Starting phenix.real_space_refine on Fri May 9 20:53:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r9x_19015/05_2025/8r9x_19015.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r9x_19015/05_2025/8r9x_19015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r9x_19015/05_2025/8r9x_19015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r9x_19015/05_2025/8r9x_19015.map" model { file = "/net/cci-nas-00/data/ceres_data/8r9x_19015/05_2025/8r9x_19015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r9x_19015/05_2025/8r9x_19015.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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 18 5.16 5 C 2381 2.51 5 N 612 2.21 5 O 771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3782 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1844 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain: "H" Number of atoms: 929 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Conformer: "B" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} bond proxies already assigned to first conformer: 930 Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 812 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.95, per 1000 atoms: 1.04 Number of scatterers: 3782 At special positions: 0 Unit cell: (97.09, 68.474, 70.518, 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 18 16.00 O 771 8.00 N 612 7.00 C 2381 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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 ALPHA1-3 " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " BETA1-6 " NAG B 1 " - " FUC B 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1101 " - " ASN A 162 " " NAG A1102 " - " ASN A 169 " " NAG A1103 " - " ASN A 251 " " NAG B 1 " - " ASN A 99 " " NAG C 1 " - " ASN A 184 " " NAG D 1 " - " ASN A 241 " " NAG E 1 " - " ASN A 74 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 569.0 milliseconds 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 854 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 9 sheets defined 8.9% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.790A pdb=" N LEU A 68 " --> pdb=" O ASN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 124 removed outlier: 3.650A pdb=" N MET A 120 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 121 " --> pdb=" O GLY A 118 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 122 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.711A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 88 removed outlier: 3.600A pdb=" N GLY A 81 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 256 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR A 250 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 removed outlier: 4.618A pdb=" N GLN A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE A 206 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 105 removed outlier: 7.251A pdb=" N ILE A 141 " --> pdb=" O CYS A 157 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N CYS A 157 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS A 181 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.918A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.663A pdb=" N TYR H 111 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.346A pdb=" N LEU L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.767A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) 127 hydrogen bonds defined for protein. 318 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: 0.98 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1174 1.34 - 1.46: 912 1.46 - 1.57: 1756 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3866 Sorted by residual: bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.59e+00 bond pdb=" CA SER A 43 " pdb=" CB SER A 43 " ideal model delta sigma weight residual 1.530 1.498 0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 NAG A1102 " pdb=" O5 NAG A1102 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" N SER A 43 " pdb=" CA SER A 43 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 1.97e+00 ... (remaining 3861 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 5111 1.63 - 3.26: 129 3.26 - 4.89: 20 4.89 - 6.52: 8 6.52 - 8.15: 1 Bond angle restraints: 5269 Sorted by residual: angle pdb=" N LEU A 58 " pdb=" CA LEU A 58 " pdb=" C LEU A 58 " ideal model delta sigma weight residual 109.81 115.70 -5.89 2.21e+00 2.05e-01 7.09e+00 angle pdb=" CA LEU A 106 " pdb=" CB LEU A 106 " pdb=" CG LEU A 106 " ideal model delta sigma weight residual 116.30 124.45 -8.15 3.50e+00 8.16e-02 5.42e+00 angle pdb=" C1 BMA D 3 " pdb=" O5 BMA D 3 " pdb=" C5 BMA D 3 " ideal model delta sigma weight residual 118.82 112.31 6.51 3.00e+00 1.11e-01 4.71e+00 angle pdb=" C3 BMA D 3 " pdb=" C2 BMA D 3 " pdb=" O2 BMA D 3 " ideal model delta sigma weight residual 112.95 106.48 6.47 3.00e+00 1.11e-01 4.65e+00 angle pdb=" C3 MAN D 4 " pdb=" C2 MAN D 4 " pdb=" O2 MAN D 4 " ideal model delta sigma weight residual 111.77 105.37 6.40 3.00e+00 1.11e-01 4.56e+00 ... (remaining 5264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.65: 2226 21.65 - 43.30: 196 43.30 - 64.94: 23 64.94 - 86.59: 11 86.59 - 108.24: 5 Dihedral angle restraints: 2461 sinusoidal: 1118 harmonic: 1343 Sorted by residual: dihedral pdb=" CA LEU A 58 " pdb=" C LEU A 58 " pdb=" N PRO A 59 " pdb=" CA PRO A 59 " ideal model delta harmonic sigma weight residual 180.00 150.41 29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA PHE A 182 " pdb=" C PHE A 182 " pdb=" N THR A 183 " pdb=" CA THR A 183 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.53 108.24 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 2458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 494 0.044 - 0.089: 104 0.089 - 0.133: 46 0.133 - 0.177: 2 0.177 - 0.221: 1 Chirality restraints: 647 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.50 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 241 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" C3 FUC B 3 " pdb=" C2 FUC B 3 " pdb=" C4 FUC B 3 " pdb=" O3 FUC B 3 " both_signs ideal model delta sigma weight residual False -2.45 -2.59 0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 644 not shown) Planarity restraints: 655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 58 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO A 59 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 59 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 59 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 3 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.03e+00 pdb=" C VAL L 3 " -0.018 2.00e-02 2.50e+03 pdb=" O VAL L 3 " 0.007 2.00e-02 2.50e+03 pdb=" N MET L 4 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA L 43 " -0.015 5.00e-02 4.00e+02 2.28e-02 8.34e-01 pdb=" N PRO L 44 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO L 44 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO L 44 " -0.013 5.00e-02 4.00e+02 ... (remaining 652 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1005 2.80 - 3.33: 3150 3.33 - 3.85: 6103 3.85 - 4.38: 7321 4.38 - 4.90: 13218 Nonbonded interactions: 30797 Sorted by model distance: nonbonded pdb=" NH1 ARG A 48 " pdb=" OD2 ASP A 134 " model vdw 2.277 3.120 nonbonded pdb=" O THR L 20 " pdb=" OG1 THR L 20 " model vdw 2.292 3.040 nonbonded pdb=" NH1 ARG L 61 " pdb=" OE1 GLN L 79 " model vdw 2.307 3.120 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.362 3.040 nonbonded pdb=" O ASN A 251 " pdb=" OG1 THR A 252 " model vdw 2.379 3.040 ... (remaining 30792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.820 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 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 : 0.004 0.032 3886 Z= 0.195 Angle : 0.669 8.147 5324 Z= 0.302 Chirality : 0.044 0.221 647 Planarity : 0.003 0.050 648 Dihedral : 16.479 108.236 1592 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 20.95 % Favored : 79.05 % 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: -0.47 (0.41), residues: 456 helix: -0.35 (1.07), residues: 25 sheet: -0.02 (0.41), residues: 176 loop : -0.44 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 112 HIS 0.003 0.001 HIS A 168 PHE 0.011 0.001 PHE A 237 TYR 0.009 0.001 TYR A 222 ARG 0.002 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 7) link_NAG-ASN : angle 1.72565 ( 21) link_ALPHA1-6 : bond 0.00394 ( 1) link_ALPHA1-6 : angle 1.58731 ( 3) link_BETA1-4 : bond 0.00429 ( 5) link_BETA1-4 : angle 2.24744 ( 15) link_ALPHA1-3 : bond 0.00732 ( 1) link_ALPHA1-3 : angle 1.15123 ( 3) hydrogen bonds : bond 0.23497 ( 122) hydrogen bonds : angle 8.84192 ( 318) link_BETA1-6 : bond 0.00164 ( 1) link_BETA1-6 : angle 1.53286 ( 3) SS BOND : bond 0.00090 ( 5) SS BOND : angle 0.37937 ( 10) covalent geometry : bond 0.00414 ( 3866) covalent geometry : angle 0.65022 ( 5269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2339 time to fit residues: 23.0626 Evaluate side-chains 74 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 4.9990 chunk 34 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.0970 chunk 22 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN H 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.074552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.057489 restraints weight = 20990.994| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 4.92 r_work: 0.2514 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3886 Z= 0.138 Angle : 0.645 7.748 5324 Z= 0.323 Chirality : 0.043 0.179 647 Planarity : 0.004 0.048 648 Dihedral : 9.983 82.589 815 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.99 % Allowed : 21.20 % Favored : 75.81 % 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: -0.28 (0.40), residues: 456 helix: 0.31 (1.17), residues: 25 sheet: 0.17 (0.41), residues: 163 loop : -0.40 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 47 HIS 0.002 0.001 HIS A 236 PHE 0.012 0.001 PHE A 237 TYR 0.014 0.001 TYR H 80 ARG 0.007 0.001 ARG L 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 7) link_NAG-ASN : angle 1.59860 ( 21) link_ALPHA1-6 : bond 0.00284 ( 1) link_ALPHA1-6 : angle 2.56840 ( 3) link_BETA1-4 : bond 0.00247 ( 5) link_BETA1-4 : angle 1.91480 ( 15) link_ALPHA1-3 : bond 0.01041 ( 1) link_ALPHA1-3 : angle 2.39697 ( 3) hydrogen bonds : bond 0.04189 ( 122) hydrogen bonds : angle 6.00899 ( 318) link_BETA1-6 : bond 0.00148 ( 1) link_BETA1-6 : angle 1.46285 ( 3) SS BOND : bond 0.00126 ( 5) SS BOND : angle 0.45684 ( 10) covalent geometry : bond 0.00311 ( 3866) covalent geometry : angle 0.62564 ( 5269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8856 (t0) cc_final: 0.8615 (t0) REVERT: A 139 ASP cc_start: 0.9250 (t0) cc_final: 0.9014 (m-30) REVERT: A 197 ASP cc_start: 0.9017 (t0) cc_final: 0.8773 (t0) REVERT: H 1 GLU cc_start: 0.8188 (tp30) cc_final: 0.7744 (tp30) REVERT: L 79 GLN cc_start: 0.8876 (mt0) cc_final: 0.8657 (mt0) outliers start: 12 outliers final: 5 residues processed: 86 average time/residue: 0.2065 time to fit residues: 20.8520 Evaluate side-chains 80 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain L residue 2 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 27 optimal weight: 0.0670 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- 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 = 0.3034 r_free = 0.3034 target = 0.073539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.057508 restraints weight = 14938.590| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 4.27 r_work: 0.2540 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3886 Z= 0.144 Angle : 0.605 7.964 5324 Z= 0.302 Chirality : 0.043 0.204 647 Planarity : 0.004 0.047 648 Dihedral : 9.310 78.723 815 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.49 % Allowed : 20.70 % Favored : 76.81 % 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: -0.25 (0.40), residues: 456 helix: 0.53 (1.20), residues: 25 sheet: 0.29 (0.41), residues: 158 loop : -0.47 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 112 HIS 0.002 0.001 HIS A 236 PHE 0.010 0.001 PHE A 206 TYR 0.014 0.001 TYR A 222 ARG 0.005 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 7) link_NAG-ASN : angle 1.53544 ( 21) link_ALPHA1-6 : bond 0.00352 ( 1) link_ALPHA1-6 : angle 2.46359 ( 3) link_BETA1-4 : bond 0.00236 ( 5) link_BETA1-4 : angle 1.96982 ( 15) link_ALPHA1-3 : bond 0.01278 ( 1) link_ALPHA1-3 : angle 1.82273 ( 3) hydrogen bonds : bond 0.03858 ( 122) hydrogen bonds : angle 5.47508 ( 318) link_BETA1-6 : bond 0.00001 ( 1) link_BETA1-6 : angle 1.40297 ( 3) SS BOND : bond 0.00127 ( 5) SS BOND : angle 0.36717 ( 10) covalent geometry : bond 0.00332 ( 3866) covalent geometry : angle 0.58556 ( 5269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8899 (t0) cc_final: 0.8606 (t0) REVERT: A 120 MET cc_start: 0.8554 (tpp) cc_final: 0.8182 (tpp) REVERT: A 139 ASP cc_start: 0.9157 (t0) cc_final: 0.8926 (m-30) REVERT: A 151 GLU cc_start: 0.8178 (pm20) cc_final: 0.7894 (pm20) REVERT: A 197 ASP cc_start: 0.9111 (t0) cc_final: 0.8774 (t0) REVERT: H 1 GLU cc_start: 0.8195 (tp30) cc_final: 0.7730 (tp30) REVERT: H 3 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7628 (mmm-85) REVERT: L 11 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7984 (tt) REVERT: L 79 GLN cc_start: 0.8930 (mt0) cc_final: 0.8628 (mt0) outliers start: 10 outliers final: 7 residues processed: 83 average time/residue: 0.2206 time to fit residues: 21.3560 Evaluate side-chains 81 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain L residue 11 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 6 optimal weight: 0.0020 chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- 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 = 0.3046 r_free = 0.3046 target = 0.074070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.057161 restraints weight = 21488.244| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 4.98 r_work: 0.2512 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3886 Z= 0.138 Angle : 0.610 7.867 5324 Z= 0.303 Chirality : 0.043 0.224 647 Planarity : 0.004 0.046 648 Dihedral : 8.694 74.424 815 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.74 % Allowed : 21.45 % Favored : 75.81 % 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: -0.14 (0.40), residues: 456 helix: 0.64 (1.21), residues: 25 sheet: 0.41 (0.42), residues: 158 loop : -0.43 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 112 HIS 0.001 0.000 HIS A 236 PHE 0.010 0.001 PHE A 237 TYR 0.014 0.001 TYR A 222 ARG 0.007 0.001 ARG A 48 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 7) link_NAG-ASN : angle 1.49142 ( 21) link_ALPHA1-6 : bond 0.00431 ( 1) link_ALPHA1-6 : angle 2.47630 ( 3) link_BETA1-4 : bond 0.00182 ( 5) link_BETA1-4 : angle 1.92152 ( 15) link_ALPHA1-3 : bond 0.01119 ( 1) link_ALPHA1-3 : angle 1.89195 ( 3) hydrogen bonds : bond 0.03492 ( 122) hydrogen bonds : angle 5.17672 ( 318) link_BETA1-6 : bond 0.00006 ( 1) link_BETA1-6 : angle 1.42748 ( 3) SS BOND : bond 0.00169 ( 5) SS BOND : angle 0.38520 ( 10) covalent geometry : bond 0.00317 ( 3866) covalent geometry : angle 0.59081 ( 5269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 48 ARG cc_start: 0.9488 (mtm110) cc_final: 0.8756 (ttp80) REVERT: A 54 ASP cc_start: 0.8945 (t0) cc_final: 0.8629 (t0) REVERT: A 120 MET cc_start: 0.8590 (tpp) cc_final: 0.8236 (tpp) REVERT: A 197 ASP cc_start: 0.9185 (t0) cc_final: 0.8799 (t0) REVERT: H 1 GLU cc_start: 0.8329 (tp30) cc_final: 0.7941 (tp30) REVERT: H 3 ARG cc_start: 0.8215 (mmm-85) cc_final: 0.7767 (mmm-85) REVERT: H 76 LYS cc_start: 0.9560 (mtpp) cc_final: 0.9302 (mtmm) REVERT: H 87 ARG cc_start: 0.8419 (ptp-170) cc_final: 0.7743 (ptp-170) REVERT: L 79 GLN cc_start: 0.8941 (mt0) cc_final: 0.8636 (mt0) outliers start: 11 outliers final: 8 residues processed: 81 average time/residue: 0.2209 time to fit residues: 20.9371 Evaluate side-chains 80 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain L residue 2 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 28 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 27 optimal weight: 0.0370 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 0.0470 chunk 38 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.075012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.057968 restraints weight = 21624.012| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 5.06 r_work: 0.2535 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3886 Z= 0.119 Angle : 0.609 7.893 5324 Z= 0.301 Chirality : 0.042 0.230 647 Planarity : 0.003 0.044 648 Dihedral : 8.345 71.511 815 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.49 % Allowed : 21.20 % Favored : 75.31 % 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: -0.09 (0.40), residues: 456 helix: 0.65 (1.21), residues: 25 sheet: 0.46 (0.42), residues: 158 loop : -0.40 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 112 HIS 0.002 0.001 HIS A 236 PHE 0.010 0.001 PHE A 237 TYR 0.013 0.001 TYR H 59 ARG 0.007 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 7) link_NAG-ASN : angle 1.46490 ( 21) link_ALPHA1-6 : bond 0.00513 ( 1) link_ALPHA1-6 : angle 2.42445 ( 3) link_BETA1-4 : bond 0.00279 ( 5) link_BETA1-4 : angle 1.87088 ( 15) link_ALPHA1-3 : bond 0.01380 ( 1) link_ALPHA1-3 : angle 2.02146 ( 3) hydrogen bonds : bond 0.03321 ( 122) hydrogen bonds : angle 5.00794 ( 318) link_BETA1-6 : bond 0.00033 ( 1) link_BETA1-6 : angle 1.37813 ( 3) SS BOND : bond 0.00104 ( 5) SS BOND : angle 0.41138 ( 10) covalent geometry : bond 0.00269 ( 3866) covalent geometry : angle 0.59118 ( 5269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 48 ARG cc_start: 0.9444 (mtm110) cc_final: 0.8675 (ttp80) REVERT: A 54 ASP cc_start: 0.8956 (t0) cc_final: 0.8622 (t0) REVERT: A 106 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8576 (pp) REVERT: A 120 MET cc_start: 0.8547 (tpp) cc_final: 0.8201 (tpp) REVERT: A 197 ASP cc_start: 0.9228 (t0) cc_final: 0.8796 (t0) REVERT: H 1 GLU cc_start: 0.8395 (tp30) cc_final: 0.8120 (tp30) REVERT: H 87 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7999 (ptt-90) REVERT: L 11 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8141 (tp) REVERT: L 79 GLN cc_start: 0.8930 (mt0) cc_final: 0.8615 (mt0) outliers start: 14 outliers final: 9 residues processed: 83 average time/residue: 0.2197 time to fit residues: 21.4325 Evaluate side-chains 84 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 11 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.0570 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.9102 ------------------------------------------------------------------------------- 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 = 0.3044 r_free = 0.3044 target = 0.072415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.056653 restraints weight = 19808.872| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 4.59 r_work: 0.2558 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3886 Z= 0.159 Angle : 0.608 7.809 5324 Z= 0.303 Chirality : 0.043 0.237 647 Planarity : 0.004 0.045 648 Dihedral : 8.190 70.251 815 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.24 % Allowed : 23.19 % Favored : 74.56 % 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: -0.11 (0.40), residues: 456 helix: 0.60 (1.20), residues: 25 sheet: 0.41 (0.42), residues: 159 loop : -0.39 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP H 112 HIS 0.002 0.001 HIS A 236 PHE 0.010 0.001 PHE A 237 TYR 0.014 0.001 TYR A 222 ARG 0.007 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 7) link_NAG-ASN : angle 1.51720 ( 21) link_ALPHA1-6 : bond 0.00406 ( 1) link_ALPHA1-6 : angle 2.54080 ( 3) link_BETA1-4 : bond 0.00223 ( 5) link_BETA1-4 : angle 1.94320 ( 15) link_ALPHA1-3 : bond 0.01246 ( 1) link_ALPHA1-3 : angle 2.06062 ( 3) hydrogen bonds : bond 0.03378 ( 122) hydrogen bonds : angle 4.99002 ( 318) link_BETA1-6 : bond 0.00075 ( 1) link_BETA1-6 : angle 1.43849 ( 3) SS BOND : bond 0.00126 ( 5) SS BOND : angle 0.40452 ( 10) covalent geometry : bond 0.00367 ( 3866) covalent geometry : angle 0.58867 ( 5269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.9439 (mtm110) cc_final: 0.8696 (ttp80) REVERT: A 54 ASP cc_start: 0.8968 (t0) cc_final: 0.8640 (t0) REVERT: A 120 MET cc_start: 0.8701 (tpp) cc_final: 0.8390 (tpp) REVERT: A 197 ASP cc_start: 0.9200 (t0) cc_final: 0.8877 (t0) REVERT: H 73 ASP cc_start: 0.8301 (t0) cc_final: 0.7756 (t0) REVERT: L 79 GLN cc_start: 0.8848 (mt0) cc_final: 0.8225 (mm110) outliers start: 9 outliers final: 8 residues processed: 79 average time/residue: 0.2204 time to fit residues: 20.3629 Evaluate side-chains 81 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain H residue 117 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 41 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3055 r_free = 0.3055 target = 0.072922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.057321 restraints weight = 19747.950| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 4.58 r_work: 0.2573 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3886 Z= 0.128 Angle : 0.599 7.834 5324 Z= 0.298 Chirality : 0.042 0.242 647 Planarity : 0.003 0.044 648 Dihedral : 7.866 67.329 815 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.99 % Allowed : 22.19 % Favored : 74.81 % 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: -0.07 (0.40), residues: 456 helix: 0.63 (1.20), residues: 25 sheet: 0.44 (0.42), residues: 159 loop : -0.37 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 112 HIS 0.002 0.001 HIS A 236 PHE 0.010 0.001 PHE A 237 TYR 0.013 0.001 TYR A 222 ARG 0.008 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 7) link_NAG-ASN : angle 1.44767 ( 21) link_ALPHA1-6 : bond 0.00522 ( 1) link_ALPHA1-6 : angle 2.48118 ( 3) link_BETA1-4 : bond 0.00258 ( 5) link_BETA1-4 : angle 1.86376 ( 15) link_ALPHA1-3 : bond 0.01260 ( 1) link_ALPHA1-3 : angle 2.06271 ( 3) hydrogen bonds : bond 0.03206 ( 122) hydrogen bonds : angle 4.88310 ( 318) link_BETA1-6 : bond 0.00010 ( 1) link_BETA1-6 : angle 1.38919 ( 3) SS BOND : bond 0.00103 ( 5) SS BOND : angle 0.36067 ( 10) covalent geometry : bond 0.00296 ( 3866) covalent geometry : angle 0.58089 ( 5269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.9437 (mtm110) cc_final: 0.8887 (ttp80) REVERT: A 54 ASP cc_start: 0.8989 (t0) cc_final: 0.8657 (t0) REVERT: A 120 MET cc_start: 0.8694 (tpp) cc_final: 0.8384 (tpp) REVERT: A 139 ASP cc_start: 0.9129 (m-30) cc_final: 0.8893 (m-30) REVERT: A 197 ASP cc_start: 0.9223 (t0) cc_final: 0.8943 (t0) REVERT: H 3 ARG cc_start: 0.8387 (mmm-85) cc_final: 0.8142 (mmm-85) REVERT: H 73 ASP cc_start: 0.8338 (t0) cc_final: 0.8046 (t0) REVERT: L 79 GLN cc_start: 0.8821 (mt0) cc_final: 0.8444 (mt0) outliers start: 12 outliers final: 10 residues processed: 82 average time/residue: 0.2281 time to fit residues: 21.7398 Evaluate side-chains 84 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain L residue 2 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3062 r_free = 0.3062 target = 0.073262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.057692 restraints weight = 21934.075| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 4.73 r_work: 0.2566 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3886 Z= 0.145 Angle : 0.616 7.840 5324 Z= 0.306 Chirality : 0.043 0.248 647 Planarity : 0.004 0.046 648 Dihedral : 7.738 66.092 815 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.74 % Allowed : 22.44 % Favored : 74.81 % 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: 0.01 (0.41), residues: 456 helix: 0.62 (1.20), residues: 25 sheet: 0.57 (0.42), residues: 163 loop : -0.38 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 112 HIS 0.001 0.000 HIS A 236 PHE 0.010 0.001 PHE A 237 TYR 0.017 0.001 TYR H 59 ARG 0.007 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 7) link_NAG-ASN : angle 1.50233 ( 21) link_ALPHA1-6 : bond 0.00496 ( 1) link_ALPHA1-6 : angle 2.50656 ( 3) link_BETA1-4 : bond 0.00225 ( 5) link_BETA1-4 : angle 1.90841 ( 15) link_ALPHA1-3 : bond 0.01196 ( 1) link_ALPHA1-3 : angle 2.07969 ( 3) hydrogen bonds : bond 0.03290 ( 122) hydrogen bonds : angle 4.84710 ( 318) link_BETA1-6 : bond 0.00063 ( 1) link_BETA1-6 : angle 1.42801 ( 3) SS BOND : bond 0.00153 ( 5) SS BOND : angle 0.34770 ( 10) covalent geometry : bond 0.00335 ( 3866) covalent geometry : angle 0.59725 ( 5269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8993 (t0) cc_final: 0.8665 (t0) REVERT: A 120 MET cc_start: 0.8711 (tpp) cc_final: 0.8422 (tpp) REVERT: A 139 ASP cc_start: 0.9149 (m-30) cc_final: 0.8920 (m-30) REVERT: A 197 ASP cc_start: 0.9241 (t0) cc_final: 0.8971 (t0) REVERT: H 3 ARG cc_start: 0.8357 (mmm-85) cc_final: 0.8097 (mmm-85) REVERT: H 73 ASP cc_start: 0.8319 (t0) cc_final: 0.8025 (t0) REVERT: L 11 LEU cc_start: 0.8638 (tp) cc_final: 0.8335 (tt) REVERT: L 79 GLN cc_start: 0.8843 (mt0) cc_final: 0.8493 (mt0) outliers start: 11 outliers final: 10 residues processed: 84 average time/residue: 0.2331 time to fit residues: 22.8058 Evaluate side-chains 86 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain L residue 2 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 15 optimal weight: 0.0670 chunk 32 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.3056 r_free = 0.3056 target = 0.072944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.059283 restraints weight = 8683.771| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 3.13 r_work: 0.2658 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3886 Z= 0.135 Angle : 0.624 7.825 5324 Z= 0.308 Chirality : 0.043 0.249 647 Planarity : 0.004 0.045 648 Dihedral : 7.588 64.714 815 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.74 % Allowed : 22.44 % Favored : 74.81 % 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: 0.02 (0.41), residues: 456 helix: 0.65 (1.20), residues: 25 sheet: 0.55 (0.42), residues: 163 loop : -0.35 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP H 112 HIS 0.001 0.000 HIS A 236 PHE 0.014 0.001 PHE L 71 TYR 0.015 0.001 TYR H 59 ARG 0.008 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 7) link_NAG-ASN : angle 1.46529 ( 21) link_ALPHA1-6 : bond 0.00557 ( 1) link_ALPHA1-6 : angle 2.48865 ( 3) link_BETA1-4 : bond 0.00247 ( 5) link_BETA1-4 : angle 1.86278 ( 15) link_ALPHA1-3 : bond 0.01212 ( 1) link_ALPHA1-3 : angle 2.05899 ( 3) hydrogen bonds : bond 0.03203 ( 122) hydrogen bonds : angle 4.82598 ( 318) link_BETA1-6 : bond 0.00039 ( 1) link_BETA1-6 : angle 1.41199 ( 3) SS BOND : bond 0.00196 ( 5) SS BOND : angle 0.36179 ( 10) covalent geometry : bond 0.00316 ( 3866) covalent geometry : angle 0.60612 ( 5269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.9315 (mtm110) cc_final: 0.8649 (ttp80) REVERT: A 54 ASP cc_start: 0.8921 (t0) cc_final: 0.8589 (t0) REVERT: A 120 MET cc_start: 0.8612 (tpp) cc_final: 0.8324 (tpp) REVERT: A 139 ASP cc_start: 0.9061 (m-30) cc_final: 0.8836 (m-30) REVERT: A 197 ASP cc_start: 0.9132 (t0) cc_final: 0.8877 (t0) REVERT: H 3 ARG cc_start: 0.8311 (mmm-85) cc_final: 0.8047 (mmm-85) REVERT: H 73 ASP cc_start: 0.8282 (t0) cc_final: 0.7983 (t0) REVERT: L 11 LEU cc_start: 0.8655 (tp) cc_final: 0.8343 (tt) REVERT: L 79 GLN cc_start: 0.8770 (mt0) cc_final: 0.8395 (mt0) outliers start: 11 outliers final: 11 residues processed: 82 average time/residue: 0.2148 time to fit residues: 20.6957 Evaluate side-chains 85 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain L residue 2 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 0.0670 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 = 0.3084 r_free = 0.3084 target = 0.074365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.059868 restraints weight = 12218.526| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 3.76 r_work: 0.2634 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3886 Z= 0.114 Angle : 0.611 7.949 5324 Z= 0.304 Chirality : 0.042 0.251 647 Planarity : 0.004 0.042 648 Dihedral : 7.346 62.592 815 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.49 % Allowed : 22.94 % Favored : 74.56 % 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: 0.00 (0.41), residues: 456 helix: 0.67 (1.20), residues: 25 sheet: 0.58 (0.42), residues: 158 loop : -0.38 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP H 112 HIS 0.002 0.001 HIS A 236 PHE 0.013 0.001 PHE L 71 TYR 0.012 0.001 TYR A 222 ARG 0.009 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 7) link_NAG-ASN : angle 1.41948 ( 21) link_ALPHA1-6 : bond 0.00609 ( 1) link_ALPHA1-6 : angle 2.41068 ( 3) link_BETA1-4 : bond 0.00292 ( 5) link_BETA1-4 : angle 1.77172 ( 15) link_ALPHA1-3 : bond 0.01243 ( 1) link_ALPHA1-3 : angle 2.02227 ( 3) hydrogen bonds : bond 0.03089 ( 122) hydrogen bonds : angle 4.76730 ( 318) link_BETA1-6 : bond 0.00033 ( 1) link_BETA1-6 : angle 1.34808 ( 3) SS BOND : bond 0.00197 ( 5) SS BOND : angle 0.37239 ( 10) covalent geometry : bond 0.00266 ( 3866) covalent geometry : angle 0.59444 ( 5269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.9328 (mtm110) cc_final: 0.8667 (ttp80) REVERT: A 54 ASP cc_start: 0.8919 (t0) cc_final: 0.8587 (t0) REVERT: A 120 MET cc_start: 0.8618 (tpp) cc_final: 0.8329 (tpp) REVERT: A 197 ASP cc_start: 0.9158 (t0) cc_final: 0.8893 (t0) REVERT: H 3 ARG cc_start: 0.8343 (mmm-85) cc_final: 0.8079 (mmm-85) REVERT: H 73 ASP cc_start: 0.8240 (t0) cc_final: 0.7939 (t0) REVERT: L 11 LEU cc_start: 0.8648 (tp) cc_final: 0.8336 (tt) REVERT: L 79 GLN cc_start: 0.8785 (mt0) cc_final: 0.8175 (mm110) outliers start: 10 outliers final: 10 residues processed: 79 average time/residue: 0.2412 time to fit residues: 22.2900 Evaluate side-chains 81 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain L residue 2 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3062 r_free = 0.3062 target = 0.073429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.057438 restraints weight = 21837.941| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 4.85 r_work: 0.2570 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3886 Z= 0.132 Angle : 0.620 7.413 5324 Z= 0.309 Chirality : 0.042 0.251 647 Planarity : 0.004 0.041 648 Dihedral : 7.299 62.123 815 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.49 % Allowed : 22.94 % Favored : 74.56 % 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: -0.00 (0.41), residues: 456 helix: 0.61 (1.19), residues: 25 sheet: 0.61 (0.42), residues: 158 loop : -0.40 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP H 112 HIS 0.001 0.000 HIS A 236 PHE 0.026 0.001 PHE A 173 TYR 0.013 0.001 TYR A 222 ARG 0.009 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 7) link_NAG-ASN : angle 1.44930 ( 21) link_ALPHA1-6 : bond 0.00569 ( 1) link_ALPHA1-6 : angle 2.45826 ( 3) link_BETA1-4 : bond 0.00250 ( 5) link_BETA1-4 : angle 1.81924 ( 15) link_ALPHA1-3 : bond 0.01177 ( 1) link_ALPHA1-3 : angle 2.01025 ( 3) hydrogen bonds : bond 0.03161 ( 122) hydrogen bonds : angle 4.77868 ( 318) link_BETA1-6 : bond 0.00010 ( 1) link_BETA1-6 : angle 1.39765 ( 3) SS BOND : bond 0.00199 ( 5) SS BOND : angle 0.36625 ( 10) covalent geometry : bond 0.00308 ( 3866) covalent geometry : angle 0.60301 ( 5269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2499.08 seconds wall clock time: 44 minutes 19.80 seconds (2659.80 seconds total)