Starting phenix.real_space_refine on Sat May 10 02:11:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cx9_45982/05_2025/9cx9_45982.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cx9_45982/05_2025/9cx9_45982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cx9_45982/05_2025/9cx9_45982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cx9_45982/05_2025/9cx9_45982.map" model { file = "/net/cci-nas-00/data/ceres_data/9cx9_45982/05_2025/9cx9_45982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cx9_45982/05_2025/9cx9_45982.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 11 5.16 5 C 2930 2.51 5 N 789 2.21 5 O 895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4631 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 901 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "L" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 805 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 98 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 2550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2550 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 295} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 277 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain breaks: 1 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP%COO:plan': 1} Unresolved non-hydrogen planarities: 109 Time building chain proxies: 3.80, per 1000 atoms: 0.82 Number of scatterers: 4631 At special positions: 0 Unit cell: (62.208, 116.122, 116.122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 P 6 15.00 O 895 8.00 N 789 7.00 C 2930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS B 95 " 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 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 524.6 milliseconds 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1144 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 13 sheets defined 3.4% alpha, 39.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.033A pdb=" N ASN A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 9 Processing sheet with id=AA2, first strand: chain 'H' and resid 61 through 62 removed outlier: 4.227A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ARG H 103 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LEU H 110 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 61 through 62 removed outlier: 4.227A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13 removed outlier: 7.227A pdb=" N SER L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 46 through 47 removed outlier: 3.581A pdb=" N GLN L 91 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 49 through 51 Processing sheet with id=AA8, first strand: chain 'V' and resid 361 through 364 removed outlier: 3.537A pdb=" N LYS A 10 " --> pdb=" O ALA V 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 26 through 28 removed outlier: 7.052A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.622A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL A 53 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN A 85 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A 55 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN A 83 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL A 81 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL A 59 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 79 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AB2, first strand: chain 'A' and resid 183 through 186 Processing sheet with id=AB3, first strand: chain 'A' and resid 207 through 208 removed outlier: 4.004A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE A 231 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLU A 257 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE A 233 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N MET A 255 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL A 235 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 118 through 122 158 hydrogen bonds defined for protein. 411 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 835 1.33 - 1.45: 1179 1.45 - 1.57: 2680 1.57 - 1.69: 16 1.69 - 1.81: 17 Bond restraints: 4727 Sorted by residual: bond pdb=" N GLU A 110 " pdb=" CA GLU A 110 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.58e+00 bond pdb=" C PRO A 264 " pdb=" O PRO A 264 " ideal model delta sigma weight residual 1.235 1.206 0.029 1.30e-02 5.92e+03 5.14e+00 bond pdb=" C TYR A 272 " pdb=" N THR A 273 " ideal model delta sigma weight residual 1.331 1.303 0.029 1.30e-02 5.92e+03 4.81e+00 bond pdb=" N SER A 266 " pdb=" CA SER A 266 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.40e-02 5.10e+03 4.80e+00 bond pdb=" N ALA A 263 " pdb=" CA ALA A 263 " ideal model delta sigma weight residual 1.451 1.484 -0.033 1.60e-02 3.91e+03 4.36e+00 ... (remaining 4722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 6209 1.60 - 3.19: 189 3.19 - 4.79: 26 4.79 - 6.38: 8 6.38 - 7.98: 3 Bond angle restraints: 6435 Sorted by residual: angle pdb=" C TYR A 272 " pdb=" N THR A 273 " pdb=" CA THR A 273 " ideal model delta sigma weight residual 121.89 115.05 6.84 1.74e+00 3.30e-01 1.54e+01 angle pdb=" C TYR L 94 " pdb=" N VAL L 95 " pdb=" CA VAL L 95 " ideal model delta sigma weight residual 120.24 122.51 -2.27 6.30e-01 2.52e+00 1.30e+01 angle pdb=" CA PHE A 268 " pdb=" C PHE A 268 " pdb=" N SER A 269 " ideal model delta sigma weight residual 116.37 120.57 -4.20 1.19e+00 7.06e-01 1.25e+01 angle pdb=" C VAL A 271 " pdb=" N TYR A 272 " pdb=" CA TYR A 272 " ideal model delta sigma weight residual 123.32 129.53 -6.21 1.88e+00 2.83e-01 1.09e+01 angle pdb=" N ALA A 258 " pdb=" CA ALA A 258 " pdb=" C ALA A 258 " ideal model delta sigma weight residual 113.72 109.49 4.23 1.30e+00 5.92e-01 1.06e+01 ... (remaining 6430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 2552 16.82 - 33.65: 210 33.65 - 50.47: 67 50.47 - 67.29: 12 67.29 - 84.12: 8 Dihedral angle restraints: 2849 sinusoidal: 1074 harmonic: 1775 Sorted by residual: dihedral pdb=" CB CYS L 24 " pdb=" SG CYS L 24 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 56.47 36.53 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" CA SER A 269 " pdb=" C SER A 269 " pdb=" N LYS A 270 " pdb=" CA LYS A 270 " ideal model delta harmonic sigma weight residual -180.00 -161.43 -18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual -86.00 -113.64 27.64 1 1.00e+01 1.00e-02 1.10e+01 ... (remaining 2846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 432 0.028 - 0.055: 183 0.055 - 0.083: 53 0.083 - 0.110: 42 0.110 - 0.138: 25 Chirality restraints: 735 Sorted by residual: chirality pdb=" CA LEU A 108 " pdb=" N LEU A 108 " pdb=" C LEU A 108 " pdb=" CB LEU A 108 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE A 119 " pdb=" N ILE A 119 " pdb=" C ILE A 119 " pdb=" CB ILE A 119 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA VAL B 137 " pdb=" N VAL B 137 " pdb=" C VAL B 137 " pdb=" CB VAL B 137 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 732 not shown) Planarity restraints: 818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 272 " -0.100 2.00e-02 2.50e+03 5.18e-02 5.36e+01 pdb=" CG TYR A 272 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 272 " 0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR A 272 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR A 272 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 272 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR A 272 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR A 272 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 272 " -0.026 2.00e-02 2.50e+03 5.51e-02 3.03e+01 pdb=" C TYR A 272 " 0.095 2.00e-02 2.50e+03 pdb=" O TYR A 272 " -0.037 2.00e-02 2.50e+03 pdb=" N THR A 273 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN L 80 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO L 81 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO L 81 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 81 " 0.018 5.00e-02 4.00e+02 ... (remaining 815 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1277 2.81 - 3.33: 3756 3.33 - 3.85: 6987 3.85 - 4.38: 7851 4.38 - 4.90: 14445 Nonbonded interactions: 34316 Sorted by model distance: nonbonded pdb=" OE1 GLU L 82 " pdb=" OD1 ASP L 83 " model vdw 2.285 3.040 nonbonded pdb=" NH2 ARG A 62 " pdb=" OD2 ASP A 143 " model vdw 2.348 3.120 nonbonded pdb=" O ALA A 301 " pdb=" OH TYR A 321 " model vdw 2.358 3.040 nonbonded pdb=" NE2 GLN A 130 " pdb=" O LYS A 284 " model vdw 2.363 3.120 nonbonded pdb=" OG1 THR A 98 " pdb=" OE1 GLU A 102 " model vdw 2.381 3.040 ... (remaining 34311 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.630 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 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 : 0.003 0.033 4730 Z= 0.179 Angle : 0.668 7.978 6441 Z= 0.380 Chirality : 0.044 0.138 735 Planarity : 0.004 0.055 818 Dihedral : 14.875 84.117 1696 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.21 % Allowed : 19.92 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.36), residues: 582 helix: -0.54 (1.54), residues: 13 sheet: 0.08 (0.34), residues: 250 loop : -1.04 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 106 HIS 0.003 0.001 HIS A 159 PHE 0.013 0.001 PHE A 268 TYR 0.100 0.002 TYR A 272 ARG 0.010 0.001 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.24300 ( 145) hydrogen bonds : angle 10.46749 ( 411) SS BOND : bond 0.00177 ( 3) SS BOND : angle 0.51264 ( 6) covalent geometry : bond 0.00313 ( 4727) covalent geometry : angle 0.66838 ( 6435) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.555 Fit side-chains REVERT: A 26 ASP cc_start: 0.6766 (m-30) cc_final: 0.6323 (p0) REVERT: A 130 GLN cc_start: 0.7953 (tt0) cc_final: 0.7605 (tt0) outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 0.2000 time to fit residues: 18.1756 Evaluate side-chains 68 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN L 4 GLN A 172 GLN A 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.161069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.140250 restraints weight = 7052.465| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.85 r_work: 0.3698 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 4730 Z= 0.241 Angle : 0.660 5.991 6441 Z= 0.350 Chirality : 0.048 0.166 735 Planarity : 0.005 0.035 818 Dihedral : 5.688 37.009 674 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.45 % Allowed : 16.56 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.34), residues: 582 helix: -1.53 (1.30), residues: 15 sheet: -0.00 (0.33), residues: 232 loop : -1.19 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.006 0.001 HIS A 210 PHE 0.020 0.002 PHE H 105 TYR 0.029 0.002 TYR A 272 ARG 0.008 0.001 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.05074 ( 145) hydrogen bonds : angle 7.05074 ( 411) SS BOND : bond 0.00407 ( 3) SS BOND : angle 1.05677 ( 6) covalent geometry : bond 0.00560 ( 4727) covalent geometry : angle 0.65916 ( 6435) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.545 Fit side-chains REVERT: A 77 LYS cc_start: 0.7803 (tptt) cc_final: 0.7559 (tptt) outliers start: 26 outliers final: 20 residues processed: 80 average time/residue: 0.1904 time to fit residues: 19.0968 Evaluate side-chains 84 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 56 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.163341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.144180 restraints weight = 7083.211| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.20 r_work: 0.3699 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4730 Z= 0.133 Angle : 0.568 6.044 6441 Z= 0.297 Chirality : 0.045 0.141 735 Planarity : 0.004 0.034 818 Dihedral : 5.451 38.456 674 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.82 % Allowed : 19.92 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.35), residues: 582 helix: -0.34 (1.52), residues: 13 sheet: 0.12 (0.33), residues: 232 loop : -1.14 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.004 0.001 HIS A 210 PHE 0.011 0.001 PHE H 105 TYR 0.017 0.001 TYR A 272 ARG 0.006 0.000 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 145) hydrogen bonds : angle 6.38069 ( 411) SS BOND : bond 0.00296 ( 3) SS BOND : angle 0.73398 ( 6) covalent geometry : bond 0.00302 ( 4727) covalent geometry : angle 0.56794 ( 6435) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.542 Fit side-chains REVERT: A 77 LYS cc_start: 0.7919 (tptt) cc_final: 0.7614 (tptt) outliers start: 23 outliers final: 18 residues processed: 82 average time/residue: 0.1885 time to fit residues: 19.5011 Evaluate side-chains 82 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 48 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.161522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.142216 restraints weight = 7106.139| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.18 r_work: 0.3668 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4730 Z= 0.195 Angle : 0.609 6.502 6441 Z= 0.320 Chirality : 0.046 0.154 735 Planarity : 0.004 0.034 818 Dihedral : 5.656 37.746 674 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 6.08 % Allowed : 20.13 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.34), residues: 582 helix: -0.62 (1.44), residues: 13 sheet: 0.11 (0.33), residues: 232 loop : -1.25 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 50 HIS 0.004 0.001 HIS A 210 PHE 0.018 0.002 PHE H 105 TYR 0.022 0.002 TYR A 272 ARG 0.004 0.000 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 145) hydrogen bonds : angle 6.14437 ( 411) SS BOND : bond 0.00377 ( 3) SS BOND : angle 0.88627 ( 6) covalent geometry : bond 0.00454 ( 4727) covalent geometry : angle 0.60862 ( 6435) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.561 Fit side-chains REVERT: A 77 LYS cc_start: 0.8008 (tptt) cc_final: 0.7574 (tptt) outliers start: 29 outliers final: 22 residues processed: 87 average time/residue: 0.1912 time to fit residues: 20.8488 Evaluate side-chains 89 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.159828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.139272 restraints weight = 7303.326| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.88 r_work: 0.3685 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4730 Z= 0.230 Angle : 0.665 7.723 6441 Z= 0.348 Chirality : 0.047 0.143 735 Planarity : 0.005 0.036 818 Dihedral : 5.961 39.183 674 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.29 % Allowed : 20.13 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.34), residues: 582 helix: -1.07 (1.28), residues: 13 sheet: -0.13 (0.33), residues: 231 loop : -1.34 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 50 HIS 0.005 0.001 HIS A 210 PHE 0.021 0.002 PHE H 105 TYR 0.024 0.002 TYR A 272 ARG 0.005 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 145) hydrogen bonds : angle 6.20316 ( 411) SS BOND : bond 0.00371 ( 3) SS BOND : angle 0.83451 ( 6) covalent geometry : bond 0.00538 ( 4727) covalent geometry : angle 0.66436 ( 6435) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.511 Fit side-chains REVERT: A 77 LYS cc_start: 0.7852 (tptt) cc_final: 0.7368 (tptt) outliers start: 30 outliers final: 28 residues processed: 86 average time/residue: 0.1743 time to fit residues: 18.9486 Evaluate side-chains 90 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 50 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 4 GLN A 130 GLN A 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.160455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.140902 restraints weight = 7109.027| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.23 r_work: 0.3670 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4730 Z= 0.175 Angle : 0.621 6.445 6441 Z= 0.320 Chirality : 0.046 0.143 735 Planarity : 0.004 0.035 818 Dihedral : 5.826 38.385 674 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 6.50 % Allowed : 22.22 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.34), residues: 582 helix: -1.21 (1.27), residues: 13 sheet: -0.12 (0.33), residues: 231 loop : -1.28 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 50 HIS 0.004 0.001 HIS A 210 PHE 0.018 0.002 PHE A 87 TYR 0.017 0.002 TYR A 272 ARG 0.006 0.000 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 145) hydrogen bonds : angle 6.00488 ( 411) SS BOND : bond 0.00318 ( 3) SS BOND : angle 0.75195 ( 6) covalent geometry : bond 0.00409 ( 4727) covalent geometry : angle 0.62057 ( 6435) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.549 Fit side-chains REVERT: H 89 LEU cc_start: 0.7752 (mm) cc_final: 0.7431 (mt) REVERT: A 77 LYS cc_start: 0.7820 (tptt) cc_final: 0.7528 (tptt) outliers start: 31 outliers final: 30 residues processed: 82 average time/residue: 0.1790 time to fit residues: 18.5388 Evaluate side-chains 91 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 50 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.0030 chunk 53 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.160657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.141499 restraints weight = 7040.176| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.22 r_work: 0.3669 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4730 Z= 0.169 Angle : 0.619 7.885 6441 Z= 0.317 Chirality : 0.045 0.143 735 Planarity : 0.004 0.035 818 Dihedral : 5.801 37.940 674 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 7.13 % Allowed : 22.43 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.34), residues: 582 helix: -1.28 (1.29), residues: 13 sheet: -0.06 (0.33), residues: 231 loop : -1.25 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 50 HIS 0.004 0.001 HIS A 210 PHE 0.015 0.002 PHE H 105 TYR 0.017 0.002 TYR A 272 ARG 0.007 0.001 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 145) hydrogen bonds : angle 5.89898 ( 411) SS BOND : bond 0.00311 ( 3) SS BOND : angle 0.76005 ( 6) covalent geometry : bond 0.00395 ( 4727) covalent geometry : angle 0.61875 ( 6435) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.428 Fit side-chains REVERT: H 31 ASN cc_start: 0.8189 (t0) cc_final: 0.7736 (m-40) REVERT: H 89 LEU cc_start: 0.7762 (mm) cc_final: 0.7433 (mt) REVERT: A 77 LYS cc_start: 0.7764 (tptt) cc_final: 0.7375 (tptt) REVERT: A 165 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7992 (ptp-110) outliers start: 34 outliers final: 31 residues processed: 85 average time/residue: 0.1854 time to fit residues: 19.8319 Evaluate side-chains 92 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 39 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 4 GLN A 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.159797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.140767 restraints weight = 7058.112| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.19 r_work: 0.3673 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4730 Z= 0.188 Angle : 0.632 6.176 6441 Z= 0.325 Chirality : 0.046 0.144 735 Planarity : 0.004 0.036 818 Dihedral : 5.906 38.829 674 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 7.34 % Allowed : 22.64 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.34), residues: 582 helix: -1.52 (1.23), residues: 13 sheet: -0.07 (0.33), residues: 231 loop : -1.26 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 50 HIS 0.005 0.001 HIS H 38 PHE 0.019 0.002 PHE A 87 TYR 0.018 0.002 TYR A 272 ARG 0.007 0.001 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 145) hydrogen bonds : angle 5.94764 ( 411) SS BOND : bond 0.00342 ( 3) SS BOND : angle 0.78026 ( 6) covalent geometry : bond 0.00439 ( 4727) covalent geometry : angle 0.63223 ( 6435) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 63 time to evaluate : 0.535 Fit side-chains REVERT: H 31 ASN cc_start: 0.8062 (t0) cc_final: 0.7527 (m-40) REVERT: H 89 LEU cc_start: 0.7849 (mm) cc_final: 0.7596 (mt) REVERT: A 77 LYS cc_start: 0.7732 (tptt) cc_final: 0.7374 (tptt) REVERT: A 165 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7975 (ptp-110) outliers start: 35 outliers final: 32 residues processed: 86 average time/residue: 0.1821 time to fit residues: 19.6831 Evaluate side-chains 94 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 61 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 40 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 0.0070 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.161687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.142686 restraints weight = 7056.941| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.23 r_work: 0.3697 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4730 Z= 0.137 Angle : 0.609 12.288 6441 Z= 0.308 Chirality : 0.045 0.140 735 Planarity : 0.004 0.034 818 Dihedral : 5.685 39.418 674 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 6.29 % Allowed : 23.27 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.35), residues: 582 helix: -1.41 (1.26), residues: 13 sheet: 0.07 (0.33), residues: 231 loop : -1.09 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 106 HIS 0.004 0.001 HIS A 210 PHE 0.013 0.002 PHE A 27 TYR 0.014 0.001 TYR A 272 ARG 0.008 0.001 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.03132 ( 145) hydrogen bonds : angle 5.72797 ( 411) SS BOND : bond 0.00294 ( 3) SS BOND : angle 0.72034 ( 6) covalent geometry : bond 0.00319 ( 4727) covalent geometry : angle 0.60898 ( 6435) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.542 Fit side-chains REVERT: H 89 LEU cc_start: 0.7748 (mm) cc_final: 0.7461 (mt) REVERT: A 77 LYS cc_start: 0.7707 (tptt) cc_final: 0.7391 (tptt) REVERT: A 320 SER cc_start: 0.8207 (p) cc_final: 0.7927 (t) outliers start: 30 outliers final: 29 residues processed: 82 average time/residue: 0.1919 time to fit residues: 19.7760 Evaluate side-chains 91 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 10 optimal weight: 0.1980 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 4 GLN A 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.160506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.141423 restraints weight = 7006.994| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.21 r_work: 0.3692 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4730 Z= 0.168 Angle : 0.629 11.560 6441 Z= 0.320 Chirality : 0.045 0.141 735 Planarity : 0.004 0.037 818 Dihedral : 5.793 41.709 674 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 6.08 % Allowed : 23.27 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.34), residues: 582 helix: -1.66 (1.18), residues: 13 sheet: 0.05 (0.33), residues: 231 loop : -1.14 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 50 HIS 0.005 0.001 HIS A 210 PHE 0.016 0.002 PHE H 105 TYR 0.022 0.002 TYR A 113 ARG 0.008 0.001 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 145) hydrogen bonds : angle 5.77564 ( 411) SS BOND : bond 0.00318 ( 3) SS BOND : angle 0.73212 ( 6) covalent geometry : bond 0.00393 ( 4727) covalent geometry : angle 0.62861 ( 6435) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.696 Fit side-chains REVERT: H 31 ASN cc_start: 0.7904 (t0) cc_final: 0.7419 (m110) REVERT: H 89 LEU cc_start: 0.7775 (mm) cc_final: 0.7497 (mt) REVERT: A 77 LYS cc_start: 0.7813 (tptt) cc_final: 0.7431 (tptt) outliers start: 29 outliers final: 29 residues processed: 81 average time/residue: 0.1822 time to fit residues: 18.6830 Evaluate side-chains 91 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 4 optimal weight: 0.6980 chunk 56 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 0.0980 chunk 41 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 42 optimal weight: 0.0370 chunk 46 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.161265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.142305 restraints weight = 7051.506| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.22 r_work: 0.3703 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4730 Z= 0.155 Angle : 0.616 11.073 6441 Z= 0.312 Chirality : 0.045 0.143 735 Planarity : 0.004 0.037 818 Dihedral : 5.762 43.430 674 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.50 % Allowed : 23.06 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.34), residues: 582 helix: -1.48 (1.24), residues: 13 sheet: 0.06 (0.33), residues: 231 loop : -1.12 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 106 HIS 0.004 0.001 HIS A 210 PHE 0.014 0.002 PHE H 105 TYR 0.020 0.002 TYR A 113 ARG 0.008 0.001 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 145) hydrogen bonds : angle 5.73852 ( 411) SS BOND : bond 0.00289 ( 3) SS BOND : angle 0.67816 ( 6) covalent geometry : bond 0.00363 ( 4727) covalent geometry : angle 0.61586 ( 6435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2993.87 seconds wall clock time: 52 minutes 23.34 seconds (3143.34 seconds total)