Starting phenix.real_space_refine on Tue Feb 11 07:13:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ym8_33924/02_2025/7ym8_33924.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ym8_33924/02_2025/7ym8_33924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ym8_33924/02_2025/7ym8_33924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ym8_33924/02_2025/7ym8_33924.map" model { file = "/net/cci-nas-00/data/ceres_data/7ym8_33924/02_2025/7ym8_33924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ym8_33924/02_2025/7ym8_33924.cif" } resolution = 2.92 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= 0.109 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 26 5.16 5 C 2805 2.51 5 N 704 2.21 5 O 752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4287 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1238 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 1, 'TRANS': 167} Chain breaks: 2 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 120 Chain: "A" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2108 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 887 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'J5C': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.15, per 1000 atoms: 0.73 Number of scatterers: 4287 At special positions: 0 Unit cell: (59.5375, 58.455, 138.56, 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 26 16.00 O 752 8.00 N 704 7.00 C 2805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 94 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 505.5 milliseconds 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1038 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 51.8% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'B' and resid 27 through 33 Processing helix chain 'B' and resid 77 through 82 removed outlier: 3.666A pdb=" N CYS B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 128 through 133 removed outlier: 3.708A pdb=" N ALA B 132 " --> pdb=" O GLN B 128 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 133' Processing helix chain 'B' and resid 169 through 184 removed outlier: 4.243A pdb=" N PHE B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 179 " --> pdb=" O ILE B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 225 removed outlier: 3.722A pdb=" N ARG B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 53 removed outlier: 3.586A pdb=" N ILE A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 79 removed outlier: 3.664A pdb=" N ILE A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 95 through 129 Processing helix chain 'A' and resid 141 through 159 Processing helix chain 'A' and resid 184 through 211 removed outlier: 5.603A pdb=" N LEU A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Proline residue: A 196 - end of helix Processing helix chain 'A' and resid 263 through 286 removed outlier: 3.931A pdb=" N GLU A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 304 through 326 removed outlier: 3.775A pdb=" N PHE A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N CYS A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) Proline residue: A 323 - end of helix Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 330 through 341 removed outlier: 3.875A pdb=" N GLN A 338 " --> pdb=" O LYS A 334 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 52 through 58 removed outlier: 9.826A pdb=" N ALA B 87 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ARG B 17 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE B 89 " --> pdb=" O ARG B 17 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 19 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL B 91 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AA3, first strand: chain 'D' and resid 11 through 13 removed outlier: 3.585A pdb=" N SER D 115 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N MET D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 705 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: 1.21 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 669 1.32 - 1.44: 1248 1.44 - 1.56: 2438 1.56 - 1.68: 1 1.68 - 1.81: 35 Bond restraints: 4391 Sorted by residual: bond pdb=" C9 J5C A 501 " pdb=" N13 J5C A 501 " ideal model delta sigma weight residual 1.277 1.463 -0.186 2.00e-02 2.50e+03 8.67e+01 bond pdb=" C9 J5C A 501 " pdb=" N10 J5C A 501 " ideal model delta sigma weight residual 1.373 1.465 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C11 J5C A 501 " pdb=" C12 J5C A 501 " ideal model delta sigma weight residual 1.540 1.490 0.050 2.00e-02 2.50e+03 6.37e+00 bond pdb=" C5 J5C A 501 " pdb=" O15 J5C A 501 " ideal model delta sigma weight residual 1.356 1.400 -0.044 2.00e-02 2.50e+03 4.89e+00 bond pdb=" C MET A 292 " pdb=" N PRO A 293 " ideal model delta sigma weight residual 1.334 1.376 -0.043 2.34e-02 1.83e+03 3.31e+00 ... (remaining 4386 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 5724 1.78 - 3.56: 211 3.56 - 5.34: 37 5.34 - 7.13: 13 7.13 - 8.91: 4 Bond angle restraints: 5989 Sorted by residual: angle pdb=" C ARG B 117 " pdb=" N THR B 118 " pdb=" CA THR B 118 " ideal model delta sigma weight residual 122.46 127.56 -5.10 1.41e+00 5.03e-01 1.31e+01 angle pdb=" N LEU A 80 " pdb=" CA LEU A 80 " pdb=" C LEU A 80 " ideal model delta sigma weight residual 109.81 117.34 -7.53 2.21e+00 2.05e-01 1.16e+01 angle pdb=" CA THR B 118 " pdb=" CB THR B 118 " pdb=" CG2 THR B 118 " ideal model delta sigma weight residual 110.50 115.96 -5.46 1.70e+00 3.46e-01 1.03e+01 angle pdb=" N ASN A 322 " pdb=" CA ASN A 322 " pdb=" C ASN A 322 " ideal model delta sigma weight residual 113.16 117.48 -4.32 1.42e+00 4.96e-01 9.26e+00 angle pdb=" N10 J5C A 501 " pdb=" C9 J5C A 501 " pdb=" N13 J5C A 501 " ideal model delta sigma weight residual 116.22 107.31 8.91 3.00e+00 1.11e-01 8.82e+00 ... (remaining 5984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.45: 2347 20.45 - 40.90: 199 40.90 - 61.34: 34 61.34 - 81.79: 8 81.79 - 102.24: 3 Dihedral angle restraints: 2591 sinusoidal: 976 harmonic: 1615 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 94 " pdb=" CB CYS D 94 " ideal model delta sinusoidal sigma weight residual 93.00 59.87 33.13 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" CA ILE A 325 " pdb=" C ILE A 325 " pdb=" N TYR A 326 " pdb=" CA TYR A 326 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CAR Y01 A 502 " pdb=" CAV Y01 A 502 " pdb=" CBC Y01 A 502 " pdb=" CAZ Y01 A 502 " ideal model delta sinusoidal sigma weight residual 55.40 -46.84 102.24 1 3.00e+01 1.11e-03 1.29e+01 ... (remaining 2588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 411 0.038 - 0.077: 191 0.077 - 0.115: 67 0.115 - 0.154: 16 0.154 - 0.192: 7 Chirality restraints: 692 Sorted by residual: chirality pdb=" CB VAL B 85 " pdb=" CA VAL B 85 " pdb=" CG1 VAL B 85 " pdb=" CG2 VAL B 85 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.21e-01 chirality pdb=" CA THR B 118 " pdb=" N THR B 118 " pdb=" C THR B 118 " pdb=" CB THR B 118 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CB ILE A 126 " pdb=" CA ILE A 126 " pdb=" CG1 ILE A 126 " pdb=" CG2 ILE A 126 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 689 not shown) Planarity restraints: 740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 80 " -0.041 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO A 81 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 326 " 0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO A 327 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 286 " -0.038 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO A 287 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " -0.032 5.00e-02 4.00e+02 ... (remaining 737 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1415 2.84 - 3.36: 3748 3.36 - 3.87: 7189 3.87 - 4.39: 8184 4.39 - 4.90: 14266 Nonbonded interactions: 34802 Sorted by model distance: nonbonded pdb=" O LEU A 74 " pdb=" OG1 THR A 78 " model vdw 2.331 3.040 nonbonded pdb=" O ALA B 23 " pdb=" OG SER B 26 " model vdw 2.353 3.040 nonbonded pdb=" O SER D 83 " pdb=" OG SER D 83 " model vdw 2.369 3.040 nonbonded pdb=" NH2 ARG A 124 " pdb=" OG SER A 329 " model vdw 2.384 3.120 nonbonded pdb=" O GLN B 101 " pdb=" ND2 ASN B 105 " model vdw 2.396 3.120 ... (remaining 34797 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.000 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:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 0.186 4391 Z= 0.451 Angle : 0.860 8.907 5989 Z= 0.462 Chirality : 0.051 0.192 692 Planarity : 0.007 0.061 740 Dihedral : 16.010 102.240 1547 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.62 (0.30), residues: 544 helix: -2.14 (0.24), residues: 271 sheet: -1.98 (0.50), residues: 100 loop : -2.68 (0.41), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 165 HIS 0.005 0.001 HIS B 191 PHE 0.017 0.002 PHE A 94 TYR 0.035 0.002 TYR D 37 ARG 0.005 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.456 Fit side-chains REVERT: B 17 ARG cc_start: 0.7374 (mtp85) cc_final: 0.7150 (ttp-110) REVERT: B 21 LEU cc_start: 0.7899 (mt) cc_final: 0.7671 (mp) REVERT: B 204 GLU cc_start: 0.6596 (mp0) cc_final: 0.6389 (mp0) REVERT: A 61 THR cc_start: 0.8518 (m) cc_final: 0.8288 (p) REVERT: A 203 MET cc_start: 0.8882 (mmp) cc_final: 0.8631 (mmm) REVERT: D 105 TYR cc_start: 0.7753 (m-10) cc_final: 0.7372 (m-10) outliers start: 0 outliers final: 1 residues processed: 74 average time/residue: 0.8222 time to fit residues: 64.3886 Evaluate side-chains 56 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 HIS B 112 ASN B 226 ASN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 HIS D 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.171363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129888 restraints weight = 4384.792| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.64 r_work: 0.3113 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4391 Z= 0.229 Angle : 0.571 5.697 5989 Z= 0.296 Chirality : 0.043 0.135 692 Planarity : 0.005 0.046 740 Dihedral : 9.848 83.463 681 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.56 % Allowed : 13.72 % Favored : 83.72 % 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: -1.84 (0.34), residues: 544 helix: -0.37 (0.29), residues: 276 sheet: -1.59 (0.52), residues: 101 loop : -2.18 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.003 0.001 HIS B 191 PHE 0.013 0.002 PHE A 94 TYR 0.017 0.001 TYR D 37 ARG 0.003 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.469 Fit side-chains REVERT: B 17 ARG cc_start: 0.7886 (mtp85) cc_final: 0.7491 (ttm110) REVERT: B 226 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.7483 (t0) REVERT: A 61 THR cc_start: 0.8753 (m) cc_final: 0.8408 (p) REVERT: A 203 MET cc_start: 0.9092 (mmp) cc_final: 0.8808 (mmm) outliers start: 11 outliers final: 5 residues processed: 67 average time/residue: 0.8094 time to fit residues: 57.3489 Evaluate side-chains 64 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain D residue 21 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.169173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.126768 restraints weight = 4394.983| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.59 r_work: 0.3092 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4391 Z= 0.260 Angle : 0.574 7.536 5989 Z= 0.293 Chirality : 0.043 0.125 692 Planarity : 0.004 0.044 740 Dihedral : 9.160 69.436 679 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.56 % Allowed : 17.44 % Favored : 80.00 % 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: -1.14 (0.36), residues: 544 helix: 0.23 (0.30), residues: 276 sheet: -1.31 (0.52), residues: 101 loop : -1.88 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.003 0.001 HIS B 191 PHE 0.014 0.002 PHE A 94 TYR 0.019 0.002 TYR D 37 ARG 0.004 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.483 Fit side-chains REVERT: B 17 ARG cc_start: 0.7850 (mtp85) cc_final: 0.7422 (ttm110) REVERT: B 21 LEU cc_start: 0.7942 (mt) cc_final: 0.7566 (mp) REVERT: B 226 ASN cc_start: 0.8343 (m110) cc_final: 0.7478 (t0) REVERT: A 31 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7886 (t) REVERT: A 36 LEU cc_start: 0.8029 (mt) cc_final: 0.7509 (tp) REVERT: A 61 THR cc_start: 0.8742 (m) cc_final: 0.8382 (p) REVERT: A 203 MET cc_start: 0.9087 (mmp) cc_final: 0.8819 (mmm) REVERT: A 294 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7402 (mp) REVERT: A 305 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7187 (tt0) outliers start: 11 outliers final: 5 residues processed: 68 average time/residue: 0.8770 time to fit residues: 62.7771 Evaluate side-chains 66 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain D residue 21 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.170691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.128391 restraints weight = 4419.213| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.59 r_work: 0.3065 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4391 Z= 0.206 Angle : 0.531 5.803 5989 Z= 0.272 Chirality : 0.042 0.124 692 Planarity : 0.004 0.041 740 Dihedral : 7.784 64.305 679 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.33 % Allowed : 17.91 % Favored : 79.77 % 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: -0.63 (0.36), residues: 544 helix: 0.66 (0.31), residues: 276 sheet: -1.10 (0.53), residues: 101 loop : -1.66 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 165 HIS 0.003 0.001 HIS A 56 PHE 0.012 0.001 PHE A 94 TYR 0.016 0.001 TYR D 37 ARG 0.003 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.471 Fit side-chains REVERT: B 17 ARG cc_start: 0.7834 (mtp85) cc_final: 0.7194 (ttp-110) REVERT: B 21 LEU cc_start: 0.7867 (mt) cc_final: 0.7487 (mp) REVERT: B 176 ARG cc_start: 0.6547 (ttp-170) cc_final: 0.6334 (ttp-170) REVERT: B 182 ILE cc_start: 0.7132 (OUTLIER) cc_final: 0.6765 (mp) REVERT: B 226 ASN cc_start: 0.8394 (m110) cc_final: 0.7451 (t0) REVERT: A 36 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7528 (tp) REVERT: A 61 THR cc_start: 0.8786 (m) cc_final: 0.8341 (p) REVERT: A 162 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7252 (tp) REVERT: A 203 MET cc_start: 0.9062 (mmp) cc_final: 0.8741 (mmm) REVERT: A 294 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7358 (mp) REVERT: A 305 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7234 (tt0) outliers start: 10 outliers final: 2 residues processed: 68 average time/residue: 0.9410 time to fit residues: 67.1168 Evaluate side-chains 65 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain D residue 21 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.169605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.126995 restraints weight = 4461.808| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.62 r_work: 0.3085 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4391 Z= 0.233 Angle : 0.530 6.105 5989 Z= 0.273 Chirality : 0.042 0.124 692 Planarity : 0.004 0.041 740 Dihedral : 7.169 63.451 679 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.79 % Allowed : 17.91 % Favored : 79.30 % 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: -0.47 (0.37), residues: 544 helix: 0.78 (0.31), residues: 276 sheet: -1.06 (0.52), residues: 101 loop : -1.53 (0.48), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.003 0.001 HIS B 191 PHE 0.013 0.001 PHE A 94 TYR 0.018 0.001 TYR D 53 ARG 0.002 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.407 Fit side-chains REVERT: B 17 ARG cc_start: 0.7894 (mtp85) cc_final: 0.7263 (ttp-110) REVERT: B 182 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.6902 (mp) REVERT: B 226 ASN cc_start: 0.8446 (m110) cc_final: 0.7598 (t0) REVERT: A 36 LEU cc_start: 0.8052 (mt) cc_final: 0.7590 (tp) REVERT: A 162 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7295 (tp) REVERT: A 203 MET cc_start: 0.9068 (mmp) cc_final: 0.8809 (mmm) REVERT: A 205 CYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7397 (m) REVERT: A 294 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7409 (mp) REVERT: A 305 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7285 (tt0) outliers start: 12 outliers final: 3 residues processed: 71 average time/residue: 0.8705 time to fit residues: 65.1437 Evaluate side-chains 67 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain D residue 21 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 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 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.170587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.128188 restraints weight = 4433.075| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.78 r_work: 0.3083 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4391 Z= 0.205 Angle : 0.515 5.878 5989 Z= 0.266 Chirality : 0.042 0.125 692 Planarity : 0.004 0.040 740 Dihedral : 7.095 63.683 679 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.26 % Allowed : 18.14 % Favored : 78.60 % 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: -0.26 (0.37), residues: 544 helix: 0.92 (0.32), residues: 276 sheet: -0.94 (0.53), residues: 101 loop : -1.41 (0.49), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 165 HIS 0.002 0.001 HIS A 56 PHE 0.011 0.001 PHE A 94 TYR 0.022 0.001 TYR D 53 ARG 0.003 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.447 Fit side-chains REVERT: B 17 ARG cc_start: 0.7914 (mtp85) cc_final: 0.7291 (ttp-110) REVERT: B 182 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.6902 (mp) REVERT: B 226 ASN cc_start: 0.8433 (m110) cc_final: 0.7605 (t0) REVERT: A 36 LEU cc_start: 0.8060 (mt) cc_final: 0.7598 (tp) REVERT: A 162 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7336 (tp) REVERT: A 203 MET cc_start: 0.9058 (mmp) cc_final: 0.8779 (mmm) REVERT: A 205 CYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7426 (m) REVERT: A 305 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7235 (tt0) outliers start: 14 outliers final: 6 residues processed: 68 average time/residue: 0.9157 time to fit residues: 65.4940 Evaluate side-chains 66 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain D residue 21 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 46 optimal weight: 0.0770 chunk 36 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.171839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.130290 restraints weight = 4432.773| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.59 r_work: 0.3164 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4391 Z= 0.181 Angle : 0.502 5.621 5989 Z= 0.259 Chirality : 0.041 0.125 692 Planarity : 0.004 0.040 740 Dihedral : 7.037 63.790 679 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.49 % Allowed : 18.14 % Favored : 78.37 % 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: -0.05 (0.37), residues: 544 helix: 1.02 (0.32), residues: 279 sheet: -0.81 (0.53), residues: 101 loop : -1.23 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 106 HIS 0.002 0.001 HIS A 56 PHE 0.010 0.001 PHE B 56 TYR 0.023 0.001 TYR D 53 ARG 0.003 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.446 Fit side-chains REVERT: B 17 ARG cc_start: 0.7926 (mtp85) cc_final: 0.7324 (ttp-110) REVERT: B 182 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6877 (mp) REVERT: B 226 ASN cc_start: 0.8386 (m110) cc_final: 0.7633 (t0) REVERT: A 36 LEU cc_start: 0.8036 (mt) cc_final: 0.7601 (tp) REVERT: A 162 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7342 (tp) REVERT: A 203 MET cc_start: 0.9045 (mmp) cc_final: 0.8750 (mmm) REVERT: A 205 CYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7423 (m) REVERT: A 294 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7466 (mp) REVERT: A 305 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7236 (tt0) outliers start: 15 outliers final: 5 residues processed: 72 average time/residue: 0.9179 time to fit residues: 69.4785 Evaluate side-chains 64 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain D residue 21 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.170811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.128507 restraints weight = 4392.555| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.63 r_work: 0.3113 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4391 Z= 0.221 Angle : 0.533 6.180 5989 Z= 0.274 Chirality : 0.043 0.133 692 Planarity : 0.004 0.039 740 Dihedral : 7.098 63.452 679 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.72 % Allowed : 18.60 % Favored : 77.67 % 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 (0.37), residues: 544 helix: 0.97 (0.32), residues: 279 sheet: -0.77 (0.54), residues: 97 loop : -1.26 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 165 HIS 0.002 0.001 HIS B 191 PHE 0.012 0.001 PHE A 94 TYR 0.024 0.001 TYR D 53 ARG 0.004 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.459 Fit side-chains REVERT: B 17 ARG cc_start: 0.7919 (mtp85) cc_final: 0.7297 (ttp-110) REVERT: B 182 ILE cc_start: 0.7264 (OUTLIER) cc_final: 0.6894 (mp) REVERT: B 226 ASN cc_start: 0.8381 (m110) cc_final: 0.7649 (t0) REVERT: A 36 LEU cc_start: 0.8046 (mt) cc_final: 0.7596 (tp) REVERT: A 167 GLN cc_start: 0.5842 (OUTLIER) cc_final: 0.5193 (mt0) REVERT: A 203 MET cc_start: 0.9049 (mmp) cc_final: 0.8788 (mmm) REVERT: A 205 CYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7410 (m) REVERT: A 294 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7461 (mp) REVERT: A 305 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7274 (tt0) outliers start: 16 outliers final: 8 residues processed: 70 average time/residue: 0.9354 time to fit residues: 68.6831 Evaluate side-chains 68 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 46 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 28 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 47 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: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.171125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.128534 restraints weight = 4486.832| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.62 r_work: 0.3108 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4391 Z= 0.217 Angle : 0.533 5.991 5989 Z= 0.274 Chirality : 0.043 0.126 692 Planarity : 0.004 0.040 740 Dihedral : 7.107 63.510 679 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.02 % Allowed : 19.77 % Favored : 77.21 % 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: -0.08 (0.37), residues: 544 helix: 0.97 (0.32), residues: 279 sheet: -0.71 (0.55), residues: 97 loop : -1.26 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 165 HIS 0.002 0.001 HIS A 56 PHE 0.011 0.001 PHE A 94 TYR 0.024 0.001 TYR D 53 ARG 0.009 0.001 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.432 Fit side-chains REVERT: B 17 ARG cc_start: 0.7883 (mtp85) cc_final: 0.7331 (ttp-110) REVERT: B 182 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6872 (mp) REVERT: B 226 ASN cc_start: 0.8344 (m110) cc_final: 0.7597 (t0) REVERT: A 36 LEU cc_start: 0.8012 (mt) cc_final: 0.7544 (tp) REVERT: A 167 GLN cc_start: 0.5805 (OUTLIER) cc_final: 0.5161 (mt0) REVERT: A 203 MET cc_start: 0.9049 (mmp) cc_final: 0.8773 (mmm) REVERT: A 205 CYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7366 (m) REVERT: A 294 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7428 (mp) REVERT: A 305 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7281 (tt0) outliers start: 13 outliers final: 8 residues processed: 66 average time/residue: 0.9610 time to fit residues: 66.5171 Evaluate side-chains 67 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 28 optimal weight: 0.0980 chunk 35 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.167812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.124901 restraints weight = 4404.275| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.60 r_work: 0.3102 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4391 Z= 0.226 Angle : 0.546 6.759 5989 Z= 0.278 Chirality : 0.043 0.124 692 Planarity : 0.004 0.039 740 Dihedral : 7.140 63.517 679 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.26 % Allowed : 19.53 % Favored : 77.21 % 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: -0.07 (0.37), residues: 544 helix: 0.98 (0.32), residues: 279 sheet: -0.69 (0.55), residues: 97 loop : -1.25 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 165 HIS 0.003 0.001 HIS B 191 PHE 0.012 0.001 PHE A 94 TYR 0.025 0.001 TYR D 53 ARG 0.009 0.001 ARG B 181 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.425 Fit side-chains REVERT: B 17 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7331 (ttp-110) REVERT: B 182 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6829 (mp) REVERT: B 226 ASN cc_start: 0.8445 (m110) cc_final: 0.7675 (t0) REVERT: A 36 LEU cc_start: 0.8002 (mt) cc_final: 0.7522 (tp) REVERT: A 167 GLN cc_start: 0.5807 (OUTLIER) cc_final: 0.5163 (mt0) REVERT: A 203 MET cc_start: 0.9049 (mmp) cc_final: 0.8781 (mmm) REVERT: A 205 CYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7369 (m) REVERT: A 294 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7431 (mp) REVERT: A 305 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7299 (tt0) outliers start: 14 outliers final: 8 residues processed: 67 average time/residue: 0.9582 time to fit residues: 67.3171 Evaluate side-chains 68 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 28 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 0.0020 chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.173636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.131647 restraints weight = 4408.110| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.75 r_work: 0.3132 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4391 Z= 0.160 Angle : 0.508 6.216 5989 Z= 0.260 Chirality : 0.041 0.124 692 Planarity : 0.004 0.039 740 Dihedral : 6.989 64.045 679 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.79 % Allowed : 20.23 % Favored : 76.98 % 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: 0.15 (0.38), residues: 544 helix: 1.18 (0.32), residues: 279 sheet: -0.56 (0.56), residues: 97 loop : -1.24 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 106 HIS 0.003 0.001 HIS A 56 PHE 0.010 0.001 PHE B 56 TYR 0.020 0.001 TYR D 53 ARG 0.010 0.001 ARG B 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3357.61 seconds wall clock time: 59 minutes 48.14 seconds (3588.14 seconds total)