Starting phenix.real_space_refine on Thu Jun 5 04:57:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qbi_13887/06_2025/7qbi_13887.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qbi_13887/06_2025/7qbi_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7qbi_13887/06_2025/7qbi_13887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qbi_13887/06_2025/7qbi_13887.map" model { file = "/net/cci-nas-00/data/ceres_data/7qbi_13887/06_2025/7qbi_13887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qbi_13887/06_2025/7qbi_13887.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 4, 'ASP:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 6, 'ARG:plan': 4} 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: {'GLN:plan1': 4, 'ASP:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 6, 'ARG:plan': 4} 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.90, per 1000 atoms: 0.78 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: 1.50 Conformation dependent library (CDL) restraints added in 573.7 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: 0.45 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: 1.34 Time building geometry restraints manager: 1.74 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 - 23.62: 3413 23.62 - 47.23: 160 47.23 - 70.85: 29 70.85 - 94.47: 12 94.47 - 118.08: 4 Dihedral angle restraints: 3618 sinusoidal: 1792 harmonic: 1826 Sorted by residual: dihedral pdb=" CAR Y01 I 102 " pdb=" CAV Y01 I 102 " pdb=" CBC Y01 I 102 " pdb=" CAZ Y01 I 102 " ideal model delta sinusoidal sigma weight residual 55.40 -62.68 118.08 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" CAR Y01 K 102 " pdb=" CAV Y01 K 102 " pdb=" CBC Y01 K 102 " pdb=" CAZ Y01 K 102 " ideal model delta sinusoidal sigma weight residual 55.40 -60.15 115.55 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" CAZ Y01 I 102 " pdb=" CAV Y01 I 102 " pdb=" CBC Y01 I 102 " pdb=" OAW Y01 I 102 " ideal model delta sinusoidal sigma weight residual -174.31 -59.08 -115.23 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 3615 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: 0.02 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: 0.570 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 16.360 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 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 : 14.753 118.083 2438 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.31), 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 TRP 0.016 0.002 TRP A 70 HIS 0.003 0.001 HIS A 94 PHE 0.025 0.003 PHE B 171 TYR 0.026 0.003 TYR A 266 ARG 0.007 0.001 ARG A 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00116 ( 4) link_NAG-ASN : angle 1.78406 ( 12) hydrogen bonds : bond 0.11871 ( 372) hydrogen bonds : angle 5.74241 ( 1086) covalent geometry : bond 0.00818 ( 5126) covalent geometry : angle 1.06429 ( 7092) *********************** 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 : 0.539 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: 0.1547 time to fit residues: 23.2042 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 : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 2 HIS K 2 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.193386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.154748 restraints weight = 6308.486| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.28 r_work: 0.3595 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5130 Z= 0.207 Angle : 0.698 7.274 7104 Z= 0.329 Chirality : 0.040 0.139 924 Planarity : 0.004 0.028 800 Dihedral : 10.803 90.862 1592 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.33), residues: 614 helix: 1.31 (0.23), residues: 448 sheet: None (None), residues: 0 loop : -0.36 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 1 HIS 0.003 0.001 HIS B 94 PHE 0.017 0.002 PHE A 171 TYR 0.010 0.002 TYR B 106 ARG 0.002 0.000 ARG B 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 4) link_NAG-ASN : angle 1.69251 ( 12) hydrogen bonds : bond 0.03996 ( 372) hydrogen bonds : angle 3.79487 ( 1086) covalent geometry : bond 0.00496 ( 5126) covalent geometry : angle 0.69554 ( 7092) *********************** 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 116 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.613 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2090 time to fit residues: 31.9644 Evaluate side-chains 94 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 59 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.182112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.142809 restraints weight = 6493.991| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.40 r_work: 0.3501 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2418 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= 0.125 Angle : 0.591 7.598 7104 Z= 0.278 Chirality : 0.037 0.134 924 Planarity : 0.003 0.025 800 Dihedral : 9.590 79.422 1592 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.87 % Allowed : 14.41 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.33), residues: 614 helix: 2.49 (0.24), residues: 434 sheet: None (None), residues: 0 loop : -0.61 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 3 HIS 0.002 0.001 HIS A 94 PHE 0.014 0.001 PHE B 171 TYR 0.008 0.001 TYR A 17 ARG 0.001 0.000 ARG A 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 4) link_NAG-ASN : angle 1.22170 ( 12) hydrogen bonds : bond 0.03489 ( 372) hydrogen bonds : angle 3.38378 ( 1086) covalent geometry : bond 0.00291 ( 5126) covalent geometry : angle 0.58962 ( 7092) *********************** 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 106 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.524 Fit side-chains REVERT: A 64 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8084 (tt) REVERT: A 149 GLN cc_start: 0.8356 (tt0) cc_final: 0.8085 (tt0) REVERT: B 64 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8111 (tt) REVERT: B 70 TRP cc_start: 0.7842 (OUTLIER) cc_final: 0.7432 (m100) outliers start: 4 outliers final: 1 residues processed: 104 average time/residue: 0.2068 time to fit residues: 28.6108 Evaluate side-chains 102 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 38 optimal weight: 0.0980 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4122 r_free = 0.4122 target = 0.180093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140112 restraints weight = 6655.787| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.49 r_work: 0.3440 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5130 Z= 0.161 Angle : 0.646 8.066 7104 Z= 0.296 Chirality : 0.038 0.136 924 Planarity : 0.003 0.026 800 Dihedral : 8.881 58.728 1592 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.28 % Allowed : 16.16 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.33), residues: 614 helix: 2.58 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.48 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 70 HIS 0.002 0.001 HIS A 94 PHE 0.015 0.001 PHE A 55 TYR 0.008 0.001 TYR A 128 ARG 0.002 0.000 ARG B 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 4) link_NAG-ASN : angle 1.41744 ( 12) hydrogen bonds : bond 0.03635 ( 372) hydrogen bonds : angle 3.36862 ( 1086) covalent geometry : bond 0.00385 ( 5126) covalent geometry : angle 0.64369 ( 7092) *********************** 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 114 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.547 Fit side-chains REVERT: A 64 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8187 (tp) REVERT: A 106 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.8375 (m-80) REVERT: A 149 GLN cc_start: 0.8385 (tt0) cc_final: 0.8108 (tt0) REVERT: B 64 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8209 (tp) REVERT: B 106 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8382 (m-80) outliers start: 15 outliers final: 6 residues processed: 107 average time/residue: 0.1692 time to fit residues: 24.0501 Evaluate side-chains 107 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 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 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 26 optimal weight: 0.0060 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.180707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141525 restraints weight = 6497.547| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.43 r_work: 0.3497 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2931 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= 0.117 Angle : 0.573 6.731 7104 Z= 0.268 Chirality : 0.037 0.136 924 Planarity : 0.003 0.024 800 Dihedral : 8.253 58.837 1592 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.97 % Allowed : 19.21 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.33), residues: 614 helix: 2.91 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.31 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 3 HIS 0.002 0.001 HIS K 2 PHE 0.010 0.001 PHE B 171 TYR 0.008 0.001 TYR B 128 ARG 0.002 0.000 ARG B 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 4) link_NAG-ASN : angle 1.22709 ( 12) hydrogen bonds : bond 0.03339 ( 372) hydrogen bonds : angle 3.24190 ( 1086) covalent geometry : bond 0.00271 ( 5126) covalent geometry : angle 0.57135 ( 7092) *********************** 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 109 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.540 Fit side-chains REVERT: A 64 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8293 (tp) REVERT: A 106 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.8235 (m-80) REVERT: A 149 GLN cc_start: 0.8344 (tt0) cc_final: 0.8119 (tt0) REVERT: B 64 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8249 (tt) REVERT: B 106 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8340 (m-80) outliers start: 9 outliers final: 5 residues processed: 104 average time/residue: 0.1565 time to fit residues: 21.2232 Evaluate side-chains 107 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 197 SER 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 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 58 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.177383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.137757 restraints weight = 6536.411| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.45 r_work: 0.3448 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3136 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= 0.151 Angle : 0.606 6.956 7104 Z= 0.281 Chirality : 0.038 0.134 924 Planarity : 0.003 0.025 800 Dihedral : 8.373 59.504 1592 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.84 % Allowed : 18.78 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.33), residues: 614 helix: 2.87 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.25 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 70 HIS 0.002 0.001 HIS A 94 PHE 0.015 0.001 PHE B 55 TYR 0.007 0.001 TYR B 128 ARG 0.001 0.000 ARG B 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 4) link_NAG-ASN : angle 1.36749 ( 12) hydrogen bonds : bond 0.03542 ( 372) hydrogen bonds : angle 3.27583 ( 1086) covalent geometry : bond 0.00359 ( 5126) covalent geometry : angle 0.60382 ( 7092) *********************** 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: 13 poor density : 101 time to evaluate : 0.501 Fit side-chains REVERT: A 64 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8153 (tp) REVERT: A 106 TYR cc_start: 0.8942 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: B 64 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8213 (tp) REVERT: B 106 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.8037 (m-80) outliers start: 13 outliers final: 8 residues processed: 106 average time/residue: 0.1890 time to fit residues: 26.3718 Evaluate side-chains 108 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 197 SER 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 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 0.0050 chunk 6 optimal weight: 0.5980 chunk 15 optimal weight: 30.0000 chunk 9 optimal weight: 0.0670 chunk 8 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 overall best weight: 0.3932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.179830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.140816 restraints weight = 6531.402| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.43 r_work: 0.3483 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5130 Z= 0.117 Angle : 0.565 6.426 7104 Z= 0.270 Chirality : 0.037 0.133 924 Planarity : 0.003 0.028 800 Dihedral : 7.989 59.518 1592 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.75 % Allowed : 20.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.32), residues: 614 helix: 3.04 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.16 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 3 HIS 0.002 0.001 HIS K 2 PHE 0.011 0.001 PHE B 171 TYR 0.007 0.001 TYR B 128 ARG 0.001 0.000 ARG A 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 4) link_NAG-ASN : angle 1.13782 ( 12) hydrogen bonds : bond 0.03342 ( 372) hydrogen bonds : angle 3.19084 ( 1086) covalent geometry : bond 0.00267 ( 5126) covalent geometry : angle 0.56364 ( 7092) *********************** 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 109 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.547 Fit side-chains REVERT: A 64 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8250 (tp) REVERT: B 64 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8271 (tp) REVERT: B 106 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8188 (m-80) outliers start: 8 outliers final: 4 residues processed: 104 average time/residue: 0.1591 time to fit residues: 21.7205 Evaluate side-chains 102 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.178265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139002 restraints weight = 6577.987| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.43 r_work: 0.3454 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5130 Z= 0.137 Angle : 0.595 6.734 7104 Z= 0.281 Chirality : 0.038 0.135 924 Planarity : 0.003 0.028 800 Dihedral : 8.065 59.000 1592 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.62 % Allowed : 21.18 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.32), residues: 614 helix: 3.14 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.20 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 70 HIS 0.002 0.001 HIS A 94 PHE 0.015 0.001 PHE B 55 TYR 0.007 0.001 TYR B 128 ARG 0.000 0.000 ARG A 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 4) link_NAG-ASN : angle 1.25036 ( 12) hydrogen bonds : bond 0.03399 ( 372) hydrogen bonds : angle 3.19600 ( 1086) covalent geometry : bond 0.00324 ( 5126) covalent geometry : angle 0.59317 ( 7092) *********************** 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: 12 poor density : 94 time to evaluate : 0.514 Fit side-chains REVERT: A 64 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8289 (tp) REVERT: A 89 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7590 (t80) REVERT: A 106 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: B 64 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8302 (tp) outliers start: 12 outliers final: 8 residues processed: 98 average time/residue: 0.1610 time to fit residues: 20.6640 Evaluate side-chains 106 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 89 PHE 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 64 LEU Chi-restraints excluded: chain B residue 70 TRP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 30.0000 chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.176879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137709 restraints weight = 6468.258| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.40 r_work: 0.3442 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3452 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= 0.143 Angle : 0.599 6.987 7104 Z= 0.284 Chirality : 0.038 0.135 924 Planarity : 0.003 0.029 800 Dihedral : 8.174 58.743 1592 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.62 % Allowed : 21.83 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.32), residues: 614 helix: 3.15 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.30 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 3 HIS 0.002 0.001 HIS A 94 PHE 0.013 0.001 PHE B 55 TYR 0.007 0.001 TYR A 128 ARG 0.001 0.000 ARG A 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00077 ( 4) link_NAG-ASN : angle 1.29643 ( 12) hydrogen bonds : bond 0.03473 ( 372) hydrogen bonds : angle 3.22574 ( 1086) covalent geometry : bond 0.00340 ( 5126) covalent geometry : angle 0.59671 ( 7092) *********************** 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 106 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.498 Fit side-chains REVERT: A 64 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8269 (tp) REVERT: A 106 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8025 (m-80) REVERT: B 64 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8298 (tp) outliers start: 12 outliers final: 8 residues processed: 98 average time/residue: 0.1496 time to fit residues: 19.5441 Evaluate side-chains 105 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 197 SER 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 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 41 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.0000 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.178397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.139111 restraints weight = 6544.845| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.46 r_work: 0.3457 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5130 Z= 0.121 Angle : 0.568 6.635 7104 Z= 0.273 Chirality : 0.037 0.133 924 Planarity : 0.003 0.030 800 Dihedral : 8.092 57.799 1592 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.40 % Allowed : 22.27 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.46 (0.32), residues: 614 helix: 3.26 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.26 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 3 HIS 0.002 0.001 HIS K 2 PHE 0.010 0.001 PHE B 55 TYR 0.007 0.001 TYR B 128 ARG 0.001 0.000 ARG A 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00112 ( 4) link_NAG-ASN : angle 1.17508 ( 12) hydrogen bonds : bond 0.03322 ( 372) hydrogen bonds : angle 3.17600 ( 1086) covalent geometry : bond 0.00280 ( 5126) covalent geometry : angle 0.56658 ( 7092) ********************** 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 110 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.582 Fit side-chains REVERT: A 64 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8238 (tp) REVERT: A 106 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.8087 (m-80) REVERT: B 64 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8290 (tp) REVERT: B 106 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.7994 (m-80) outliers start: 11 outliers final: 6 residues processed: 101 average time/residue: 0.1557 time to fit residues: 20.5930 Evaluate side-chains 105 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 64 LEU Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 106 TYR 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 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.176091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136561 restraints weight = 6540.024| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.44 r_work: 0.3430 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3583 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= 0.157 Angle : 0.609 7.225 7104 Z= 0.290 Chirality : 0.038 0.140 924 Planarity : 0.003 0.030 800 Dihedral : 8.428 58.574 1592 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.84 % Allowed : 21.83 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.32), residues: 614 helix: 3.14 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.38 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 3 HIS 0.002 0.001 HIS A 94 PHE 0.014 0.001 PHE B 55 TYR 0.007 0.001 TYR B 128 ARG 0.002 0.000 ARG A 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 4) link_NAG-ASN : angle 1.36422 ( 12) hydrogen bonds : bond 0.03556 ( 372) hydrogen bonds : angle 3.28873 ( 1086) covalent geometry : bond 0.00374 ( 5126) covalent geometry : angle 0.60696 ( 7092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2660.98 seconds wall clock time: 47 minutes 15.62 seconds (2835.62 seconds total)