Starting phenix.real_space_refine on Wed Mar 5 22:09:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sof_25269/03_2025/7sof_25269.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sof_25269/03_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_25269/03_2025/7sof_25269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sof_25269/03_2025/7sof_25269.map" model { file = "/net/cci-nas-00/data/ceres_data/7sof_25269/03_2025/7sof_25269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sof_25269/03_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-5624/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: 5.00, per 1000 atoms: 1.34 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: 1.12 Conformation dependent library (CDL) restraints added in 468.0 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: 0.48 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: 1.00 Time building geometry restraints manager: 1.32 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: 7.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.320 Find NCS groups from input model: 0.040 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.490 ------------------------------------------------------------------------------- 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 : 0.383 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: 0.1863 time to fit residues: 20.0312 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 : 0.381 ------------------------------------------------------------------------------- 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 = 0.156504 restraints weight = 2990.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.158260 restraints weight = 3061.158| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 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 : 0.412 Fit side-chains REVERT: L 53 ARG cc_start: 0.8070 (mtm-85) cc_final: 0.7867 (mtm110) REVERT: A 108 THR cc_start: 0.8634 (p) cc_final: 0.8214 (t) REVERT: A 138 ASP cc_start: 0.7993 (t0) cc_final: 0.7761 (t0) REVERT: A 154 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8280 (ttpp) REVERT: A 258 TRP cc_start: 0.8194 (m-90) cc_final: 0.7739 (m-90) outliers start: 5 outliers final: 2 residues processed: 69 average time/residue: 0.1969 time to fit residues: 16.5348 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 : 0.427 ------------------------------------------------------------------------------- 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: 0.9980 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.184838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.153120 restraints weight = 4165.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.155900 restraints weight = 3180.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.156678 restraints weight = 3209.277| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3834 Z= 0.364 Angle : 0.624 6.134 5248 Z= 0.325 Chirality : 0.046 0.160 626 Planarity : 0.005 0.054 652 Dihedral : 6.113 38.072 704 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.12 % Allowed : 7.06 % Favored : 88.82 % 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: 2.85 (1.62), residues: 11 sheet: 1.06 (0.37), residues: 191 loop : -0.39 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 49 HIS 0.004 0.001 HIS A 245 PHE 0.014 0.002 PHE A 238 TYR 0.017 0.002 TYR L 48 ARG 0.002 0.000 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 78 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8348 (ttpp) outliers start: 14 outliers final: 10 residues processed: 72 average time/residue: 0.2258 time to fit residues: 19.1167 Evaluate side-chains 66 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 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 284 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.161523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.129864 restraints weight = 4296.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.130473 restraints weight = 3542.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.132301 restraints weight = 3653.670| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3231 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= 0.247 Angle : 0.565 7.837 5248 Z= 0.291 Chirality : 0.046 0.160 626 Planarity : 0.004 0.047 652 Dihedral : 5.381 36.937 704 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.24 % Allowed : 8.82 % 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: 0.27 (0.38), residues: 474 helix: 3.15 (1.65), residues: 11 sheet: 0.92 (0.36), residues: 190 loop : -0.48 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 103 HIS 0.002 0.001 HIS A 245 PHE 0.012 0.002 PHE A 238 TYR 0.017 0.002 TYR L 48 ARG 0.012 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 67 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8326 (ttpp) REVERT: A 258 TRP cc_start: 0.8008 (m-90) cc_final: 0.7605 (m-90) outliers start: 11 outliers final: 9 residues processed: 64 average time/residue: 0.2195 time to fit residues: 16.6879 Evaluate side-chains 61 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 34 optimal weight: 0.4980 chunk 25 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.159734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.125808 restraints weight = 4413.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.126873 restraints weight = 3544.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.128562 restraints weight = 3585.421| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3570 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= 0.305 Angle : 0.584 8.845 5248 Z= 0.300 Chirality : 0.045 0.164 626 Planarity : 0.004 0.047 652 Dihedral : 5.433 38.509 704 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.12 % Allowed : 7.65 % Favored : 88.24 % 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 (0.38), residues: 474 helix: 3.22 (1.63), residues: 11 sheet: 0.74 (0.36), residues: 191 loop : -0.41 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 115 HIS 0.003 0.001 HIS A 245 PHE 0.013 0.002 PHE A 238 TYR 0.015 0.002 TYR A 265 ARG 0.007 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 65 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8357 (ttpp) REVERT: A 258 TRP cc_start: 0.8098 (m-90) cc_final: 0.7622 (m-90) outliers start: 14 outliers final: 11 residues processed: 60 average time/residue: 0.1958 time to fit residues: 14.2308 Evaluate side-chains 62 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 210 ILE 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: 2.9990 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 chunk 11 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.175778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143647 restraints weight = 4286.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.145920 restraints weight = 3375.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.147452 restraints weight = 3045.081| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3705 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= 0.200 Angle : 0.543 7.969 5248 Z= 0.278 Chirality : 0.044 0.160 626 Planarity : 0.004 0.043 652 Dihedral : 5.168 37.143 704 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.53 % Allowed : 9.41 % 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: 0.24 (0.39), residues: 474 helix: 3.25 (1.64), residues: 11 sheet: 0.73 (0.36), residues: 191 loop : -0.36 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 103 HIS 0.004 0.001 HIS A 207 PHE 0.012 0.001 PHE A 55 TYR 0.016 0.001 TYR A 265 ARG 0.006 0.001 ARG A 246 *********************** 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 61 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8320 (ttpp) REVERT: A 258 TRP cc_start: 0.8061 (m-90) cc_final: 0.7612 (m-90) outliers start: 12 outliers final: 9 residues processed: 57 average time/residue: 0.2159 time to fit residues: 14.7708 Evaluate side-chains 56 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 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 131 CYS 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: 0.1980 chunk 36 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.0770 chunk 45 optimal weight: 0.6980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.158706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.127587 restraints weight = 4354.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.128279 restraints weight = 4331.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.130561 restraints weight = 4807.415| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3821 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= 0.201 Angle : 0.533 7.479 5248 Z= 0.272 Chirality : 0.044 0.162 626 Planarity : 0.004 0.043 652 Dihedral : 5.021 36.779 704 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.53 % Allowed : 8.82 % Favored : 87.65 % 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: 0.23 (0.39), residues: 474 helix: 3.18 (1.65), residues: 11 sheet: 0.74 (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 0.015 0.001 PHE A 55 TYR 0.015 0.001 TYR A 265 ARG 0.007 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 64 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8328 (ttpp) outliers start: 12 outliers final: 10 residues processed: 61 average time/residue: 0.2065 time to fit residues: 15.1035 Evaluate side-chains 60 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 124 THR Chi-restraints excluded: chain A residue 131 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 40 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.164693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.133257 restraints weight = 4334.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.136387 restraints weight = 3935.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.136871 restraints weight = 4001.993| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3834 Z= 0.274 Angle : 0.578 8.038 5248 Z= 0.293 Chirality : 0.045 0.163 626 Planarity : 0.004 0.046 652 Dihedral : 5.154 37.779 704 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.53 % Allowed : 10.88 % Favored : 85.59 % 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: 0.10 (0.39), residues: 474 helix: 3.50 (1.69), residues: 11 sheet: 0.63 (0.36), residues: 191 loop : -0.47 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 115 HIS 0.002 0.001 HIS A 245 PHE 0.019 0.002 PHE A 55 TYR 0.016 0.001 TYR A 265 ARG 0.007 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 61 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8667 (ttpt) cc_final: 0.8330 (ttpp) outliers start: 12 outliers final: 11 residues processed: 57 average time/residue: 0.2119 time to fit residues: 14.3717 Evaluate side-chains 60 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.0570 chunk 45 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 0.0050 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.0770 chunk 41 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 overall best weight: 0.1470 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.160138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.130473 restraints weight = 4276.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.130275 restraints weight = 4072.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.132249 restraints weight = 4886.529| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3834 Z= 0.137 Angle : 0.513 6.861 5248 Z= 0.260 Chirality : 0.044 0.159 626 Planarity : 0.004 0.044 652 Dihedral : 4.741 34.844 704 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.35 % Allowed : 12.06 % Favored : 85.59 % 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: 0.22 (0.39), residues: 474 helix: 3.05 (1.68), residues: 11 sheet: 0.80 (0.37), residues: 191 loop : -0.44 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 103 HIS 0.005 0.001 HIS A 207 PHE 0.022 0.001 PHE A 55 TYR 0.014 0.001 TYR L 48 ARG 0.003 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 59 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8286 (ttpp) outliers start: 8 outliers final: 7 residues processed: 56 average time/residue: 0.2088 time to fit residues: 14.1288 Evaluate side-chains 57 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 24 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 131 CYS 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: 1.9990 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.156009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.123235 restraints weight = 4397.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.123441 restraints weight = 3533.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.125029 restraints weight = 3761.478| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 3834 Z= 0.467 Angle : 0.650 8.733 5248 Z= 0.331 Chirality : 0.048 0.168 626 Planarity : 0.005 0.057 652 Dihedral : 5.481 39.507 704 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.65 % Allowed : 12.06 % 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: -0.18 (0.39), residues: 474 helix: 3.41 (1.67), residues: 11 sheet: 0.49 (0.34), residues: 216 loop : -0.83 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 258 HIS 0.003 0.001 HIS A 245 PHE 0.017 0.003 PHE A 55 TYR 0.017 0.002 TYR H 96 ARG 0.005 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 59 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8348 (ttpp) outliers start: 9 outliers final: 8 residues processed: 57 average time/residue: 0.2163 time to fit residues: 14.7438 Evaluate side-chains 57 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 88 GLN A 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.160003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.127987 restraints weight = 4296.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.129787 restraints weight = 3817.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.130752 restraints weight = 3787.701| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3834 Z= 0.221 Angle : 0.575 9.169 5248 Z= 0.287 Chirality : 0.046 0.169 626 Planarity : 0.004 0.055 652 Dihedral : 5.207 37.631 704 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.35 % Allowed : 13.24 % Favored : 84.41 % 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 (0.38), residues: 474 helix: 3.56 (1.73), residues: 11 sheet: 0.56 (0.36), residues: 186 loop : -0.80 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 115 HIS 0.003 0.001 HIS A 207 PHE 0.021 0.002 PHE A 55 TYR 0.014 0.001 TYR L 48 ARG 0.003 0.001 ARG A 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1907.41 seconds wall clock time: 33 minutes 53.57 seconds (2033.57 seconds total)