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE B 220 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 74 " -0.275 9.50e-02 1.11e+02 1.23e-01 9.48e+00 pdb=" NE ARG A 74 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 74 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 74 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 74 " -0.008 2.00e-02 2.50e+03 ... (remaining 801 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 903 2.77 - 3.30: 5100 3.30 - 3.83: 8016 3.83 - 4.37: 9430 4.37 - 4.90: 16177 Nonbonded interactions: 39626 Sorted by model distance: nonbonded pdb=" OE1 GLN B 51 " pdb=" OH TYR B 98 " model vdw 2.231 3.040 nonbonded pdb=" OE1 GLN A 51 " pdb=" OH TYR A 98 " model vdw 2.232 3.040 nonbonded pdb=" O ARG B 122 " pdb=" ND1 HIS B 126 " model vdw 2.296 3.120 nonbonded pdb=" O ARG A 122 " pdb=" ND1 HIS A 126 " model vdw 2.297 3.120 nonbonded pdb=" NH2 ARG A 74 " pdb=" O ALA B 298 " model vdw 2.330 3.120 ... (remaining 39621 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'I' selection = chain 'K' } 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.450 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 : 0.008 0.109 5130 Z= 0.438 Angle : 1.066 10.390 7104 Z= 0.600 Chirality : 0.053 0.305 924 Planarity : 0.009 0.123 800 Dihedral : 14.724 86.636 1658 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.31), residues: 614 helix: -0.82 (0.22), residues: 444 sheet: None (None), residues: 0 loop : -0.86 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 74 TYR 0.026 0.003 TYR A 266 PHE 0.025 0.003 PHE B 171 TRP 0.016 0.002 TRP A 70 HIS 0.003 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00818 / 0.44 ( 5126) covalent geometry : angle 1.06429 / 0.60 ( 7092) hydrogen bonds : bond 0.11871 / 7.60 ( 372) hydrogen bonds : angle 5.74241 / 4.02 ( 1086) link_NAG-ASN : bond 0.00116 / 0.05 ( 4) link_NAG-ASN : angle 1.78406 / 1.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.174 Fit side-chains REVERT: A 120 ILE cc_start: 0.8098 (mm) cc_final: 0.7731 (mm) REVERT: B 120 ILE cc_start: 0.8135 (mm) cc_final: 0.7768 (mm) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.0634 time to fit residues: 9.7278 Evaluate side-chains 104 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 ASN I 2 HIS K 2 HIS B 216 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.184449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146058 restraints weight = 6585.824| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.38 r_work: 0.3512 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5130 Z= 0.157 Angle : 0.615 7.133 7104 Z= 0.298 Chirality : 0.037 0.134 924 Planarity : 0.004 0.024 800 Dihedral : 9.774 75.041 812 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.33), residues: 614 helix: 1.45 (0.23), residues: 448 sheet: None (None), residues: 0 loop : -0.34 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 74 TYR 0.009 0.001 TYR B 17 PHE 0.017 0.001 PHE A 171 TRP 0.004 0.001 TRP A 70 HIS 0.002 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 5126) covalent geometry : angle 0.61231 / 0.30 ( 7092) hydrogen bonds : bond 0.03697 / 2.37 ( 372) hydrogen bonds : angle 3.68683 / 2.63 ( 1086) link_NAG-ASN : bond 0.00199 / 0.09 ( 4) link_NAG-ASN : angle 1.52643 / 0.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.185 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.0606 time to fit residues: 9.2590 Evaluate side-chains 97 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 ASN B 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.181495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.142119 restraints weight = 6551.214| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.41 r_work: 0.3493 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5130 Z= 0.135 Angle : 0.573 7.052 7104 Z= 0.276 Chirality : 0.037 0.136 924 Planarity : 0.003 0.024 800 Dihedral : 9.045 73.818 812 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.75 % Allowed : 13.32 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.33), residues: 614 helix: 2.50 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.53 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 74 TYR 0.008 0.001 TYR B 128 PHE 0.016 0.001 PHE A 12 TRP 0.003 0.001 TRP I 1 HIS 0.002 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 5126) covalent geometry : angle 0.57064 / 0.28 ( 7092) hydrogen bonds : bond 0.03527 / 2.27 ( 372) hydrogen bonds : angle 3.40310 / 2.43 ( 1086) link_NAG-ASN : bond 0.00061 / 0.03 ( 4) link_NAG-ASN : angle 1.33966 / 0.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.184 Fit side-chains REVERT: A 64 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8191 (tt) REVERT: A 149 GLN cc_start: 0.8360 (tt0) cc_final: 0.8095 (tt0) REVERT: B 64 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8178 (tt) REVERT: B 70 TRP cc_start: 0.7857 (OUTLIER) cc_final: 0.7456 (m100) outliers start: 8 outliers final: 5 residues processed: 106 average time/residue: 0.0685 time to fit residues: 9.5785 Evaluate side-chains 108 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 23 optimal weight: 0.0060 chunk 51 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 ASN B 216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.182497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.142310 restraints weight = 6538.265| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.49 r_work: 0.3474 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5130 Z= 0.137 Angle : 0.576 6.964 7104 Z= 0.274 Chirality : 0.037 0.135 924 Planarity : 0.003 0.024 800 Dihedral : 9.137 73.557 812 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.28 % Allowed : 15.07 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.33), residues: 614 helix: 2.72 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.44 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 74 TYR 0.008 0.001 TYR A 128 PHE 0.012 0.001 PHE A 55 TRP 0.005 0.001 TRP A 70 HIS 0.002 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 5126) covalent geometry : angle 0.57403 / 0.27 ( 7092) hydrogen bonds : bond 0.03465 / 2.23 ( 372) hydrogen bonds : angle 3.32873 / 2.37 ( 1086) link_NAG-ASN : bond 0.00063 / 0.03 ( 4) link_NAG-ASN : angle 1.33571 / 0.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.188 Fit side-chains REVERT: A 64 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8171 (tt) REVERT: A 106 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: A 149 GLN cc_start: 0.8345 (tt0) cc_final: 0.8073 (tt0) REVERT: B 64 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8240 (tp) REVERT: B 106 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.8365 (m-80) outliers start: 15 outliers final: 5 residues processed: 106 average time/residue: 0.0645 time to fit residues: 9.1185 Evaluate side-chains 104 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 19 optimal weight: 0.0570 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.182234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141906 restraints weight = 6600.114| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.50 r_work: 0.3477 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5130 Z= 0.131 Angle : 0.565 6.782 7104 Z= 0.269 Chirality : 0.037 0.134 924 Planarity : 0.003 0.025 800 Dihedral : 9.250 73.234 812 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.40 % Allowed : 17.69 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.33), residues: 614 helix: 2.86 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.31 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 122 TYR 0.009 0.001 TYR B 128 PHE 0.012 0.001 PHE A 55 TRP 0.004 0.001 TRP K 3 HIS 0.002 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 5126) covalent geometry : angle 0.56295 / 0.27 ( 7092) hydrogen bonds : bond 0.03407 / 2.19 ( 372) hydrogen bonds : angle 3.29495 / 2.34 ( 1086) link_NAG-ASN : bond 0.00045 / 0.02 ( 4) link_NAG-ASN : angle 1.35943 / 0.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.174 Fit side-chains REVERT: A 64 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8305 (tp) REVERT: A 149 GLN cc_start: 0.8339 (tt0) cc_final: 0.8123 (tt0) REVERT: B 64 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8316 (tp) REVERT: B 225 LYS cc_start: 0.6787 (ttmt) cc_final: 0.6524 (ttmt) outliers start: 11 outliers final: 8 residues processed: 109 average time/residue: 0.0611 time to fit residues: 8.9389 Evaluate side-chains 110 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 2 optimal weight: 0.0060 chunk 1 optimal weight: 0.0670 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.182567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.143514 restraints weight = 6585.573| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.43 r_work: 0.3522 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5130 Z= 0.107 Angle : 0.528 6.592 7104 Z= 0.258 Chirality : 0.035 0.131 924 Planarity : 0.003 0.027 800 Dihedral : 8.995 71.797 812 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.53 % Allowed : 20.52 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.25 (0.32), residues: 614 helix: 3.03 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.11 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 76 TYR 0.009 0.001 TYR A 128 PHE 0.012 0.001 PHE A 171 TRP 0.005 0.001 TRP K 3 HIS 0.003 0.001 HIS K 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 5126) covalent geometry : angle 0.52705 / 0.26 ( 7092) hydrogen bonds : bond 0.03207 / 2.07 ( 372) hydrogen bonds : angle 3.20100 / 2.29 ( 1086) link_NAG-ASN : bond 0.00121 / 0.06 ( 4) link_NAG-ASN : angle 1.07996 / 0.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.142 Fit side-chains REVERT: A 64 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8152 (tt) REVERT: A 106 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.8496 (m-80) REVERT: B 64 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8167 (tt) REVERT: B 106 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.8486 (m-80) outliers start: 7 outliers final: 3 residues processed: 109 average time/residue: 0.0636 time to fit residues: 9.1945 Evaluate side-chains 109 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.177634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.137795 restraints weight = 6534.048| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.46 r_work: 0.3446 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5130 Z= 0.159 Angle : 0.607 7.104 7104 Z= 0.288 Chirality : 0.038 0.135 924 Planarity : 0.003 0.028 800 Dihedral : 9.502 74.198 812 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.28 % Allowed : 19.21 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.17 (0.32), residues: 614 helix: 2.96 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.13 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 74 TYR 0.007 0.001 TYR B 111 PHE 0.017 0.001 PHE A 55 TRP 0.002 0.001 TRP K 1 HIS 0.002 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 5126) covalent geometry : angle 0.60474 / 0.29 ( 7092) hydrogen bonds : bond 0.03571 / 2.29 ( 372) hydrogen bonds : angle 3.32208 / 2.38 ( 1086) link_NAG-ASN : bond 0.00029 / 0.01 ( 4) link_NAG-ASN : angle 1.41201 / 0.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.139 Fit side-chains REVERT: A 64 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8201 (tp) REVERT: A 106 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.8028 (m-80) REVERT: A 225 LYS cc_start: 0.7040 (ttmt) cc_final: 0.6615 (ttmt) REVERT: B 64 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8227 (tp) REVERT: B 106 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.7956 (m-80) REVERT: B 225 LYS cc_start: 0.7025 (ttmt) cc_final: 0.6636 (ttmt) outliers start: 15 outliers final: 9 residues processed: 105 average time/residue: 0.0660 time to fit residues: 9.1919 Evaluate side-chains 111 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 58 optimal weight: 0.0040 chunk 12 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.178461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138875 restraints weight = 6554.898| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.46 r_work: 0.3461 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5130 Z= 0.134 Angle : 0.569 6.462 7104 Z= 0.274 Chirality : 0.037 0.132 924 Planarity : 0.003 0.029 800 Dihedral : 9.555 73.392 812 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.75 % Allowed : 20.09 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.32 (0.32), residues: 614 helix: 3.09 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.12 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 76 TYR 0.009 0.001 TYR B 128 PHE 0.012 0.001 PHE B 55 TRP 0.004 0.001 TRP I 3 HIS 0.002 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 5126) covalent geometry : angle 0.56754 / 0.27 ( 7092) hydrogen bonds : bond 0.03423 / 2.19 ( 372) hydrogen bonds : angle 3.25631 / 2.33 ( 1086) link_NAG-ASN : bond 0.00073 / 0.04 ( 4) link_NAG-ASN : angle 1.27263 / 0.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.177 Fit side-chains REVERT: A 64 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8316 (tp) REVERT: A 106 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.8051 (m-80) REVERT: B 64 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8321 (tp) REVERT: B 106 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.8037 (m-80) outliers start: 8 outliers final: 4 residues processed: 100 average time/residue: 0.0645 time to fit residues: 8.4711 Evaluate side-chains 106 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 7 optimal weight: 0.0570 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 46 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.178750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139633 restraints weight = 6484.307| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.42 r_work: 0.3467 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5130 Z= 0.125 Angle : 0.562 6.405 7104 Z= 0.270 Chirality : 0.037 0.137 924 Planarity : 0.003 0.030 800 Dihedral : 9.551 73.278 812 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.40 % Allowed : 20.31 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.44 (0.32), residues: 614 helix: 3.20 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.12 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 74 TYR 0.008 0.001 TYR B 128 PHE 0.012 0.001 PHE B 171 TRP 0.004 0.001 TRP K 3 HIS 0.002 0.001 HIS I 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 5126) covalent geometry : angle 0.55998 / 0.27 ( 7092) hydrogen bonds : bond 0.03329 / 2.14 ( 372) hydrogen bonds : angle 3.19045 / 2.27 ( 1086) link_NAG-ASN : bond 0.00064 / 0.03 ( 4) link_NAG-ASN : angle 1.22390 / 0.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.117 Fit side-chains REVERT: A 64 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8297 (tp) REVERT: A 106 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.7981 (m-80) REVERT: B 64 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8307 (tp) REVERT: B 106 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.7980 (m-80) outliers start: 11 outliers final: 7 residues processed: 103 average time/residue: 0.0678 time to fit residues: 9.1836 Evaluate side-chains 110 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.177512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137550 restraints weight = 6551.775| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.45 r_work: 0.3439 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5130 Z= 0.152 Angle : 0.596 6.734 7104 Z= 0.286 Chirality : 0.038 0.138 924 Planarity : 0.003 0.030 800 Dihedral : 9.817 74.234 812 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.84 % Allowed : 19.87 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.33), residues: 614 helix: 2.95 (0.23), residues: 448 sheet: None (None), residues: 0 loop : -0.25 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 122 TYR 0.007 0.001 TYR B 128 PHE 0.015 0.001 PHE B 55 TRP 0.003 0.001 TRP I 1 HIS 0.002 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 5126) covalent geometry : angle 0.59375 / 0.29 ( 7092) hydrogen bonds : bond 0.03525 / 2.25 ( 372) hydrogen bonds : angle 3.26630 / 2.33 ( 1086) link_NAG-ASN : bond 0.00035 / 0.02 ( 4) link_NAG-ASN : angle 1.38573 / 0.85 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.211 Fit side-chains REVERT: A 64 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8254 (tp) REVERT: A 106 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: B 64 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8263 (tp) REVERT: B 106 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.8018 (m-80) outliers start: 13 outliers final: 9 residues processed: 105 average time/residue: 0.0617 time to fit residues: 8.6837 Evaluate side-chains 114 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 TRP Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 0.0070 chunk 49 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.178328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138615 restraints weight = 6620.231| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.46 r_work: 0.3456 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5130 Z= 0.133 Angle : 0.574 6.424 7104 Z= 0.277 Chirality : 0.037 0.134 924 Planarity : 0.003 0.031 800 Dihedral : 9.663 73.598 812 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.06 % Allowed : 19.65 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.31 (0.33), residues: 614 helix: 3.02 (0.23), residues: 448 sheet: None (None), residues: 0 loop : -0.25 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 74 TYR 0.008 0.001 TYR B 128 PHE 0.012 0.001 PHE B 55 TRP 0.005 0.001 TRP A 295 HIS 0.002 0.001 HIS I 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 5126) covalent geometry : angle 0.57182 / 0.28 ( 7092) hydrogen bonds : bond 0.03413 / 2.18 ( 372) hydrogen bonds : angle 3.24247 / 2.32 ( 1086) link_NAG-ASN : bond 0.00066 / 0.03 ( 4) link_NAG-ASN : angle 1.26498 / 0.79 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1220.63 seconds wall clock time: 21 minutes 43.51 seconds (1303.51 seconds total)