Starting phenix.real_space_refine on Wed Mar 5 23:56:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dm4_27526/03_2025/8dm4_27526.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm4_27526/03_2025/8dm4_27526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dm4_27526/03_2025/8dm4_27526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm4_27526/03_2025/8dm4_27526.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm4_27526/03_2025/8dm4_27526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm4_27526/03_2025/8dm4_27526.cif" } resolution = 2.45 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2563 2.51 5 N 653 2.21 5 O 784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4018 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2096 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 11, 'TRANS': 245} Chain breaks: 3 Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 976 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "L" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.52, per 1000 atoms: 0.88 Number of scatterers: 4018 At special positions: 0 Unit cell: (101, 61, 97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 784 8.00 N 653 7.00 C 2563 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 113 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 404.0 milliseconds 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 924 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 10 sheets defined 1.6% alpha, 47.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 106 through 110 removed outlier: 4.019A pdb=" N THR H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 30 removed outlier: 7.905A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.872A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.766A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25 removed outlier: 3.711A pdb=" N VAL H 37 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU H 102 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.409A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET H 53 " --> pdb=" O GLY H 69 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP H 55 " --> pdb=" O MET H 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.409A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 121 through 123 Processing sheet with id=AA9, first strand: chain 'L' and resid 24 through 27 Processing sheet with id=AB1, first strand: chain 'L' and resid 30 through 32 removed outlier: 4.284A pdb=" N ASP L 130 " --> pdb=" O SER L 31 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN L 62 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU L 71 " --> pdb=" O GLN L 62 " (cutoff:3.500A) 159 hydrogen bonds defined for protein. 399 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: 0.92 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1249 1.34 - 1.46: 1064 1.46 - 1.58: 1777 1.58 - 1.70: 0 1.70 - 1.82: 27 Bond restraints: 4117 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.76e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 ... (remaining 4112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 5350 2.08 - 4.16: 220 4.16 - 6.23: 18 6.23 - 8.31: 3 8.31 - 10.39: 3 Bond angle restraints: 5594 Sorted by residual: angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 121.54 131.93 -10.39 1.91e+00 2.74e-01 2.96e+01 angle pdb=" C LEU A 141 " pdb=" N ASP A 142 " pdb=" CA ASP A 142 " ideal model delta sigma weight residual 122.93 118.21 4.72 1.45e+00 4.76e-01 1.06e+01 angle pdb=" CA CYS A 131 " pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " ideal model delta sigma weight residual 114.40 121.47 -7.07 2.30e+00 1.89e-01 9.45e+00 angle pdb=" CA ASP A 198 " pdb=" CB ASP A 198 " pdb=" CG ASP A 198 " ideal model delta sigma weight residual 112.60 115.65 -3.05 1.00e+00 1.00e+00 9.29e+00 angle pdb=" N THR L 34 " pdb=" CA THR L 34 " pdb=" C THR L 34 " ideal model delta sigma weight residual 110.35 106.53 3.82 1.38e+00 5.25e-01 7.64e+00 ... (remaining 5589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 2302 17.82 - 35.63: 148 35.63 - 53.45: 27 53.45 - 71.27: 13 71.27 - 89.09: 4 Dihedral angle restraints: 2494 sinusoidal: 1051 harmonic: 1443 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -51.05 -34.95 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CA VAL H 24 " pdb=" C VAL H 24 " pdb=" N GLU H 25 " pdb=" CA GLU H 25 " ideal model delta harmonic sigma weight residual -180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA VAL A 90 " pdb=" C VAL A 90 " pdb=" N TYR A 91 " pdb=" CA TYR A 91 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 2491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 424 0.051 - 0.102: 159 0.102 - 0.152: 44 0.152 - 0.203: 4 0.203 - 0.254: 3 Chirality restraints: 634 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB THR L 56 " pdb=" CA THR L 56 " pdb=" OG1 THR L 56 " pdb=" CG2 THR L 56 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ASP A 198 " pdb=" N ASP A 198 " pdb=" C ASP A 198 " pdb=" CB ASP A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 631 not shown) Planarity restraints: 711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 27 " -0.048 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO L 28 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO L 28 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 28 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 273 " -0.237 9.50e-02 1.11e+02 1.07e-01 7.74e+00 pdb=" NE ARG A 273 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 273 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 273 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 273 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 210 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.57e+00 pdb=" C ILE A 210 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE A 210 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN A 211 " -0.016 2.00e-02 2.50e+03 ... (remaining 708 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 865 2.79 - 3.32: 3144 3.32 - 3.84: 6623 3.84 - 4.37: 7758 4.37 - 4.90: 13925 Nonbonded interactions: 32315 Sorted by model distance: nonbonded pdb=" OG SER L 90 " pdb=" OG1 THR L 97 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP H 109 " pdb=" OH TYR H 113 " model vdw 2.279 3.040 nonbonded pdb=" O SER L 45 " pdb=" OG1 THR L 94 " model vdw 2.307 3.040 nonbonded pdb=" OG SER A 247 " pdb=" OH TYR H 46 " model vdw 2.365 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.368 3.040 ... (remaining 32310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.540 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.030 Find NCS groups from input model: 0.040 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.006 0.045 4117 Z= 0.383 Angle : 0.904 10.390 5594 Z= 0.484 Chirality : 0.057 0.254 634 Planarity : 0.008 0.107 706 Dihedral : 13.358 89.087 1558 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.23 % Allowed : 0.92 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.05 (0.37), residues: 485 helix: None (None), residues: 0 sheet: 0.55 (0.34), residues: 230 loop : -0.55 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP H 66 HIS 0.003 0.001 HIS A 69 PHE 0.025 0.003 PHE A 175 TYR 0.032 0.003 TYR A 145 ARG 0.016 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.385 Fit side-chains REVERT: A 80 ASP cc_start: 0.6299 (t0) cc_final: 0.6086 (t0) REVERT: A 100 ILE cc_start: 0.8408 (mp) cc_final: 0.8064 (tp) REVERT: H 52 SER cc_start: 0.7982 (m) cc_final: 0.7705 (p) REVERT: H 65 GLU cc_start: 0.6701 (pt0) cc_final: 0.6168 (pm20) REVERT: H 107 SER cc_start: 0.7089 (m) cc_final: 0.6425 (t) REVERT: H 131 TYR cc_start: 0.8106 (t80) cc_final: 0.7868 (t80) REVERT: H 134 MET cc_start: 0.8612 (mtm) cc_final: 0.8405 (mpp) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 1.0695 time to fit residues: 111.2443 Evaluate side-chains 72 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 30 ASN L 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.144334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.100357 restraints weight = 5622.689| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.23 r_work: 0.3209 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4117 Z= 0.229 Angle : 0.598 8.442 5594 Z= 0.312 Chirality : 0.045 0.214 634 Planarity : 0.004 0.055 706 Dihedral : 7.413 57.756 665 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.75 % Allowed : 10.76 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.28 (0.37), residues: 485 helix: None (None), residues: 0 sheet: 0.76 (0.35), residues: 215 loop : -0.25 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 66 HIS 0.003 0.001 HIS A 245 PHE 0.018 0.002 PHE A 175 TYR 0.014 0.002 TYR A 28 ARG 0.006 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.442 Fit side-chains REVERT: A 80 ASP cc_start: 0.6620 (t0) cc_final: 0.6164 (t0) REVERT: A 115 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8206 (mm110) REVERT: A 169 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: A 173 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8269 (mp10) REVERT: H 65 GLU cc_start: 0.7384 (pt0) cc_final: 0.6722 (pm20) REVERT: H 100 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6671 (ttp) REVERT: H 109 ASP cc_start: 0.7164 (t0) cc_final: 0.6914 (t0) REVERT: H 131 TYR cc_start: 0.8153 (t80) cc_final: 0.7896 (t80) REVERT: H 134 MET cc_start: 0.8768 (mtm) cc_final: 0.8457 (mpp) REVERT: L 132 LYS cc_start: 0.7608 (mmmm) cc_final: 0.7387 (mmmm) outliers start: 12 outliers final: 6 residues processed: 71 average time/residue: 1.3858 time to fit residues: 101.5820 Evaluate side-chains 74 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 0.0570 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS L 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.143585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.099846 restraints weight = 5578.265| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.21 r_work: 0.3200 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4117 Z= 0.228 Angle : 0.571 5.600 5594 Z= 0.301 Chirality : 0.045 0.200 634 Planarity : 0.004 0.045 706 Dihedral : 6.756 55.271 665 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.97 % Allowed : 12.36 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.41 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.84 (0.35), residues: 213 loop : -0.14 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.006 0.001 HIS A 245 PHE 0.019 0.002 PHE A 175 TYR 0.013 0.002 TYR A 28 ARG 0.004 0.001 ARG L 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.651 Fit side-chains REVERT: A 14 GLN cc_start: 0.7688 (mt0) cc_final: 0.7449 (mt0) REVERT: A 80 ASP cc_start: 0.6656 (t0) cc_final: 0.6210 (t0) REVERT: A 137 ASN cc_start: 0.8469 (m110) cc_final: 0.7992 (t0) REVERT: A 169 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7784 (tm-30) REVERT: A 173 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8250 (mp10) REVERT: A 177 MET cc_start: 0.7999 (pmt) cc_final: 0.7740 (pmt) REVERT: H 65 GLU cc_start: 0.7463 (pt0) cc_final: 0.7136 (pt0) REVERT: H 78 MET cc_start: 0.7021 (tpp) cc_final: 0.6110 (tpt) REVERT: H 100 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.7000 (tmm) REVERT: H 109 ASP cc_start: 0.7268 (t0) cc_final: 0.7052 (t0) REVERT: H 131 TYR cc_start: 0.8222 (t80) cc_final: 0.7950 (t80) REVERT: H 134 MET cc_start: 0.8752 (mtm) cc_final: 0.8478 (mpp) REVERT: L 117 THR cc_start: 0.8444 (p) cc_final: 0.8195 (p) REVERT: L 132 LYS cc_start: 0.7617 (mmmm) cc_final: 0.7364 (mmmm) outliers start: 13 outliers final: 5 residues processed: 72 average time/residue: 1.8371 time to fit residues: 137.2964 Evaluate side-chains 72 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN L 55 ASN L 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.140689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.097402 restraints weight = 5504.833| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.15 r_work: 0.3161 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 4117 Z= 0.359 Angle : 0.624 6.590 5594 Z= 0.327 Chirality : 0.047 0.207 634 Planarity : 0.004 0.043 706 Dihedral : 6.617 50.213 665 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.20 % Allowed : 13.27 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 485 helix: None (None), residues: 0 sheet: 0.80 (0.35), residues: 212 loop : -0.22 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 66 HIS 0.005 0.001 HIS A 245 PHE 0.028 0.002 PHE A 175 TYR 0.016 0.002 TYR A 28 ARG 0.004 0.001 ARG L 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.468 Fit side-chains REVERT: A 14 GLN cc_start: 0.7747 (mt0) cc_final: 0.7520 (mt0) REVERT: A 80 ASP cc_start: 0.6733 (t0) cc_final: 0.6287 (t0) REVERT: A 137 ASN cc_start: 0.8489 (m110) cc_final: 0.8067 (t0) REVERT: A 169 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: A 173 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8291 (mp10) REVERT: H 65 GLU cc_start: 0.7542 (pt0) cc_final: 0.7215 (pt0) REVERT: H 78 MET cc_start: 0.7074 (tpp) cc_final: 0.6163 (tpt) REVERT: H 100 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7272 (ttp) REVERT: H 134 MET cc_start: 0.8796 (mtm) cc_final: 0.8422 (mpp) REVERT: H 135 ASP cc_start: 0.8367 (m-30) cc_final: 0.8157 (m-30) outliers start: 14 outliers final: 6 residues processed: 72 average time/residue: 1.3578 time to fit residues: 101.3020 Evaluate side-chains 71 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 55 ASN L 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.141413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.097748 restraints weight = 5749.071| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.22 r_work: 0.3176 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4117 Z= 0.297 Angle : 0.595 6.017 5594 Z= 0.315 Chirality : 0.046 0.202 634 Planarity : 0.004 0.041 706 Dihedral : 6.333 50.959 665 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.52 % Allowed : 15.33 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.38 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.87 (0.35), residues: 212 loop : -0.21 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 66 HIS 0.005 0.001 HIS A 245 PHE 0.024 0.002 PHE A 175 TYR 0.014 0.002 TYR A 28 ARG 0.003 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.450 Fit side-chains REVERT: A 80 ASP cc_start: 0.6760 (t0) cc_final: 0.6316 (t0) REVERT: A 169 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7810 (tm-30) REVERT: A 173 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8273 (mp10) REVERT: H 48 LEU cc_start: 0.8174 (tp) cc_final: 0.7959 (mt) REVERT: H 65 GLU cc_start: 0.7548 (pt0) cc_final: 0.7163 (pt0) REVERT: H 78 MET cc_start: 0.7034 (tpp) cc_final: 0.6125 (tpt) REVERT: H 100 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7254 (ttp) REVERT: H 134 MET cc_start: 0.8774 (mtm) cc_final: 0.8522 (mpp) outliers start: 11 outliers final: 5 residues processed: 71 average time/residue: 1.2132 time to fit residues: 89.1835 Evaluate side-chains 73 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 38 optimal weight: 0.0670 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 GLN L 55 ASN L 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.142871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.099460 restraints weight = 5561.373| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.25 r_work: 0.3196 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4117 Z= 0.194 Angle : 0.559 5.144 5594 Z= 0.297 Chirality : 0.045 0.191 634 Planarity : 0.004 0.040 706 Dihedral : 5.888 51.425 665 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.29 % Allowed : 16.25 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.47 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.94 (0.35), residues: 212 loop : -0.16 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.006 0.001 HIS A 245 PHE 0.016 0.001 PHE A 175 TYR 0.011 0.001 TYR A 28 ARG 0.005 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.435 Fit side-chains REVERT: A 14 GLN cc_start: 0.7766 (mt0) cc_final: 0.7408 (mt0) REVERT: A 80 ASP cc_start: 0.6743 (t0) cc_final: 0.6279 (t0) REVERT: A 137 ASN cc_start: 0.8455 (m110) cc_final: 0.7915 (t0) REVERT: A 169 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7784 (tm-30) REVERT: A 173 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8172 (mp10) REVERT: H 48 LEU cc_start: 0.7981 (tp) cc_final: 0.7733 (mt) REVERT: H 53 MET cc_start: 0.7916 (tpp) cc_final: 0.7591 (tpt) REVERT: H 65 GLU cc_start: 0.7483 (pt0) cc_final: 0.7067 (pt0) REVERT: H 78 MET cc_start: 0.6937 (tpp) cc_final: 0.6036 (tpt) REVERT: H 100 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.7055 (ttp) REVERT: H 109 ASP cc_start: 0.7390 (t0) cc_final: 0.7157 (t0) outliers start: 10 outliers final: 4 residues processed: 70 average time/residue: 1.3308 time to fit residues: 96.4436 Evaluate side-chains 71 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 GLN L 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.142038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.098745 restraints weight = 5632.940| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.25 r_work: 0.3181 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4117 Z= 0.251 Angle : 0.576 5.311 5594 Z= 0.305 Chirality : 0.045 0.194 634 Planarity : 0.004 0.040 706 Dihedral : 5.778 50.941 665 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.29 % Allowed : 18.08 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.42 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.88 (0.35), residues: 214 loop : -0.18 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 66 HIS 0.006 0.001 HIS A 245 PHE 0.020 0.002 PHE A 175 TYR 0.013 0.001 TYR A 28 ARG 0.005 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.491 Fit side-chains REVERT: A 14 GLN cc_start: 0.7731 (mt0) cc_final: 0.7359 (mt0) REVERT: A 80 ASP cc_start: 0.6753 (t0) cc_final: 0.6278 (t0) REVERT: A 131 CYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7837 (m) REVERT: A 137 ASN cc_start: 0.8445 (m110) cc_final: 0.7926 (t0) REVERT: A 169 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7774 (tm-30) REVERT: A 173 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8186 (mp10) REVERT: A 177 MET cc_start: 0.7967 (pmt) cc_final: 0.7757 (pmt) REVERT: H 65 GLU cc_start: 0.7455 (pt0) cc_final: 0.7021 (pt0) REVERT: H 100 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7093 (ttp) outliers start: 10 outliers final: 5 residues processed: 69 average time/residue: 1.4415 time to fit residues: 103.0959 Evaluate side-chains 74 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 2 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 0.0870 chunk 25 optimal weight: 3.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 GLN L 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.143264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.100280 restraints weight = 5522.893| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.25 r_work: 0.3207 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4117 Z= 0.179 Angle : 0.553 4.916 5594 Z= 0.293 Chirality : 0.044 0.187 634 Planarity : 0.003 0.039 706 Dihedral : 5.573 51.532 665 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.52 % Allowed : 18.31 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.41 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.97 (0.36), residues: 204 loop : -0.23 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.007 0.001 HIS A 245 PHE 0.018 0.001 PHE H 70 TYR 0.011 0.001 TYR A 28 ARG 0.005 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.464 Fit side-chains REVERT: A 14 GLN cc_start: 0.7724 (mt0) cc_final: 0.7394 (mt0) REVERT: A 80 ASP cc_start: 0.6703 (t0) cc_final: 0.6225 (t0) REVERT: A 131 CYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7700 (m) REVERT: A 137 ASN cc_start: 0.8472 (m110) cc_final: 0.7952 (t0) REVERT: A 169 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: A 173 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8151 (mp10) REVERT: A 177 MET cc_start: 0.7967 (pmt) cc_final: 0.7681 (pmt) REVERT: H 65 GLU cc_start: 0.7415 (pt0) cc_final: 0.6967 (pt0) REVERT: H 100 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6977 (ttp) outliers start: 11 outliers final: 4 residues processed: 70 average time/residue: 1.0763 time to fit residues: 78.3576 Evaluate side-chains 70 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.0570 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 6 optimal weight: 0.2980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 GLN L 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.143305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.100275 restraints weight = 5615.018| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.25 r_work: 0.3206 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4117 Z= 0.195 Angle : 0.566 6.134 5594 Z= 0.300 Chirality : 0.045 0.190 634 Planarity : 0.004 0.039 706 Dihedral : 5.497 51.381 665 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.52 % Allowed : 17.85 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.38 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.83 (0.35), residues: 212 loop : -0.17 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 66 HIS 0.002 0.000 HIS A 69 PHE 0.019 0.001 PHE H 70 TYR 0.011 0.001 TYR H 132 ARG 0.005 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.475 Fit side-chains REVERT: A 14 GLN cc_start: 0.7717 (mt0) cc_final: 0.7290 (mt0) REVERT: A 80 ASP cc_start: 0.6696 (t0) cc_final: 0.6246 (t0) REVERT: A 131 CYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7664 (m) REVERT: A 137 ASN cc_start: 0.8482 (m110) cc_final: 0.7973 (t0) REVERT: A 169 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7793 (tm-30) REVERT: A 177 MET cc_start: 0.8005 (pmt) cc_final: 0.7720 (pmt) REVERT: H 65 GLU cc_start: 0.7394 (pt0) cc_final: 0.6969 (pt0) REVERT: H 100 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7007 (ttp) REVERT: L 132 LYS cc_start: 0.7781 (mmmm) cc_final: 0.7407 (mmmm) outliers start: 11 outliers final: 5 residues processed: 70 average time/residue: 1.1437 time to fit residues: 83.0511 Evaluate side-chains 71 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 GLN L 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.142121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.099030 restraints weight = 5595.582| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.25 r_work: 0.3187 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4117 Z= 0.251 Angle : 0.588 6.242 5594 Z= 0.311 Chirality : 0.046 0.194 634 Planarity : 0.004 0.039 706 Dihedral : 5.613 50.883 665 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.29 % Allowed : 18.54 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.30 (0.37), residues: 485 helix: None (None), residues: 0 sheet: 0.77 (0.35), residues: 214 loop : -0.22 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 60 HIS 0.003 0.001 HIS A 69 PHE 0.021 0.002 PHE H 70 TYR 0.013 0.002 TYR H 132 ARG 0.007 0.001 ARG A 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.455 Fit side-chains REVERT: A 14 GLN cc_start: 0.7721 (mt0) cc_final: 0.7379 (mt0) REVERT: A 80 ASP cc_start: 0.6685 (t0) cc_final: 0.6226 (t0) REVERT: A 131 CYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7743 (m) REVERT: A 137 ASN cc_start: 0.8433 (m110) cc_final: 0.7963 (t0) REVERT: A 169 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7765 (tm-30) REVERT: A 177 MET cc_start: 0.8043 (pmt) cc_final: 0.7730 (pmt) REVERT: H 65 GLU cc_start: 0.7471 (pt0) cc_final: 0.7052 (pt0) REVERT: H 67 MET cc_start: 0.7980 (ttm) cc_final: 0.7774 (ttp) REVERT: H 100 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.7019 (ttp) outliers start: 10 outliers final: 7 residues processed: 71 average time/residue: 1.1098 time to fit residues: 81.9475 Evaluate side-chains 73 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 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 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.142326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.099006 restraints weight = 5471.110| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.21 r_work: 0.3187 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4117 Z= 0.237 Angle : 0.586 5.880 5594 Z= 0.310 Chirality : 0.045 0.193 634 Planarity : 0.004 0.039 706 Dihedral : 5.600 51.019 665 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.29 % Allowed : 18.54 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.26 (0.37), residues: 485 helix: None (None), residues: 0 sheet: 0.75 (0.35), residues: 214 loop : -0.26 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 60 HIS 0.003 0.001 HIS A 245 PHE 0.021 0.002 PHE H 70 TYR 0.012 0.001 TYR H 132 ARG 0.007 0.001 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5283.61 seconds wall clock time: 94 minutes 2.54 seconds (5642.54 seconds total)