Starting phenix.real_space_refine on Wed Jul 1 21:27:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lxx_23578/07_2026/7lxx_23578.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lxx_23578/07_2026/7lxx_23578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7lxx_23578/07_2026/7lxx_23578.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lxx_23578/07_2026/7lxx_23578.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lxx_23578/07_2026/7lxx_23578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lxx_23578/07_2026/7lxx_23578.map" model { file = "/net/cci-nas-00/data/ceres_data/7lxx_23578/07_2026/7lxx_23578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lxx_23578/07_2026/7lxx_23578.cif" } resolution = 3.0 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= 0.029 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 10 5.16 5 C 1724 2.51 5 N 466 2.21 5 O 540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2740 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 971 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 123} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 777 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain breaks: 5 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 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 chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.70, per 1000 atoms: 0.26 Number of scatterers: 2740 At special positions: 0 Unit cell: (71.4, 86.1, 71.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 540 8.00 N 466 7.00 C 1724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.07 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 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 BETA1-4 " NAG B 1 " - " NAG B 2 " BETA1-6 " NAG B 1 " - " FUC B 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 149 " " NAG B 1 " - " ASN A 17 " Time building additional restraints: 0.19 Conformation dependent library (CDL) restraints added in 60.9 milliseconds 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 642 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 9 sheets defined 4.3% alpha, 50.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.847A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.669A pdb=" N TYR H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.530A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA8, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.464A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 83 through 84 removed outlier: 12.962A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.148A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.535A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 276 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: 0.30 Time building geometry restraints manager: 0.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 719 1.33 - 1.45: 607 1.45 - 1.57: 1465 1.57 - 1.69: 0 1.69 - 1.81: 13 Bond restraints: 2804 Sorted by residual: bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.464 -0.051 2.00e-02 2.50e+03 6.60e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.463 -0.050 2.00e-02 2.50e+03 6.20e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.461 -0.048 2.00e-02 2.50e+03 5.70e+00 bond pdb=" CD GLU A 154 " pdb=" OE2 GLU A 154 " ideal model delta sigma weight residual 1.249 1.204 0.045 1.90e-02 2.77e+03 5.54e+00 bond pdb=" CG ASP H 114 " pdb=" OD2 ASP H 114 " ideal model delta sigma weight residual 1.249 1.204 0.045 1.90e-02 2.77e+03 5.51e+00 ... (remaining 2799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 3138 1.40 - 2.81: 545 2.81 - 4.21: 89 4.21 - 5.62: 26 5.62 - 7.02: 12 Bond angle restraints: 3810 Sorted by residual: angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.05 -7.02 9.90e-01 1.02e+00 5.03e+01 angle pdb=" C ALA L 45 " pdb=" N PRO L 46 " pdb=" CA PRO L 46 " ideal model delta sigma weight residual 119.85 126.55 -6.70 1.01e+00 9.80e-01 4.40e+01 angle pdb=" C ARG L 56 " pdb=" N PRO L 57 " pdb=" CA PRO L 57 " ideal model delta sigma weight residual 119.78 126.60 -6.82 1.03e+00 9.43e-01 4.38e+01 angle pdb=" C ASP A 138 " pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta sigma weight residual 120.14 126.93 -6.79 1.06e+00 8.90e-01 4.10e+01 angle pdb=" C THR A 250 " pdb=" N PRO A 251 " pdb=" CA PRO A 251 " ideal model delta sigma weight residual 119.85 126.28 -6.43 1.01e+00 9.80e-01 4.05e+01 ... (remaining 3805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 1513 14.98 - 29.95: 55 29.95 - 44.93: 9 44.93 - 59.90: 5 59.90 - 74.87: 4 Dihedral angle restraints: 1586 sinusoidal: 580 harmonic: 1006 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 120.22 -27.22 1 1.00e+01 1.00e-02 1.06e+01 dihedral pdb=" CG ARG H 67 " pdb=" CD ARG H 67 " pdb=" NE ARG H 67 " pdb=" CZ ARG H 67 " ideal model delta sinusoidal sigma weight residual 180.00 141.04 38.96 2 1.50e+01 4.44e-03 8.43e+00 dihedral pdb=" CB GLU A 154 " pdb=" CG GLU A 154 " pdb=" CD GLU A 154 " pdb=" OE1 GLU A 154 " ideal model delta sinusoidal sigma weight residual 0.00 74.87 -74.87 1 3.00e+01 1.11e-03 7.88e+00 ... (remaining 1583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 309 0.061 - 0.121: 95 0.121 - 0.181: 14 0.181 - 0.241: 7 0.241 - 0.302: 2 Chirality restraints: 427 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.48 0.08 2.00e-02 2.50e+03 1.72e+01 chirality pdb=" C1 FUC B 3 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 3 " pdb=" O5 FUC B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.06e+01 chirality pdb=" C2 NAG A1301 " pdb=" C1 NAG A1301 " pdb=" C3 NAG A1301 " pdb=" N2 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.79 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 424 not shown) Planarity restraints: 481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.353 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG B 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.544 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 95 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C TYR H 95 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR H 95 " 0.019 2.00e-02 2.50e+03 pdb=" N CYS H 96 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 29 " 0.025 2.00e-02 2.50e+03 1.52e-02 4.05e+00 pdb=" CG PHE H 29 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE H 29 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE H 29 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE H 29 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 29 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE H 29 " 0.014 2.00e-02 2.50e+03 ... (remaining 478 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 1519 3.00 - 3.47: 2371 3.47 - 3.95: 4484 3.95 - 4.42: 5187 4.42 - 4.90: 8533 Nonbonded interactions: 22094 Sorted by model distance: nonbonded pdb=" OD2 ASP H 73 " pdb=" NZ LYS H 76 " model vdw 2.519 3.120 nonbonded pdb=" N ASP H 62 " pdb=" OD1 ASP H 62 " model vdw 2.529 3.120 nonbonded pdb=" O THR A 250 " pdb=" OG1 THR A 250 " model vdw 2.573 3.040 nonbonded pdb=" N ASN L 33 " pdb=" OD1 ASN L 33 " model vdw 2.579 3.120 nonbonded pdb=" N LYS H 104 " pdb=" N TRP H 105 " model vdw 2.582 2.560 ... (remaining 22089 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.720 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.210 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:8.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 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 : 0.012 0.056 2811 Z= 0.665 Angle : 1.200 7.023 3828 Z= 0.796 Chirality : 0.064 0.302 427 Planarity : 0.015 0.306 479 Dihedral : 10.116 74.874 935 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.72 (0.40), residues: 154 loop : 0.35 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 78 TYR 0.025 0.004 TYR H 103 PHE 0.025 0.004 PHE H 29 TRP 0.022 0.004 TRP L 101 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.01211 / 0.66 ( 2804) covalent geometry : angle 1.19329 / 0.80 ( 3810) SS BOND : bond 0.02145 / 1.13 ( 3) SS BOND : angle 2.19574 / 1.24 ( 6) hydrogen bonds : bond 0.16936 / 11.84 ( 105) hydrogen bonds : angle 8.24625 / 5.52 ( 276) link_BETA1-4 : bond 0.05409 / 2.85 ( 1) link_BETA1-4 : angle 2.27361 / 1.20 ( 3) link_BETA1-6 : bond 0.04677 / 2.46 ( 1) link_BETA1-6 : angle 1.86634 / 1.00 ( 3) link_NAG-ASN : bond 0.05294 / 2.64 ( 2) link_NAG-ASN : angle 2.28691 / 1.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.060 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.3217 time to fit residues: 28.6254 Evaluate side-chains 61 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.0570 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.0980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.0970 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 overall best weight: 0.1296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 56 ASN H 118 GLN L 33 ASN A 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.142499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.134899 restraints weight = 3617.594| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.18 r_work: 0.3480 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2811 Z= 0.123 Angle : 0.609 7.114 3828 Z= 0.308 Chirality : 0.044 0.170 427 Planarity : 0.004 0.033 479 Dihedral : 4.196 15.905 379 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.51 % Allowed : 11.23 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.86 (0.40), residues: 152 loop : -0.04 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 102 TYR 0.018 0.002 TYR A 248 PHE 0.012 0.002 PHE A 238 TRP 0.009 0.001 TRP H 116 HIS 0.003 0.001 HIS L 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 2804) covalent geometry : angle 0.59931 / 0.31 ( 3810) SS BOND : bond 0.00253 / 0.13 ( 3) SS BOND : angle 1.04125 / 0.56 ( 6) hydrogen bonds : bond 0.03855 / 2.76 ( 105) hydrogen bonds : angle 6.36908 / 4.24 ( 276) link_BETA1-4 : bond 0.01124 / 0.59 ( 1) link_BETA1-4 : angle 2.17580 / 1.14 ( 3) link_BETA1-6 : bond 0.00940 / 0.49 ( 1) link_BETA1-6 : angle 1.23356 / 0.65 ( 3) link_NAG-ASN : bond 0.00228 / 0.12 ( 2) link_NAG-ASN : angle 2.13513 / 1.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.098 Fit side-chains REVERT: L 84 ASP cc_start: 0.8045 (m-30) cc_final: 0.7819 (m-30) REVERT: A 102 ARG cc_start: 0.8315 (mmt90) cc_final: 0.8030 (mmt90) outliers start: 10 outliers final: 4 residues processed: 70 average time/residue: 0.3374 time to fit residues: 24.5060 Evaluate side-chains 67 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 124 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 0.0570 chunk 31 optimal weight: 0.3980 chunk 28 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.0670 chunk 23 optimal weight: 0.6980 chunk 10 optimal weight: 0.0870 chunk 3 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 overall best weight: 0.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 56 ASN L 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.139248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.131567 restraints weight = 3640.140| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.14 r_work: 0.3455 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 2811 Z= 0.147 Angle : 0.575 7.078 3828 Z= 0.292 Chirality : 0.043 0.169 427 Planarity : 0.004 0.024 479 Dihedral : 4.078 16.962 379 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.81 % Allowed : 13.33 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.74 (0.41), residues: 142 loop : -0.03 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 19 TYR 0.018 0.002 TYR A 248 PHE 0.012 0.002 PHE H 29 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 2804) covalent geometry : angle 0.56767 / 0.29 ( 3810) SS BOND : bond 0.00502 / 0.26 ( 3) SS BOND : angle 0.79212 / 0.43 ( 6) hydrogen bonds : bond 0.03456 / 2.45 ( 105) hydrogen bonds : angle 5.92282 / 3.99 ( 276) link_BETA1-4 : bond 0.00130 / 0.07 ( 1) link_BETA1-4 : angle 1.39865 / 0.71 ( 3) link_BETA1-6 : bond 0.00297 / 0.16 ( 1) link_BETA1-6 : angle 1.61032 / 0.68 ( 3) link_NAG-ASN : bond 0.00318 / 0.17 ( 2) link_NAG-ASN : angle 1.79031 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.095 Fit side-chains REVERT: H 52 SER cc_start: 0.8933 (p) cc_final: 0.8610 (t) REVERT: L 84 ASP cc_start: 0.8174 (m-30) cc_final: 0.7934 (m-30) REVERT: A 154 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7976 (tt0) outliers start: 8 outliers final: 7 residues processed: 70 average time/residue: 0.3717 time to fit residues: 26.9006 Evaluate side-chains 70 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 154 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.0970 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 0.0060 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.0050 chunk 14 optimal weight: 0.1980 chunk 20 optimal weight: 0.7980 overall best weight: 0.1608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 56 ASN H 84 ASN H 118 GLN L 41 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.139936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.132179 restraints weight = 3596.872| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.16 r_work: 0.3459 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2811 Z= 0.126 Angle : 0.559 7.021 3828 Z= 0.283 Chirality : 0.043 0.174 427 Planarity : 0.003 0.023 479 Dihedral : 3.988 16.179 379 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.91 % Allowed : 12.63 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.74 (0.42), residues: 142 loop : -0.07 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 78 TYR 0.019 0.001 TYR A 248 PHE 0.010 0.001 PHE A 238 TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 2804) covalent geometry : angle 0.55066 / 0.28 ( 3810) SS BOND : bond 0.00356 / 0.18 ( 3) SS BOND : angle 0.97036 / 0.51 ( 6) hydrogen bonds : bond 0.03084 / 2.19 ( 105) hydrogen bonds : angle 5.72610 / 3.86 ( 276) link_BETA1-4 : bond 0.00417 / 0.22 ( 1) link_BETA1-4 : angle 1.33960 / 0.61 ( 3) link_BETA1-6 : bond 0.00458 / 0.24 ( 1) link_BETA1-6 : angle 1.50188 / 0.64 ( 3) link_NAG-ASN : bond 0.00145 / 0.08 ( 2) link_NAG-ASN : angle 1.96280 / 1.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.093 Fit side-chains REVERT: H 52 SER cc_start: 0.8950 (p) cc_final: 0.8653 (t) REVERT: L 84 ASP cc_start: 0.8179 (m-30) cc_final: 0.7931 (m-30) outliers start: 14 outliers final: 6 residues processed: 76 average time/residue: 0.3114 time to fit residues: 24.5014 Evaluate side-chains 68 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 2 optimal weight: 0.2980 chunk 17 optimal weight: 0.0670 chunk 21 optimal weight: 0.2980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 56 ASN H 118 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.136217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.128377 restraints weight = 3539.324| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.15 r_work: 0.3407 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 2811 Z= 0.203 Angle : 0.630 7.717 3828 Z= 0.318 Chirality : 0.045 0.216 427 Planarity : 0.004 0.025 479 Dihedral : 4.297 16.656 379 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.21 % Allowed : 15.44 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.50 (0.42), residues: 152 loop : -0.22 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 78 TYR 0.016 0.002 TYR A 248 PHE 0.016 0.002 PHE H 29 TRP 0.010 0.002 TRP A 258 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 ( 2804) covalent geometry : angle 0.61847 / 0.32 ( 3810) SS BOND : bond 0.00483 / 0.24 ( 3) SS BOND : angle 0.89715 / 0.48 ( 6) hydrogen bonds : bond 0.03524 / 2.43 ( 105) hydrogen bonds : angle 6.15640 / 4.18 ( 276) link_BETA1-4 : bond 0.00160 / 0.08 ( 1) link_BETA1-4 : angle 1.32256 / 0.64 ( 3) link_BETA1-6 : bond 0.00212 / 0.11 ( 1) link_BETA1-6 : angle 1.86940 / 0.80 ( 3) link_NAG-ASN : bond 0.00190 / 0.10 ( 2) link_NAG-ASN : angle 2.55623 / 1.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.073 Fit side-chains REVERT: H 52 SER cc_start: 0.9041 (p) cc_final: 0.8649 (t) REVERT: L 84 ASP cc_start: 0.8249 (m-30) cc_final: 0.8045 (m-30) outliers start: 12 outliers final: 8 residues processed: 75 average time/residue: 0.2717 time to fit residues: 21.1560 Evaluate side-chains 71 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 15 optimal weight: 0.2980 chunk 10 optimal weight: 0.0070 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 6 optimal weight: 0.0770 chunk 22 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 16 optimal weight: 0.0970 chunk 23 optimal weight: 0.2980 overall best weight: 0.1154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 56 ASN H 118 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.138887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130576 restraints weight = 3582.182| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.16 r_work: 0.3437 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2811 Z= 0.113 Angle : 0.573 7.406 3828 Z= 0.290 Chirality : 0.043 0.205 427 Planarity : 0.003 0.023 479 Dihedral : 3.971 16.588 379 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.46 % Allowed : 20.00 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.47), residues: 336 helix: None (None), residues: 0 sheet: 0.51 (0.43), residues: 142 loop : -0.06 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 78 TYR 0.016 0.001 TYR A 248 PHE 0.009 0.001 PHE A 238 TRP 0.007 0.001 TRP L 101 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 2804) covalent geometry : angle 0.56069 / 0.29 ( 3810) SS BOND : bond 0.00399 / 0.20 ( 3) SS BOND : angle 1.15762 / 0.61 ( 6) hydrogen bonds : bond 0.02948 / 2.07 ( 105) hydrogen bonds : angle 5.74389 / 3.88 ( 276) link_BETA1-4 : bond 0.00264 / 0.14 ( 1) link_BETA1-4 : angle 1.37152 / 0.62 ( 3) link_BETA1-6 : bond 0.00451 / 0.24 ( 1) link_BETA1-6 : angle 1.63573 / 0.70 ( 3) link_NAG-ASN : bond 0.00127 / 0.07 ( 2) link_NAG-ASN : angle 2.45093 / 1.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.056 Fit side-chains REVERT: H 52 SER cc_start: 0.8992 (p) cc_final: 0.8693 (t) REVERT: L 84 ASP cc_start: 0.8217 (m-30) cc_final: 0.7990 (m-30) outliers start: 7 outliers final: 5 residues processed: 65 average time/residue: 0.2820 time to fit residues: 18.9706 Evaluate side-chains 63 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 0.0980 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 56 ASN H 118 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.134134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126340 restraints weight = 3577.126| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.14 r_work: 0.3381 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 2811 Z= 0.246 Angle : 0.671 7.911 3828 Z= 0.340 Chirality : 0.047 0.267 427 Planarity : 0.005 0.061 479 Dihedral : 4.458 17.700 379 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.21 % Allowed : 18.95 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.47), residues: 336 helix: None (None), residues: 0 sheet: 0.23 (0.42), residues: 154 loop : -0.27 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 102 TYR 0.017 0.002 TYR H 95 PHE 0.019 0.002 PHE H 29 TRP 0.013 0.002 TRP A 258 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.25 ( 2804) covalent geometry : angle 0.65494 / 0.34 ( 3810) SS BOND : bond 0.00449 / 0.22 ( 3) SS BOND : angle 1.23891 / 0.66 ( 6) hydrogen bonds : bond 0.03716 / 2.60 ( 105) hydrogen bonds : angle 6.39483 / 4.36 ( 276) link_BETA1-4 : bond 0.00389 / 0.20 ( 1) link_BETA1-4 : angle 1.39888 / 0.65 ( 3) link_BETA1-6 : bond 0.00222 / 0.12 ( 1) link_BETA1-6 : angle 2.03221 / 0.87 ( 3) link_NAG-ASN : bond 0.00030 / 0.02 ( 2) link_NAG-ASN : angle 3.17108 / 1.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.100 Fit side-chains REVERT: A 153 MET cc_start: 0.8190 (mtt) cc_final: 0.7937 (mtt) outliers start: 12 outliers final: 8 residues processed: 74 average time/residue: 0.3162 time to fit residues: 24.2508 Evaluate side-chains 73 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 154 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 26 optimal weight: 0.1980 chunk 15 optimal weight: 0.0020 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 0.1980 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 0.1980 chunk 6 optimal weight: 0.0970 chunk 10 optimal weight: 0.0970 overall best weight: 0.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 118 GLN ** A 239 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 = 0.3580 r_free = 0.3580 target = 0.138019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129886 restraints weight = 3590.574| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.22 r_work: 0.3418 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2811 Z= 0.119 Angle : 0.587 7.605 3828 Z= 0.299 Chirality : 0.044 0.218 427 Planarity : 0.004 0.056 479 Dihedral : 4.066 16.618 379 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.16 % Allowed : 20.35 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.47), residues: 336 helix: None (None), residues: 0 sheet: 0.42 (0.44), residues: 142 loop : -0.14 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 102 TYR 0.014 0.001 TYR A 248 PHE 0.011 0.001 PHE A 238 TRP 0.007 0.001 TRP H 116 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 2804) covalent geometry : angle 0.57425 / 0.30 ( 3810) SS BOND : bond 0.00341 / 0.17 ( 3) SS BOND : angle 1.07487 / 0.57 ( 6) hydrogen bonds : bond 0.02926 / 2.08 ( 105) hydrogen bonds : angle 5.79604 / 3.92 ( 276) link_BETA1-4 : bond 0.00481 / 0.25 ( 1) link_BETA1-4 : angle 1.41909 / 0.64 ( 3) link_BETA1-6 : bond 0.00407 / 0.21 ( 1) link_BETA1-6 : angle 1.72308 / 0.74 ( 3) link_NAG-ASN : bond 0.00114 / 0.06 ( 2) link_NAG-ASN : angle 2.62165 / 1.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.094 Fit side-chains REVERT: H 52 SER cc_start: 0.9031 (p) cc_final: 0.8714 (t) REVERT: H 65 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8114 (ttmt) outliers start: 9 outliers final: 5 residues processed: 70 average time/residue: 0.3058 time to fit residues: 22.2088 Evaluate side-chains 68 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 6 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.0770 chunk 11 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 56 ASN H 118 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.133830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.124290 restraints weight = 3670.502| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.27 r_work: 0.3395 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 2811 Z= 0.208 Angle : 0.659 7.577 3828 Z= 0.335 Chirality : 0.046 0.252 427 Planarity : 0.005 0.051 479 Dihedral : 4.328 17.281 379 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.81 % Allowed : 21.40 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.47), residues: 336 helix: None (None), residues: 0 sheet: 0.20 (0.43), residues: 154 loop : -0.24 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 102 TYR 0.016 0.002 TYR H 95 PHE 0.016 0.002 PHE H 29 TRP 0.009 0.002 TRP A 258 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 ( 2804) covalent geometry : angle 0.64549 / 0.33 ( 3810) SS BOND : bond 0.00434 / 0.22 ( 3) SS BOND : angle 1.13851 / 0.60 ( 6) hydrogen bonds : bond 0.03431 / 2.39 ( 105) hydrogen bonds : angle 6.19234 / 4.21 ( 276) link_BETA1-4 : bond 0.00467 / 0.25 ( 1) link_BETA1-4 : angle 1.38250 / 0.64 ( 3) link_BETA1-6 : bond 0.00331 / 0.17 ( 1) link_BETA1-6 : angle 1.94676 / 0.83 ( 3) link_NAG-ASN : bond 0.00079 / 0.04 ( 2) link_NAG-ASN : angle 2.86178 / 1.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.088 Fit side-chains REVERT: H 52 SER cc_start: 0.9055 (p) cc_final: 0.8690 (t) outliers start: 8 outliers final: 8 residues processed: 69 average time/residue: 0.2292 time to fit residues: 16.4643 Evaluate side-chains 70 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 28 optimal weight: 0.0980 chunk 10 optimal weight: 0.0000 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.0010 chunk 29 optimal weight: 0.3980 chunk 21 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 overall best weight: 0.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 56 ASN ** A 239 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 = 0.3575 r_free = 0.3575 target = 0.137151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.128672 restraints weight = 3622.407| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.26 r_work: 0.3432 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2811 Z= 0.114 Angle : 0.605 7.485 3828 Z= 0.308 Chirality : 0.043 0.219 427 Planarity : 0.004 0.059 479 Dihedral : 4.062 16.948 379 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.81 % Allowed : 22.11 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.47), residues: 336 helix: None (None), residues: 0 sheet: 0.34 (0.44), residues: 142 loop : -0.11 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 102 TYR 0.014 0.001 TYR A 248 PHE 0.010 0.001 PHE A 238 TRP 0.007 0.001 TRP A 152 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 2804) covalent geometry : angle 0.59290 / 0.31 ( 3810) SS BOND : bond 0.00331 / 0.17 ( 3) SS BOND : angle 1.04788 / 0.55 ( 6) hydrogen bonds : bond 0.02910 / 2.06 ( 105) hydrogen bonds : angle 5.81181 / 3.94 ( 276) link_BETA1-4 : bond 0.00411 / 0.22 ( 1) link_BETA1-4 : angle 1.42613 / 0.64 ( 3) link_BETA1-6 : bond 0.00345 / 0.18 ( 1) link_BETA1-6 : angle 1.77690 / 0.77 ( 3) link_NAG-ASN : bond 0.00123 / 0.06 ( 2) link_NAG-ASN : angle 2.56680 / 1.46 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.056 Fit side-chains REVERT: H 52 SER cc_start: 0.9018 (p) cc_final: 0.8690 (t) REVERT: H 65 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8101 (ttmt) outliers start: 8 outliers final: 6 residues processed: 67 average time/residue: 0.2205 time to fit residues: 15.3243 Evaluate side-chains 66 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 21 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 0.0980 chunk 9 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 0.0470 chunk 4 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 overall best weight: 0.1478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 56 ASN H 118 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.138279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.130060 restraints weight = 3530.482| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.15 r_work: 0.3418 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2811 Z= 0.131 Angle : 0.609 7.538 3828 Z= 0.312 Chirality : 0.043 0.208 427 Planarity : 0.004 0.039 479 Dihedral : 4.031 16.229 379 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.46 % Allowed : 21.75 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.47), residues: 336 helix: None (None), residues: 0 sheet: 0.34 (0.44), residues: 142 loop : -0.16 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 102 TYR 0.013 0.001 TYR H 95 PHE 0.010 0.001 PHE A 238 TRP 0.006 0.001 TRP A 64 HIS 0.003 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 2804) covalent geometry : angle 0.59872 / 0.31 ( 3810) SS BOND : bond 0.00365 / 0.19 ( 3) SS BOND : angle 1.01864 / 0.54 ( 6) hydrogen bonds : bond 0.03019 / 2.10 ( 105) hydrogen bonds : angle 5.80235 / 3.95 ( 276) link_BETA1-4 : bond 0.00453 / 0.24 ( 1) link_BETA1-4 : angle 1.37053 / 0.62 ( 3) link_BETA1-6 : bond 0.00367 / 0.19 ( 1) link_BETA1-6 : angle 1.73782 / 0.74 ( 3) link_NAG-ASN : bond 0.00147 / 0.07 ( 2) link_NAG-ASN : angle 2.28602 / 1.30 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1163.88 seconds wall clock time: 20 minutes 40.46 seconds (1240.46 seconds total)