Starting phenix.real_space_refine on Tue Feb 11 02:59:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sof_25269/02_2025/7sof_25269.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sof_25269/02_2025/7sof_25269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sof_25269/02_2025/7sof_25269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sof_25269/02_2025/7sof_25269.map" model { file = "/net/cci-nas-00/data/ceres_data/7sof_25269/02_2025/7sof_25269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sof_25269/02_2025/7sof_25269.cif" } resolution = 3.6 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= 0.045 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 13 5.16 5 C 2426 2.51 5 N 611 2.21 5 O 685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3735 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 730 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "H" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 916 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 117} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1966 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 13, 'TRANS': 244} Chain breaks: 4 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.04, per 1000 atoms: 1.35 Number of scatterers: 3735 At special positions: 0 Unit cell: (73.341, 91.044, 77.556, 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 13 16.00 O 685 8.00 N 611 7.00 C 2426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " 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 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 149 " " NAG A1306 " - " ASN A 17 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 625.7 milliseconds 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 912 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 6 sheets defined 4.7% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.797A pdb=" N GLU L 82 " --> pdb=" O THR L 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'A' and resid 294 through 303 Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.529A pdb=" N VAL L 10 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 48 through 54 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 59 through 61 current: chain 'H' and resid 108 through 115 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 108 through 115 current: chain 'A' and resid 116 through 121 removed outlier: 6.601A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N PHE A 140 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLU A 156 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ASP A 142 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYS A 154 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR A 144 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TRP A 152 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.484A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.711A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) 116 hydrogen bonds defined for protein. 288 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: 0.89 Time building geometry restraints manager: 1.21 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: 730 1.33 - 1.45: 971 1.45 - 1.57: 2117 1.57 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3834 Sorted by residual: bond pdb=" NE ARG A 246 " pdb=" CZ ARG A 246 " ideal model delta sigma weight residual 1.326 1.369 -0.043 1.10e-02 8.26e+03 1.50e+01 bond pdb=" NE ARG A 78 " pdb=" CZ ARG A 78 " ideal model delta sigma weight residual 1.326 1.367 -0.041 1.10e-02 8.26e+03 1.41e+01 bond pdb=" N ILE L 94 " pdb=" CA ILE L 94 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.85e+00 bond pdb=" C5 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" C5 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.17e+00 ... (remaining 3829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 4327 1.49 - 2.99: 734 2.99 - 4.48: 108 4.48 - 5.98: 52 5.98 - 7.47: 27 Bond angle restraints: 5248 Sorted by residual: angle pdb=" C GLN H 41 " pdb=" N PRO H 42 " pdb=" CA PRO H 42 " ideal model delta sigma weight residual 119.66 125.79 -6.13 7.30e-01 1.88e+00 7.05e+01 angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.20 -7.17 9.90e-01 1.02e+00 5.24e+01 angle pdb=" C GLY H 8 " pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 119.76 126.99 -7.23 1.03e+00 9.43e-01 4.93e+01 angle pdb=" C ASP A 138 " pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta sigma weight residual 119.76 126.70 -6.94 1.00e+00 1.00e+00 4.82e+01 angle pdb=" C ARG L 53 " pdb=" N PRO L 54 " pdb=" CA PRO L 54 " ideal model delta sigma weight residual 119.85 126.83 -6.98 1.01e+00 9.80e-01 4.78e+01 ... (remaining 5243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.32: 2273 21.32 - 42.64: 44 42.64 - 63.96: 5 63.96 - 85.28: 7 85.28 - 106.60: 4 Dihedral angle restraints: 2333 sinusoidal: 916 harmonic: 1417 Sorted by residual: dihedral pdb=" C THR L 93 " pdb=" N THR L 93 " pdb=" CA THR L 93 " pdb=" CB THR L 93 " ideal model delta harmonic sigma weight residual -122.00 -132.33 10.33 0 2.50e+00 1.60e-01 1.71e+01 dihedral pdb=" CA GLY H 105 " pdb=" C GLY H 105 " pdb=" N GLU H 106 " pdb=" CA GLU H 106 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.89 106.60 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 2330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 447 0.070 - 0.139: 136 0.139 - 0.209: 29 0.209 - 0.278: 4 0.278 - 0.348: 10 Chirality restraints: 626 Sorted by residual: chirality pdb=" C1 BMA B 3 " pdb=" O4 NAG B 2 " pdb=" C2 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-02 2.50e+03 3.71e+01 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 -2.47 0.07 2.00e-02 2.50e+03 1.13e+01 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.62 0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 623 not shown) Planarity restraints: 659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 96 " 0.034 2.00e-02 2.50e+03 1.80e-02 6.45e+00 pdb=" CG TYR H 96 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR H 96 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR H 96 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR H 96 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR H 96 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR H 96 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 96 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 105 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C GLY H 105 " -0.041 2.00e-02 2.50e+03 pdb=" O GLY H 105 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU H 106 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1303 " -0.026 2.00e-02 2.50e+03 2.12e-02 5.61e+00 pdb=" C7 NAG A1303 " -0.003 2.00e-02 2.50e+03 pdb=" C8 NAG A1303 " -0.016 2.00e-02 2.50e+03 pdb=" N2 NAG A1303 " 0.035 2.00e-02 2.50e+03 pdb=" O7 NAG A1303 " 0.010 2.00e-02 2.50e+03 ... (remaining 656 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 2165 3.03 - 3.50: 3156 3.50 - 3.97: 6049 3.97 - 4.43: 6775 4.43 - 4.90: 11258 Nonbonded interactions: 29403 Sorted by model distance: nonbonded pdb=" ND1 HIS A 146 " pdb=" N LYS A 147 " model vdw 2.563 3.200 nonbonded pdb=" O PRO H 14 " pdb=" OG1 THR H 15 " model vdw 2.593 3.040 nonbonded pdb=" N ASN A 148 " pdb=" O ASN A 148 " model vdw 2.603 2.496 nonbonded pdb=" N THR H 10 " pdb=" N LEU H 11 " model vdw 2.608 2.560 nonbonded pdb=" OD1 ASP H 113 " pdb=" N VAL H 114 " model vdw 2.625 3.120 ... (remaining 29398 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 group one per residue 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: 5.540 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.250 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 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 : 0.010 0.054 3834 Z= 0.681 Angle : 1.308 7.472 5248 Z= 0.869 Chirality : 0.080 0.348 626 Planarity : 0.005 0.024 652 Dihedral : 11.425 106.597 1406 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.38), residues: 474 helix: 0.56 (1.75), residues: 11 sheet: 1.23 (0.35), residues: 207 loop : -0.24 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP L 90 HIS 0.002 0.001 HIS A 207 PHE 0.014 0.003 PHE A 220 TYR 0.034 0.005 TYR H 96 ARG 0.001 0.000 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.412 Fit side-chains REVERT: L 36 GLN cc_start: 0.8889 (tt0) cc_final: 0.8628 (tt0) REVERT: H 3 THR cc_start: 0.7351 (t) cc_final: 0.7149 (m) REVERT: H 62 SER cc_start: 0.8440 (t) cc_final: 0.8090 (p) REVERT: H 124 SER cc_start: 0.6718 (p) cc_final: 0.6437 (t) REVERT: A 154 LYS cc_start: 0.8401 (ttpt) cc_final: 0.8074 (ttpp) REVERT: A 258 TRP cc_start: 0.7458 (m-90) cc_final: 0.7186 (m-90) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1852 time to fit residues: 19.7780 Evaluate side-chains 63 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.0470 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 49 GLN H 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.186913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.155501 restraints weight = 4060.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.156506 restraints weight = 2990.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.158261 restraints weight = 3060.853| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3834 Z= 0.242 Angle : 0.605 6.341 5248 Z= 0.316 Chirality : 0.047 0.154 626 Planarity : 0.005 0.051 652 Dihedral : 8.101 60.530 704 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.48 % Favored : 98.31 % Rotamer: Outliers : 1.47 % Allowed : 7.35 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.39), residues: 474 helix: 1.69 (1.55), residues: 11 sheet: 1.38 (0.38), residues: 191 loop : -0.07 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 103 HIS 0.002 0.001 HIS A 245 PHE 0.015 0.002 PHE A 55 TYR 0.026 0.002 TYR L 48 ARG 0.004 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.436 Fit side-chains REVERT: L 53 ARG cc_start: 0.8081 (mtm-85) cc_final: 0.7879 (mtm110) REVERT: A 108 THR cc_start: 0.8650 (p) cc_final: 0.8228 (t) REVERT: A 138 ASP cc_start: 0.7995 (t0) cc_final: 0.7760 (t0) REVERT: A 154 LYS cc_start: 0.8628 (ttpt) cc_final: 0.8281 (ttpp) REVERT: A 258 TRP cc_start: 0.8209 (m-90) cc_final: 0.7746 (m-90) outliers start: 5 outliers final: 2 residues processed: 69 average time/residue: 0.1803 time to fit residues: 15.2880 Evaluate side-chains 67 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain H residue 83 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.184823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.153224 restraints weight = 4162.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.156846 restraints weight = 3165.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.158667 restraints weight = 2484.238| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3834 Z= 0.353 Angle : 0.625 6.237 5248 Z= 0.325 Chirality : 0.046 0.175 626 Planarity : 0.005 0.054 652 Dihedral : 6.005 38.306 704 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.12 % Allowed : 7.35 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.38), residues: 474 helix: 2.88 (1.63), residues: 11 sheet: 1.07 (0.37), residues: 191 loop : -0.39 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 49 HIS 0.003 0.001 HIS A 245 PHE 0.014 0.002 PHE A 238 TYR 0.017 0.002 TYR L 48 ARG 0.003 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8337 (ttpp) outliers start: 14 outliers final: 9 residues processed: 71 average time/residue: 0.2375 time to fit residues: 19.9567 Evaluate side-chains 65 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 284 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 9 optimal weight: 0.2980 chunk 11 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 88 GLN A 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.162914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.131514 restraints weight = 4274.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132706 restraints weight = 3543.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.134016 restraints weight = 3563.974| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3834 Z= 0.185 Angle : 0.544 7.504 5248 Z= 0.279 Chirality : 0.045 0.159 626 Planarity : 0.004 0.046 652 Dihedral : 5.218 35.961 704 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.35 % Allowed : 10.29 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.43 (0.38), residues: 474 helix: 3.13 (1.65), residues: 11 sheet: 1.04 (0.37), residues: 190 loop : -0.38 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 103 HIS 0.003 0.001 HIS A 207 PHE 0.011 0.001 PHE A 55 TYR 0.017 0.001 TYR L 48 ARG 0.009 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8325 (ttpp) REVERT: A 258 TRP cc_start: 0.8000 (m-90) cc_final: 0.7588 (m-90) outliers start: 8 outliers final: 6 residues processed: 65 average time/residue: 0.2021 time to fit residues: 15.6986 Evaluate side-chains 62 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 0.0050 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.161716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.130042 restraints weight = 4376.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.131576 restraints weight = 3491.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.132899 restraints weight = 3481.125| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3834 Z= 0.230 Angle : 0.542 7.050 5248 Z= 0.279 Chirality : 0.045 0.165 626 Planarity : 0.004 0.045 652 Dihedral : 5.105 36.717 704 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.12 % Allowed : 7.94 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.38), residues: 474 helix: 3.29 (1.65), residues: 11 sheet: 0.95 (0.36), residues: 190 loop : -0.45 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 103 HIS 0.002 0.001 HIS A 207 PHE 0.011 0.001 PHE A 238 TYR 0.015 0.001 TYR L 48 ARG 0.009 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8676 (ttpt) cc_final: 0.8342 (ttpp) REVERT: A 258 TRP cc_start: 0.7976 (m-90) cc_final: 0.7493 (m-90) outliers start: 14 outliers final: 11 residues processed: 64 average time/residue: 0.1924 time to fit residues: 14.9486 Evaluate side-chains 64 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 45 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.163181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.131519 restraints weight = 4269.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.132634 restraints weight = 3465.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.134287 restraints weight = 3476.620| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3834 Z= 0.307 Angle : 0.578 7.843 5248 Z= 0.297 Chirality : 0.046 0.163 626 Planarity : 0.004 0.045 652 Dihedral : 5.311 38.112 704 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.71 % Allowed : 8.53 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.39), residues: 474 helix: 3.27 (1.64), residues: 11 sheet: 0.69 (0.36), residues: 191 loop : -0.38 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 115 HIS 0.002 0.001 HIS A 245 PHE 0.013 0.002 PHE A 238 TYR 0.016 0.002 TYR A 265 ARG 0.005 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8356 (ttpp) REVERT: A 258 TRP cc_start: 0.8168 (m-90) cc_final: 0.7650 (m-90) outliers start: 16 outliers final: 13 residues processed: 60 average time/residue: 0.2125 time to fit residues: 15.2826 Evaluate side-chains 63 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 9 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.157463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.126472 restraints weight = 4375.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.125739 restraints weight = 4163.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.127338 restraints weight = 4463.817| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3834 Z= 0.211 Angle : 0.536 7.040 5248 Z= 0.275 Chirality : 0.045 0.159 626 Planarity : 0.004 0.042 652 Dihedral : 5.095 36.866 704 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.53 % Allowed : 9.12 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.21 (0.39), residues: 474 helix: 3.19 (1.66), residues: 11 sheet: 0.69 (0.36), residues: 191 loop : -0.37 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 103 HIS 0.003 0.001 HIS A 207 PHE 0.016 0.002 PHE A 55 TYR 0.015 0.001 TYR A 265 ARG 0.009 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8714 (ttpt) cc_final: 0.8325 (ttpp) outliers start: 12 outliers final: 11 residues processed: 59 average time/residue: 0.1992 time to fit residues: 14.1349 Evaluate side-chains 61 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 11 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.156043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.124809 restraints weight = 4417.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.123979 restraints weight = 4402.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.126915 restraints weight = 4917.662| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3834 Z= 0.279 Angle : 0.581 7.618 5248 Z= 0.294 Chirality : 0.046 0.165 626 Planarity : 0.004 0.046 652 Dihedral : 5.201 37.688 704 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.12 % Allowed : 8.82 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.06 (0.39), residues: 474 helix: 3.61 (1.71), residues: 11 sheet: 0.54 (0.36), residues: 191 loop : -0.46 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 115 HIS 0.003 0.001 HIS A 245 PHE 0.018 0.002 PHE A 55 TYR 0.015 0.001 TYR A 265 ARG 0.006 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8350 (ttpp) outliers start: 14 outliers final: 12 residues processed: 61 average time/residue: 0.2107 time to fit residues: 15.4034 Evaluate side-chains 64 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.157816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.127355 restraints weight = 4313.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.127100 restraints weight = 4456.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.129020 restraints weight = 4303.190| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3834 Z= 0.246 Angle : 0.558 7.297 5248 Z= 0.287 Chirality : 0.045 0.158 626 Planarity : 0.004 0.054 652 Dihedral : 5.168 37.552 704 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.82 % Allowed : 9.71 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.39), residues: 474 helix: 3.20 (1.68), residues: 11 sheet: 0.53 (0.36), residues: 191 loop : -0.51 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 115 HIS 0.004 0.001 HIS A 245 PHE 0.020 0.002 PHE A 55 TYR 0.015 0.001 TYR A 265 ARG 0.004 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8332 (ttpp) outliers start: 13 outliers final: 12 residues processed: 59 average time/residue: 0.2041 time to fit residues: 14.5077 Evaluate side-chains 63 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 0.0470 chunk 31 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.159181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127928 restraints weight = 4320.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.128679 restraints weight = 3617.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.130045 restraints weight = 3821.485| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3834 Z= 0.341 Angle : 0.623 8.943 5248 Z= 0.316 Chirality : 0.047 0.161 626 Planarity : 0.005 0.057 652 Dihedral : 5.495 39.281 704 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.53 % Allowed : 11.18 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.38), residues: 474 helix: 3.60 (1.70), residues: 11 sheet: 0.56 (0.34), residues: 211 loop : -0.98 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 115 HIS 0.004 0.001 HIS A 245 PHE 0.017 0.002 PHE A 55 TYR 0.015 0.002 TYR H 96 ARG 0.004 0.001 ARG A 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: L 60 ARG cc_start: 0.7940 (mtm180) cc_final: 0.7474 (mtm180) REVERT: A 15 CYS cc_start: 0.6518 (m) cc_final: 0.6253 (m) REVERT: A 154 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8349 (ttpp) outliers start: 12 outliers final: 12 residues processed: 62 average time/residue: 0.2004 time to fit residues: 14.8901 Evaluate side-chains 66 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.178580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.147235 restraints weight = 4232.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.147596 restraints weight = 3077.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.149139 restraints weight = 3277.346| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3834 Z= 0.287 Angle : 0.599 7.582 5248 Z= 0.305 Chirality : 0.046 0.179 626 Planarity : 0.005 0.058 652 Dihedral : 5.395 38.524 704 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.82 % Allowed : 11.47 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.38), residues: 474 helix: 3.53 (1.73), residues: 11 sheet: 0.46 (0.36), residues: 186 loop : -0.86 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 115 HIS 0.003 0.001 HIS A 245 PHE 0.019 0.002 PHE A 55 TYR 0.014 0.001 TYR L 48 ARG 0.006 0.001 ARG A 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1808.90 seconds wall clock time: 32 minutes 59.03 seconds (1979.03 seconds total)