Starting phenix.real_space_refine on Fri Aug 22 14:05:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r9x_19015/08_2025/8r9x_19015.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r9x_19015/08_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_19015/08_2025/8r9x_19015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r9x_19015/08_2025/8r9x_19015.map" model { file = "/net/cci-nas-00/data/ceres_data/8r9x_19015/08_2025/8r9x_19015.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r9x_19015/08_2025/8r9x_19015.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.48, per 1000 atoms: 0.39 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: 0.47 Conformation dependent library (CDL) restraints added in 186.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.14 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: 0.61 Time building geometry restraints manager: 0.58 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: 4.530 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.640 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.770 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.002 0.000 ARG H 19 TYR 0.009 0.001 TYR A 222 PHE 0.011 0.001 PHE A 237 TRP 0.007 0.001 TRP H 112 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 3866) covalent geometry : angle 0.65022 ( 5269) SS BOND : bond 0.00090 ( 5) SS BOND : angle 0.37937 ( 10) hydrogen bonds : bond 0.23497 ( 122) hydrogen bonds : angle 8.84192 ( 318) link_ALPHA1-3 : bond 0.00732 ( 1) link_ALPHA1-3 : angle 1.15123 ( 3) 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_BETA1-6 : bond 0.00164 ( 1) link_BETA1-6 : angle 1.53286 ( 3) link_NAG-ASN : bond 0.00270 ( 7) link_NAG-ASN : angle 1.72565 ( 21) *********************** 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 : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1180 time to fit residues: 11.5958 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 : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.073893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.058963 restraints weight = 8652.282| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.29 r_work: 0.2605 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3886 Z= 0.166 Angle : 0.658 7.696 5324 Z= 0.330 Chirality : 0.044 0.175 647 Planarity : 0.004 0.050 648 Dihedral : 10.186 84.481 815 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.74 % Allowed : 21.20 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.40), residues: 456 helix: 0.31 (1.17), residues: 25 sheet: 0.16 (0.41), residues: 163 loop : -0.41 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 42 TYR 0.014 0.001 TYR H 80 PHE 0.012 0.001 PHE A 237 TRP 0.004 0.001 TRP H 112 HIS 0.003 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 3866) covalent geometry : angle 0.63808 ( 5269) SS BOND : bond 0.00133 ( 5) SS BOND : angle 0.46822 ( 10) hydrogen bonds : bond 0.04310 ( 122) hydrogen bonds : angle 6.06861 ( 318) link_ALPHA1-3 : bond 0.01063 ( 1) link_ALPHA1-3 : angle 2.34711 ( 3) link_ALPHA1-6 : bond 0.00176 ( 1) link_ALPHA1-6 : angle 2.62389 ( 3) link_BETA1-4 : bond 0.00298 ( 5) link_BETA1-4 : angle 1.94932 ( 15) link_BETA1-6 : bond 0.00122 ( 1) link_BETA1-6 : angle 1.46542 ( 3) link_NAG-ASN : bond 0.00229 ( 7) link_NAG-ASN : angle 1.64622 ( 21) *********************** 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 87 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8838 (t0) cc_final: 0.8609 (t0) REVERT: A 134 ASP cc_start: 0.8126 (t70) cc_final: 0.7892 (t70) REVERT: A 139 ASP cc_start: 0.9202 (t0) cc_final: 0.8962 (m-30) REVERT: A 197 ASP cc_start: 0.8948 (t0) cc_final: 0.8725 (t0) REVERT: H 1 GLU cc_start: 0.8084 (tp30) cc_final: 0.7697 (tp30) REVERT: L 42 ARG cc_start: 0.7937 (mmm-85) cc_final: 0.7636 (mmm160) outliers start: 11 outliers final: 6 residues processed: 84 average time/residue: 0.1020 time to fit residues: 10.0205 Evaluate side-chains 78 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 6 optimal weight: 0.0070 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.6602 ------------------------------------------------------------------------------- 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 = 0.3051 r_free = 0.3051 target = 0.074608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.057885 restraints weight = 21149.934| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 4.88 r_work: 0.2520 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3886 Z= 0.128 Angle : 0.588 7.463 5324 Z= 0.295 Chirality : 0.042 0.210 647 Planarity : 0.004 0.047 648 Dihedral : 9.174 77.640 815 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.40), residues: 456 helix: 0.56 (1.21), residues: 25 sheet: 0.30 (0.42), residues: 158 loop : -0.48 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 18 TYR 0.014 0.001 TYR A 222 PHE 0.010 0.001 PHE A 237 TRP 0.004 0.001 TRP H 112 HIS 0.002 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3866) covalent geometry : angle 0.56940 ( 5269) SS BOND : bond 0.00132 ( 5) SS BOND : angle 0.37341 ( 10) hydrogen bonds : bond 0.03735 ( 122) hydrogen bonds : angle 5.41084 ( 318) link_ALPHA1-3 : bond 0.01204 ( 1) link_ALPHA1-3 : angle 1.66924 ( 3) link_ALPHA1-6 : bond 0.00394 ( 1) link_ALPHA1-6 : angle 2.43998 ( 3) link_BETA1-4 : bond 0.00270 ( 5) link_BETA1-4 : angle 1.89365 ( 15) link_BETA1-6 : bond 0.00028 ( 1) link_BETA1-6 : angle 1.35960 ( 3) link_NAG-ASN : bond 0.00221 ( 7) link_NAG-ASN : angle 1.47653 ( 21) *********************** 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 87 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8926 (t0) cc_final: 0.8628 (t0) REVERT: A 120 MET cc_start: 0.8472 (tpp) cc_final: 0.8240 (tpp) REVERT: A 151 GLU cc_start: 0.8289 (pm20) cc_final: 0.8010 (pm20) REVERT: A 197 ASP cc_start: 0.9155 (t0) cc_final: 0.8848 (t0) REVERT: A 244 ASP cc_start: 0.8479 (t0) cc_final: 0.8035 (t0) REVERT: H 1 GLU cc_start: 0.8246 (tp30) cc_final: 0.7813 (tp30) REVERT: H 3 ARG cc_start: 0.8222 (mmm-85) cc_final: 0.7771 (mmm-85) REVERT: H 117 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9029 (tt) REVERT: L 11 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8032 (tt) REVERT: L 79 GLN cc_start: 0.8957 (mt0) cc_final: 0.8642 (mt0) outliers start: 12 outliers final: 6 residues processed: 84 average time/residue: 0.1143 time to fit residues: 11.1682 Evaluate side-chains 82 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 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 11 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.0060 chunk 0 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.074650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.059655 restraints weight = 8626.431| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.37 r_work: 0.2604 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3886 Z= 0.129 Angle : 0.602 7.512 5324 Z= 0.299 Chirality : 0.042 0.225 647 Planarity : 0.004 0.046 648 Dihedral : 8.661 74.138 815 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.49 % Allowed : 22.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.40), residues: 456 helix: 0.58 (1.20), residues: 25 sheet: 0.41 (0.42), residues: 158 loop : -0.45 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 48 TYR 0.013 0.001 TYR A 222 PHE 0.010 0.001 PHE A 237 TRP 0.003 0.001 TRP H 47 HIS 0.001 0.000 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3866) covalent geometry : angle 0.58287 ( 5269) SS BOND : bond 0.00188 ( 5) SS BOND : angle 0.42250 ( 10) hydrogen bonds : bond 0.03456 ( 122) hydrogen bonds : angle 5.16005 ( 318) link_ALPHA1-3 : bond 0.01331 ( 1) link_ALPHA1-3 : angle 2.00328 ( 3) link_ALPHA1-6 : bond 0.00462 ( 1) link_ALPHA1-6 : angle 2.45955 ( 3) link_BETA1-4 : bond 0.00251 ( 5) link_BETA1-4 : angle 1.90702 ( 15) link_BETA1-6 : bond 0.00008 ( 1) link_BETA1-6 : angle 1.39610 ( 3) link_NAG-ASN : bond 0.00235 ( 7) link_NAG-ASN : angle 1.48402 ( 21) *********************** 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 84 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.9479 (mtm110) cc_final: 0.8753 (ttp80) REVERT: A 54 ASP cc_start: 0.8913 (t0) cc_final: 0.8597 (t0) REVERT: A 120 MET cc_start: 0.8401 (tpp) cc_final: 0.8151 (tpp) REVERT: A 197 ASP cc_start: 0.9106 (t0) cc_final: 0.8734 (t0) REVERT: A 244 ASP cc_start: 0.8385 (t0) cc_final: 0.7967 (t0) REVERT: H 1 GLU cc_start: 0.8242 (tp30) cc_final: 0.7868 (tp30) REVERT: H 3 ARG cc_start: 0.8153 (mmm-85) cc_final: 0.7680 (mmm-85) REVERT: H 76 LYS cc_start: 0.9549 (mtpp) cc_final: 0.9291 (mtmm) REVERT: H 87 ARG cc_start: 0.8430 (ptp-170) cc_final: 0.7786 (ptp-170) REVERT: L 79 GLN cc_start: 0.8906 (mt0) cc_final: 0.8562 (mt0) outliers start: 10 outliers final: 9 residues processed: 81 average time/residue: 0.1098 time to fit residues: 10.3626 Evaluate side-chains 82 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 1 GLU 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 10 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3059 r_free = 0.3059 target = 0.074652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.058461 restraints weight = 15577.163| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 4.40 r_work: 0.2555 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3886 Z= 0.124 Angle : 0.594 7.574 5324 Z= 0.296 Chirality : 0.042 0.234 647 Planarity : 0.003 0.044 648 Dihedral : 8.259 70.876 815 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.24 % Allowed : 22.44 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.41), residues: 456 helix: 0.58 (1.19), residues: 25 sheet: 0.46 (0.41), residues: 168 loop : -0.38 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 87 TYR 0.014 0.001 TYR H 59 PHE 0.010 0.001 PHE A 237 TRP 0.003 0.001 TRP H 112 HIS 0.002 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 3866) covalent geometry : angle 0.57457 ( 5269) SS BOND : bond 0.00124 ( 5) SS BOND : angle 0.40607 ( 10) hydrogen bonds : bond 0.03327 ( 122) hydrogen bonds : angle 4.98512 ( 318) link_ALPHA1-3 : bond 0.01321 ( 1) link_ALPHA1-3 : angle 2.04590 ( 3) link_ALPHA1-6 : bond 0.00507 ( 1) link_ALPHA1-6 : angle 2.44045 ( 3) link_BETA1-4 : bond 0.00267 ( 5) link_BETA1-4 : angle 1.87628 ( 15) link_BETA1-6 : bond 0.00021 ( 1) link_BETA1-6 : angle 1.38409 ( 3) link_NAG-ASN : bond 0.00221 ( 7) link_NAG-ASN : angle 1.47364 ( 21) *********************** 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 90 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 48 ARG cc_start: 0.9455 (mtm110) cc_final: 0.8721 (ttp80) REVERT: A 54 ASP cc_start: 0.8965 (t0) cc_final: 0.8635 (t0) REVERT: A 120 MET cc_start: 0.8436 (tpp) cc_final: 0.8172 (tpp) REVERT: A 197 ASP cc_start: 0.9205 (t0) cc_final: 0.8803 (t0) REVERT: A 244 ASP cc_start: 0.8435 (t0) cc_final: 0.7988 (t0) REVERT: H 1 GLU cc_start: 0.8379 (tp30) cc_final: 0.8111 (tp30) REVERT: H 87 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8003 (ptt-90) REVERT: L 11 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8182 (tp) REVERT: L 79 GLN cc_start: 0.8933 (mt0) cc_final: 0.8570 (mt0) outliers start: 13 outliers final: 10 residues processed: 85 average time/residue: 0.1024 time to fit residues: 10.1758 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 : 0.157 ------------------------------------------------------------------------------- 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 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 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3066 r_free = 0.3066 target = 0.075041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.058047 restraints weight = 21224.345| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 5.03 r_work: 0.2537 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 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 = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2291 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= 0.126 Angle : 0.610 7.415 5324 Z= 0.300 Chirality : 0.042 0.240 647 Planarity : 0.003 0.044 648 Dihedral : 8.001 68.710 815 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.74 % Allowed : 22.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.40), residues: 456 helix: 0.54 (1.19), residues: 25 sheet: 0.46 (0.42), residues: 158 loop : -0.42 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 18 TYR 0.013 0.001 TYR A 222 PHE 0.009 0.001 PHE A 237 TRP 0.003 0.001 TRP H 112 HIS 0.002 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 3866) covalent geometry : angle 0.59187 ( 5269) SS BOND : bond 0.00108 ( 5) SS BOND : angle 0.37913 ( 10) hydrogen bonds : bond 0.03244 ( 122) hydrogen bonds : angle 4.90890 ( 318) link_ALPHA1-3 : bond 0.01240 ( 1) link_ALPHA1-3 : angle 2.02771 ( 3) link_ALPHA1-6 : bond 0.00528 ( 1) link_ALPHA1-6 : angle 2.46402 ( 3) link_BETA1-4 : bond 0.00257 ( 5) link_BETA1-4 : angle 1.85406 ( 15) link_BETA1-6 : bond 0.00024 ( 1) link_BETA1-6 : angle 1.39451 ( 3) link_NAG-ASN : bond 0.00222 ( 7) link_NAG-ASN : angle 1.46044 ( 21) *********************** 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 86 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.9428 (mtm110) cc_final: 0.8615 (ttp80) REVERT: A 54 ASP cc_start: 0.8957 (t0) cc_final: 0.8612 (t0) REVERT: A 120 MET cc_start: 0.8453 (tpp) cc_final: 0.8184 (tpp) REVERT: A 197 ASP cc_start: 0.9288 (t0) cc_final: 0.8901 (t0) REVERT: A 244 ASP cc_start: 0.8446 (t0) cc_final: 0.7997 (t0) REVERT: H 73 ASP cc_start: 0.8005 (t0) cc_final: 0.7703 (t0) REVERT: H 87 ARG cc_start: 0.8291 (ptp-170) cc_final: 0.8080 (ptt-90) REVERT: H 90 ASP cc_start: 0.8741 (m-30) cc_final: 0.8415 (m-30) REVERT: L 11 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8159 (tp) REVERT: L 79 GLN cc_start: 0.8917 (mt0) cc_final: 0.8550 (mt0) outliers start: 11 outliers final: 9 residues processed: 83 average time/residue: 0.1073 time to fit residues: 10.3949 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 : 0.123 ------------------------------------------------------------------------------- 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 11 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3040 r_free = 0.3040 target = 0.073399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.056549 restraints weight = 21492.073| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 4.96 r_work: 0.2511 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3886 Z= 0.153 Angle : 0.613 7.467 5324 Z= 0.306 Chirality : 0.042 0.243 647 Planarity : 0.003 0.045 648 Dihedral : 7.892 67.481 815 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.40), residues: 456 helix: 0.54 (1.19), residues: 25 sheet: 0.50 (0.42), residues: 158 loop : -0.44 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 18 TYR 0.014 0.001 TYR A 222 PHE 0.010 0.001 PHE A 237 TRP 0.003 0.001 TRP H 112 HIS 0.002 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 3866) covalent geometry : angle 0.59320 ( 5269) SS BOND : bond 0.00120 ( 5) SS BOND : angle 0.38636 ( 10) hydrogen bonds : bond 0.03326 ( 122) hydrogen bonds : angle 4.91772 ( 318) link_ALPHA1-3 : bond 0.01218 ( 1) link_ALPHA1-3 : angle 2.09265 ( 3) link_ALPHA1-6 : bond 0.00462 ( 1) link_ALPHA1-6 : angle 2.55118 ( 3) link_BETA1-4 : bond 0.00210 ( 5) link_BETA1-4 : angle 1.91906 ( 15) link_BETA1-6 : bond 0.00072 ( 1) link_BETA1-6 : angle 1.43169 ( 3) link_NAG-ASN : bond 0.00235 ( 7) link_NAG-ASN : angle 1.51402 ( 21) *********************** 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 84 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.9427 (mtm110) cc_final: 0.8835 (ttp80) REVERT: A 54 ASP cc_start: 0.8972 (t0) cc_final: 0.8627 (t0) REVERT: A 120 MET cc_start: 0.8561 (tpp) cc_final: 0.8307 (tpp) REVERT: A 197 ASP cc_start: 0.9303 (t0) cc_final: 0.8963 (t0) REVERT: A 244 ASP cc_start: 0.8495 (t0) cc_final: 0.8053 (t0) REVERT: H 3 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.8010 (mmm-85) REVERT: H 73 ASP cc_start: 0.8118 (t0) cc_final: 0.7801 (t0) REVERT: L 79 GLN cc_start: 0.8890 (mt0) cc_final: 0.8520 (mt0) outliers start: 11 outliers final: 8 residues processed: 82 average time/residue: 0.1128 time to fit residues: 10.7612 Evaluate side-chains 83 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3043 r_free = 0.3043 target = 0.073598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.056490 restraints weight = 25986.226| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 5.34 r_work: 0.2515 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2514 r_free = 0.2514 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2514 r_free = 0.2514 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2375 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= 0.146 Angle : 0.622 7.320 5324 Z= 0.309 Chirality : 0.043 0.247 647 Planarity : 0.004 0.047 648 Dihedral : 7.736 65.985 815 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.24 % Allowed : 22.69 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.41), residues: 456 helix: 0.57 (1.19), residues: 25 sheet: 0.50 (0.42), residues: 164 loop : -0.34 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 18 TYR 0.013 0.001 TYR A 222 PHE 0.010 0.001 PHE A 237 TRP 0.003 0.001 TRP H 112 HIS 0.002 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 3866) covalent geometry : angle 0.60341 ( 5269) SS BOND : bond 0.00113 ( 5) SS BOND : angle 0.35917 ( 10) hydrogen bonds : bond 0.03283 ( 122) hydrogen bonds : angle 4.88622 ( 318) link_ALPHA1-3 : bond 0.01212 ( 1) link_ALPHA1-3 : angle 2.07326 ( 3) link_ALPHA1-6 : bond 0.00487 ( 1) link_ALPHA1-6 : angle 2.51910 ( 3) link_BETA1-4 : bond 0.00224 ( 5) link_BETA1-4 : angle 1.90294 ( 15) link_BETA1-6 : bond 0.00072 ( 1) link_BETA1-6 : angle 1.42857 ( 3) link_NAG-ASN : bond 0.00225 ( 7) link_NAG-ASN : angle 1.49416 ( 21) *********************** 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 86 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8973 (t0) cc_final: 0.8625 (t0) REVERT: A 120 MET cc_start: 0.8591 (tpp) cc_final: 0.8340 (tpp) REVERT: A 139 ASP cc_start: 0.9114 (m-30) cc_final: 0.8875 (m-30) REVERT: A 197 ASP cc_start: 0.9290 (t0) cc_final: 0.8943 (t0) REVERT: A 244 ASP cc_start: 0.8493 (t0) cc_final: 0.8039 (t0) REVERT: H 3 ARG cc_start: 0.8248 (mmm-85) cc_final: 0.7986 (mmm-85) REVERT: H 73 ASP cc_start: 0.8106 (t0) cc_final: 0.7593 (t0) REVERT: H 76 LYS cc_start: 0.9590 (mtpp) cc_final: 0.9256 (mtmm) REVERT: L 79 GLN cc_start: 0.8885 (mt0) cc_final: 0.8560 (mt0) outliers start: 9 outliers final: 9 residues processed: 83 average time/residue: 0.1129 time to fit residues: 10.8923 Evaluate side-chains 85 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 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 34 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3069 r_free = 0.3069 target = 0.073658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.058943 restraints weight = 12745.836| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 3.81 r_work: 0.2634 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2539 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= 0.112 Angle : 0.609 7.607 5324 Z= 0.303 Chirality : 0.042 0.247 647 Planarity : 0.004 0.044 648 Dihedral : 7.446 63.464 815 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.00 % Allowed : 23.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.41), residues: 456 helix: 0.57 (1.18), residues: 25 sheet: 0.60 (0.42), residues: 158 loop : -0.37 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 18 TYR 0.017 0.001 TYR H 59 PHE 0.010 0.001 PHE A 237 TRP 0.004 0.001 TRP L 35 HIS 0.001 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 3866) covalent geometry : angle 0.59232 ( 5269) SS BOND : bond 0.00145 ( 5) SS BOND : angle 0.32942 ( 10) hydrogen bonds : bond 0.03122 ( 122) hydrogen bonds : angle 4.75300 ( 318) link_ALPHA1-3 : bond 0.01271 ( 1) link_ALPHA1-3 : angle 2.02279 ( 3) link_ALPHA1-6 : bond 0.00645 ( 1) link_ALPHA1-6 : angle 2.45159 ( 3) link_BETA1-4 : bond 0.00306 ( 5) link_BETA1-4 : angle 1.77331 ( 15) link_BETA1-6 : bond 0.00058 ( 1) link_BETA1-6 : angle 1.35395 ( 3) link_NAG-ASN : bond 0.00247 ( 7) link_NAG-ASN : angle 1.41150 ( 21) *********************** 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 84 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.9347 (mtm110) cc_final: 0.8703 (ttp80) REVERT: A 54 ASP cc_start: 0.8938 (t0) cc_final: 0.8612 (t0) REVERT: A 120 MET cc_start: 0.8561 (tpp) cc_final: 0.8321 (tpp) REVERT: A 197 ASP cc_start: 0.9180 (t0) cc_final: 0.8923 (t0) REVERT: A 244 ASP cc_start: 0.8447 (t0) cc_final: 0.8043 (t0) REVERT: H 3 ARG cc_start: 0.8322 (mmm-85) cc_final: 0.8059 (mmm-85) REVERT: H 73 ASP cc_start: 0.8220 (t0) cc_final: 0.7906 (t0) REVERT: L 11 LEU cc_start: 0.8697 (tp) cc_final: 0.8388 (tt) REVERT: L 79 GLN cc_start: 0.8730 (mt0) cc_final: 0.8360 (mt0) outliers start: 8 outliers final: 8 residues processed: 82 average time/residue: 0.1166 time to fit residues: 10.9840 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 : 0.149 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.072724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.058043 restraints weight = 12869.790| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.78 r_work: 0.2609 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3886 Z= 0.156 Angle : 0.628 7.209 5324 Z= 0.313 Chirality : 0.043 0.251 647 Planarity : 0.004 0.044 648 Dihedral : 7.484 63.626 815 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.00 % Allowed : 22.94 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.41), residues: 456 helix: 0.55 (1.18), residues: 25 sheet: 0.53 (0.42), residues: 158 loop : -0.39 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 18 TYR 0.030 0.001 TYR H 80 PHE 0.015 0.001 PHE L 71 TRP 0.003 0.001 TRP H 112 HIS 0.002 0.000 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 3866) covalent geometry : angle 0.60941 ( 5269) SS BOND : bond 0.00221 ( 5) SS BOND : angle 0.41021 ( 10) hydrogen bonds : bond 0.03239 ( 122) hydrogen bonds : angle 4.82944 ( 318) link_ALPHA1-3 : bond 0.01135 ( 1) link_ALPHA1-3 : angle 2.03834 ( 3) link_ALPHA1-6 : bond 0.00495 ( 1) link_ALPHA1-6 : angle 2.52482 ( 3) link_BETA1-4 : bond 0.00223 ( 5) link_BETA1-4 : angle 1.89892 ( 15) link_BETA1-6 : bond 0.00081 ( 1) link_BETA1-6 : angle 1.43887 ( 3) link_NAG-ASN : bond 0.00225 ( 7) link_NAG-ASN : angle 1.51013 ( 21) ********************** 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: 8 poor density : 75 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.9344 (mtm110) cc_final: 0.8700 (ttp80) REVERT: A 54 ASP cc_start: 0.8946 (t0) cc_final: 0.8610 (t0) REVERT: A 120 MET cc_start: 0.8648 (tpp) cc_final: 0.8414 (tpp) REVERT: A 197 ASP cc_start: 0.9141 (t0) cc_final: 0.8879 (t0) REVERT: A 244 ASP cc_start: 0.8463 (t0) cc_final: 0.8057 (t0) REVERT: H 3 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.8100 (mmm-85) REVERT: H 73 ASP cc_start: 0.8249 (t0) cc_final: 0.7940 (t0) REVERT: L 11 LEU cc_start: 0.8714 (tp) cc_final: 0.8408 (tt) REVERT: L 42 ARG cc_start: 0.8191 (mmm-85) cc_final: 0.7841 (mmm160) REVERT: L 79 GLN cc_start: 0.8739 (mt0) cc_final: 0.8358 (mt0) outliers start: 8 outliers final: 8 residues processed: 81 average time/residue: 0.1101 time to fit residues: 10.4269 Evaluate side-chains 83 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 0.0060 chunk 17 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 = 0.3073 r_free = 0.3073 target = 0.073926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.058338 restraints weight = 21553.009| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 4.75 r_work: 0.2575 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 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 = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2638 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= 0.128 Angle : 0.617 7.722 5324 Z= 0.308 Chirality : 0.042 0.248 647 Planarity : 0.004 0.044 648 Dihedral : 7.307 62.057 815 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.00 % Allowed : 23.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.41), residues: 456 helix: 0.57 (1.18), residues: 25 sheet: 0.59 (0.42), residues: 158 loop : -0.40 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 18 TYR 0.028 0.001 TYR H 80 PHE 0.012 0.001 PHE L 71 TRP 0.003 0.001 TRP H 112 HIS 0.001 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3866) covalent geometry : angle 0.60010 ( 5269) SS BOND : bond 0.00222 ( 5) SS BOND : angle 0.40550 ( 10) hydrogen bonds : bond 0.03143 ( 122) hydrogen bonds : angle 4.76477 ( 318) link_ALPHA1-3 : bond 0.01203 ( 1) link_ALPHA1-3 : angle 1.99279 ( 3) link_ALPHA1-6 : bond 0.00596 ( 1) link_ALPHA1-6 : angle 2.47215 ( 3) link_BETA1-4 : bond 0.00264 ( 5) link_BETA1-4 : angle 1.81409 ( 15) link_BETA1-6 : bond 0.00004 ( 1) link_BETA1-6 : angle 1.38649 ( 3) link_NAG-ASN : bond 0.00227 ( 7) link_NAG-ASN : angle 1.44260 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1375.66 seconds wall clock time: 24 minutes 21.27 seconds (1461.27 seconds total)