Starting phenix.real_space_refine on Thu Jul 2 00:18:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ym8_33924/07_2026/7ym8_33924.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ym8_33924/07_2026/7ym8_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_33924/07_2026/7ym8_33924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ym8_33924/07_2026/7ym8_33924.map" model { file = "/net/cci-nas-00/data/ceres_data/7ym8_33924/07_2026/7ym8_33924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ym8_33924/07_2026/7ym8_33924.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ym8_33924/07_2026/7ym8_33924.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ym8_33924/07_2026/7ym8_33924.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'ASP:plan': 6, 'ASN:plan1': 4, 'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 9, 'GLU:plan': 3, 'TRP:plan': 1} 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: {'ARG:plan': 1, 'PHE: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: 0.94, per 1000 atoms: 0.22 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: 0.28 Conformation dependent library (CDL) restraints added in 98.9 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: 0.07 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: 0.55 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 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 - 16.64: 2227 16.64 - 33.29: 224 33.29 - 49.93: 62 49.93 - 66.57: 16 66.57 - 83.21: 4 Dihedral angle restraints: 2533 sinusoidal: 918 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=" CA ILE A 126 " pdb=" C ILE A 126 " pdb=" N GLY A 127 " pdb=" CA GLY A 127 " ideal model delta harmonic sigma weight residual 180.00 163.85 16.15 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 2530 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: 1.670 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: 0.050 Check model and map are aligned: 0.020 Set scattering table: 0.000 Process input model: 4.750 Find NCS groups from input model: 0.020 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:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 4393 Z= 0.292 Angle : 0.860 8.907 5993 Z= 0.462 Chirality : 0.051 0.192 692 Planarity : 0.007 0.061 740 Dihedral : 15.400 83.214 1489 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.02 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.000 ARG D 101 TYR 0.035 0.002 TYR D 37 PHE 0.017 0.002 PHE A 94 TRP 0.013 0.002 TRP A 165 HIS 0.005 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.29 ( 4391) covalent geometry : angle 0.86015 / 0.46 ( 5989) SS BOND : bond 0.00103 / 0.05 ( 2) SS BOND : angle 0.59332 / 0.37 ( 4) hydrogen bonds : bond 0.14542 / 10.27 ( 240) hydrogen bonds : angle 7.40661 / 5.29 ( 705) *********************** 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 : 0.155 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: 0.6390 (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: 0.3634 time to fit residues: 28.3303 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 : 0.163 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3859 r_free = 0.3859 target = 0.171457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130189 restraints weight = 4418.907| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.62 r_work: 0.3116 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4393 Z= 0.156 Angle : 0.555 5.609 5993 Z= 0.291 Chirality : 0.043 0.131 692 Planarity : 0.005 0.045 740 Dihedral : 7.903 73.209 623 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.56 % Allowed : 13.49 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.34), residues: 544 helix: -0.33 (0.29), residues: 276 sheet: -1.58 (0.52), residues: 101 loop : -2.15 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 166 TYR 0.019 0.001 TYR D 37 PHE 0.013 0.002 PHE A 94 TRP 0.011 0.001 TRP A 165 HIS 0.003 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 4391) covalent geometry : angle 0.55507 / 0.29 ( 5989) SS BOND : bond 0.00074 / 0.04 ( 2) SS BOND : angle 0.43361 / 0.27 ( 4) hydrogen bonds : bond 0.04617 / 3.19 ( 240) hydrogen bonds : angle 5.20747 / 3.79 ( 705) *********************** 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 74 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.181 Fit side-chains REVERT: B 17 ARG cc_start: 0.7898 (mtp85) cc_final: 0.7496 (ttm110) REVERT: B 226 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.7483 (t0) REVERT: A 36 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7540 (tp) REVERT: A 61 THR cc_start: 0.8757 (m) cc_final: 0.8412 (p) REVERT: A 203 MET cc_start: 0.9091 (mmp) cc_final: 0.8807 (mmm) outliers start: 11 outliers final: 5 residues processed: 68 average time/residue: 0.3579 time to fit residues: 25.7391 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 : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain A residue 36 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 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 40 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3843 r_free = 0.3843 target = 0.170131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.127890 restraints weight = 4413.811| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.58 r_work: 0.3104 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4393 Z= 0.150 Angle : 0.537 5.791 5993 Z= 0.279 Chirality : 0.042 0.125 692 Planarity : 0.004 0.043 740 Dihedral : 7.727 72.624 621 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.79 % Allowed : 16.98 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.36), residues: 544 helix: 0.33 (0.30), residues: 277 sheet: -1.25 (0.53), residues: 101 loop : -1.84 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 166 TYR 0.018 0.002 TYR D 37 PHE 0.013 0.001 PHE A 94 TRP 0.009 0.001 TRP A 165 HIS 0.003 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 4391) covalent geometry : angle 0.53733 / 0.28 ( 5989) SS BOND : bond 0.00067 / 0.03 ( 2) SS BOND : angle 0.47699 / 0.31 ( 4) hydrogen bonds : bond 0.04373 / 2.98 ( 240) hydrogen bonds : angle 4.97582 / 3.63 ( 705) *********************** 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 73 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.156 Fit side-chains REVERT: B 17 ARG cc_start: 0.7861 (mtp85) cc_final: 0.7220 (ttp-110) REVERT: B 21 LEU cc_start: 0.7921 (mt) cc_final: 0.7549 (mp) REVERT: B 226 ASN cc_start: 0.8391 (m110) cc_final: 0.7453 (t0) REVERT: A 31 VAL cc_start: 0.8068 (OUTLIER) cc_final: 0.7852 (t) REVERT: A 61 THR cc_start: 0.8733 (m) cc_final: 0.8380 (p) REVERT: A 162 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7344 (tp) REVERT: A 203 MET cc_start: 0.9079 (mmp) cc_final: 0.8788 (mmm) REVERT: A 294 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7395 (mp) REVERT: A 305 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7182 (tt0) outliers start: 12 outliers final: 4 residues processed: 68 average time/residue: 0.3776 time to fit residues: 27.0048 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 : 0.152 ------------------------------------------------------------------------------- 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 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 0.0370 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.172138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.129692 restraints weight = 4360.669| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.60 r_work: 0.3129 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4393 Z= 0.116 Angle : 0.496 5.182 5993 Z= 0.257 Chirality : 0.041 0.125 692 Planarity : 0.004 0.040 740 Dihedral : 7.507 71.845 621 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.79 % Allowed : 17.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.37), residues: 544 helix: 0.85 (0.31), residues: 276 sheet: -1.06 (0.53), residues: 101 loop : -1.62 (0.47), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.013 0.001 TYR D 37 PHE 0.010 0.001 PHE A 94 TRP 0.006 0.001 TRP A 102 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 4391) covalent geometry : angle 0.49613 / 0.26 ( 5989) SS BOND : bond 0.00062 / 0.03 ( 2) SS BOND : angle 0.48378 / 0.31 ( 4) hydrogen bonds : bond 0.03879 / 2.62 ( 240) hydrogen bonds : angle 4.69751 / 3.44 ( 705) *********************** 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 75 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.094 Fit side-chains REVERT: B 17 ARG cc_start: 0.7886 (mtp85) cc_final: 0.7255 (ttp-110) REVERT: B 21 LEU cc_start: 0.7837 (mt) cc_final: 0.7538 (mp) REVERT: B 182 ILE cc_start: 0.7158 (OUTLIER) cc_final: 0.6776 (mp) REVERT: B 226 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.7527 (t0) REVERT: A 36 LEU cc_start: 0.8055 (mt) cc_final: 0.7602 (tp) REVERT: A 61 THR cc_start: 0.8729 (m) cc_final: 0.8385 (p) REVERT: A 162 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7366 (tp) REVERT: A 203 MET cc_start: 0.9071 (mmp) cc_final: 0.8801 (mmm) REVERT: A 294 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7390 (mp) REVERT: A 305 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7228 (tt0) outliers start: 12 outliers final: 2 residues processed: 70 average time/residue: 0.4106 time to fit residues: 30.0767 Evaluate side-chains 68 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 226 ASN 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 18 optimal weight: 0.0980 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3878 r_free = 0.3878 target = 0.172952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.130664 restraints weight = 4386.807| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.63 r_work: 0.3120 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4393 Z= 0.123 Angle : 0.503 5.723 5993 Z= 0.259 Chirality : 0.041 0.125 692 Planarity : 0.004 0.040 740 Dihedral : 7.430 71.138 621 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.33 % Allowed : 18.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.37), residues: 544 helix: 1.03 (0.32), residues: 276 sheet: -0.95 (0.53), residues: 101 loop : -1.52 (0.48), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 166 TYR 0.018 0.001 TYR D 53 PHE 0.010 0.001 PHE B 56 TRP 0.006 0.001 TRP A 165 HIS 0.002 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 4391) covalent geometry : angle 0.50353 / 0.26 ( 5989) SS BOND : bond 0.00079 / 0.04 ( 2) SS BOND : angle 0.44905 / 0.29 ( 4) hydrogen bonds : bond 0.03882 / 2.61 ( 240) hydrogen bonds : angle 4.62275 / 3.39 ( 705) *********************** 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 71 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.146 Fit side-chains REVERT: B 17 ARG cc_start: 0.7914 (mtp85) cc_final: 0.7285 (ttp-110) REVERT: B 21 LEU cc_start: 0.7875 (mt) cc_final: 0.7531 (mp) REVERT: B 182 ILE cc_start: 0.7130 (OUTLIER) cc_final: 0.6740 (mp) REVERT: B 226 ASN cc_start: 0.8430 (m110) cc_final: 0.7563 (t0) REVERT: A 36 LEU cc_start: 0.8038 (mt) cc_final: 0.7601 (tp) REVERT: A 61 THR cc_start: 0.8745 (m) cc_final: 0.8328 (p) REVERT: A 162 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7351 (tp) REVERT: A 203 MET cc_start: 0.9058 (mmp) cc_final: 0.8744 (mmm) REVERT: A 205 CYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7369 (m) REVERT: A 294 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7430 (mp) REVERT: A 305 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7253 (tt0) outliers start: 10 outliers final: 4 residues processed: 68 average time/residue: 0.3897 time to fit residues: 27.7306 Evaluate side-chains 67 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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 38 LEU Chi-restraints excluded: chain A residue 45 ILE 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 40 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 30 optimal weight: 0.0070 chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 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 = 0.3864 r_free = 0.3864 target = 0.171787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.130797 restraints weight = 4518.295| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.64 r_work: 0.3132 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4393 Z= 0.120 Angle : 0.501 5.300 5993 Z= 0.258 Chirality : 0.041 0.125 692 Planarity : 0.004 0.039 740 Dihedral : 7.386 70.990 621 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.49 % Allowed : 17.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.37), residues: 544 helix: 1.19 (0.32), residues: 274 sheet: -0.82 (0.53), residues: 101 loop : -1.39 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 166 TYR 0.021 0.001 TYR D 53 PHE 0.010 0.001 PHE B 56 TRP 0.006 0.001 TRP A 165 HIS 0.002 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 4391) covalent geometry : angle 0.50065 / 0.26 ( 5989) SS BOND : bond 0.00076 / 0.04 ( 2) SS BOND : angle 0.44639 / 0.29 ( 4) hydrogen bonds : bond 0.03833 / 2.58 ( 240) hydrogen bonds : angle 4.55999 / 3.35 ( 705) *********************** 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 76 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.119 Fit side-chains REVERT: B 17 ARG cc_start: 0.7920 (mtp85) cc_final: 0.7289 (ttp-110) REVERT: B 21 LEU cc_start: 0.7861 (mt) cc_final: 0.7522 (mp) REVERT: B 182 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6791 (mp) REVERT: B 226 ASN cc_start: 0.8410 (m110) cc_final: 0.7586 (t0) REVERT: A 28 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6543 (tp) REVERT: A 36 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7584 (tp) REVERT: A 162 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7290 (tp) REVERT: A 167 GLN cc_start: 0.5756 (OUTLIER) cc_final: 0.5236 (mt0) REVERT: A 203 MET cc_start: 0.9057 (mmp) cc_final: 0.8761 (mmm) REVERT: A 205 CYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7393 (m) REVERT: A 294 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7433 (mp) REVERT: A 305 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7260 (tt0) outliers start: 15 outliers final: 5 residues processed: 72 average time/residue: 0.3230 time to fit residues: 24.4437 Evaluate side-chains 71 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.088 ------------------------------------------------------------------------------- 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 28 LEU Chi-restraints excluded: chain A residue 36 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 5.9990 chunk 4 optimal weight: 0.0470 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 0.0070 chunk 51 optimal weight: 0.0270 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3879 r_free = 0.3879 target = 0.172940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.131695 restraints weight = 4433.557| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.69 r_work: 0.3124 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4393 Z= 0.125 Angle : 0.513 5.443 5993 Z= 0.264 Chirality : 0.042 0.133 692 Planarity : 0.004 0.039 740 Dihedral : 7.382 70.876 621 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.37), residues: 544 helix: 1.20 (0.32), residues: 274 sheet: -0.76 (0.53), residues: 101 loop : -1.32 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.023 0.001 TYR D 53 PHE 0.010 0.001 PHE B 56 TRP 0.007 0.001 TRP A 165 HIS 0.002 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 4391) covalent geometry : angle 0.51300 / 0.26 ( 5989) SS BOND : bond 0.00081 / 0.04 ( 2) SS BOND : angle 0.44326 / 0.29 ( 4) hydrogen bonds : bond 0.03870 / 2.60 ( 240) hydrogen bonds : angle 4.54498 / 3.34 ( 705) *********************** 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 69 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.150 Fit side-chains REVERT: B 17 ARG cc_start: 0.7955 (mtp85) cc_final: 0.7340 (ttp-110) REVERT: B 182 ILE cc_start: 0.7184 (OUTLIER) cc_final: 0.6795 (mp) REVERT: B 226 ASN cc_start: 0.8410 (m110) cc_final: 0.7609 (t0) REVERT: A 36 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7604 (tp) REVERT: A 162 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7295 (tp) REVERT: A 167 GLN cc_start: 0.5986 (OUTLIER) cc_final: 0.5365 (mt0) REVERT: A 195 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8044 (tp) REVERT: A 203 MET cc_start: 0.9058 (mmp) cc_final: 0.8763 (mmm) REVERT: A 205 CYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7424 (m) REVERT: A 294 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7452 (mp) REVERT: A 305 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7268 (tt0) outliers start: 15 outliers final: 5 residues processed: 66 average time/residue: 0.3377 time to fit residues: 23.4434 Evaluate side-chains 66 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 36 LEU 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 195 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 26 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.0970 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 GLN ** 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 = 0.3859 r_free = 0.3859 target = 0.171240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.129095 restraints weight = 4435.312| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.60 r_work: 0.3112 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4393 Z= 0.142 Angle : 0.526 5.761 5993 Z= 0.270 Chirality : 0.042 0.126 692 Planarity : 0.004 0.038 740 Dihedral : 7.435 71.388 621 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.02 % Allowed : 18.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.37), residues: 544 helix: 1.15 (0.32), residues: 274 sheet: -0.76 (0.53), residues: 101 loop : -1.29 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 166 TYR 0.024 0.001 TYR D 53 PHE 0.011 0.001 PHE A 94 TRP 0.007 0.001 TRP A 165 HIS 0.002 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 4391) covalent geometry : angle 0.52593 / 0.27 ( 5989) SS BOND : bond 0.00086 / 0.04 ( 2) SS BOND : angle 0.47557 / 0.31 ( 4) hydrogen bonds : bond 0.04032 / 2.72 ( 240) hydrogen bonds : angle 4.58982 / 3.37 ( 705) *********************** 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 68 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.151 Fit side-chains REVERT: B 17 ARG cc_start: 0.7939 (mtp85) cc_final: 0.7321 (ttp-110) REVERT: B 182 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.6877 (mp) REVERT: B 226 ASN cc_start: 0.8401 (m110) cc_final: 0.7636 (t0) REVERT: A 36 LEU cc_start: 0.8010 (mt) cc_final: 0.7580 (tp) REVERT: A 203 MET cc_start: 0.9046 (mmp) cc_final: 0.8786 (mmm) REVERT: A 205 CYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7409 (m) REVERT: A 294 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7453 (mp) REVERT: A 305 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7272 (tt0) outliers start: 13 outliers final: 8 residues processed: 65 average time/residue: 0.3405 time to fit residues: 23.1639 Evaluate side-chains 66 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.090 ------------------------------------------------------------------------------- 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 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 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.171150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.128874 restraints weight = 4430.097| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.62 r_work: 0.3107 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4393 Z= 0.143 Angle : 0.526 5.799 5993 Z= 0.270 Chirality : 0.042 0.122 692 Planarity : 0.004 0.039 740 Dihedral : 7.449 71.412 621 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.37), residues: 544 helix: 1.13 (0.32), residues: 274 sheet: -0.71 (0.54), residues: 97 loop : -1.32 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 166 TYR 0.024 0.001 TYR D 53 PHE 0.011 0.001 PHE A 94 TRP 0.007 0.001 TRP A 165 HIS 0.003 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 4391) covalent geometry : angle 0.52616 / 0.27 ( 5989) SS BOND : bond 0.00092 / 0.05 ( 2) SS BOND : angle 0.47515 / 0.31 ( 4) hydrogen bonds : bond 0.04042 / 2.72 ( 240) hydrogen bonds : angle 4.59373 / 3.38 ( 705) *********************** 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 70 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.095 Fit side-chains REVERT: B 17 ARG cc_start: 0.7936 (mtp85) cc_final: 0.7399 (ttp-110) REVERT: B 21 LEU cc_start: 0.7854 (mt) cc_final: 0.7544 (mp) REVERT: B 182 ILE cc_start: 0.7203 (OUTLIER) cc_final: 0.6862 (mp) REVERT: B 226 ASN cc_start: 0.8401 (m110) cc_final: 0.7666 (t0) REVERT: A 36 LEU cc_start: 0.8013 (mt) cc_final: 0.7574 (tp) REVERT: A 203 MET cc_start: 0.9044 (mmp) cc_final: 0.8784 (mmm) REVERT: A 205 CYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7421 (m) REVERT: A 294 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7457 (mp) REVERT: A 305 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: D 108 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7949 (pt0) outliers start: 14 outliers final: 7 residues processed: 67 average time/residue: 0.3644 time to fit residues: 25.5523 Evaluate side-chains 66 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 108 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.170666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.128222 restraints weight = 4447.935| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.59 r_work: 0.3122 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4393 Z= 0.137 Angle : 0.524 5.636 5993 Z= 0.268 Chirality : 0.042 0.126 692 Planarity : 0.004 0.038 740 Dihedral : 7.424 71.097 621 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.26 % Allowed : 18.60 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.37), residues: 544 helix: 1.11 (0.32), residues: 278 sheet: -0.65 (0.54), residues: 97 loop : -1.24 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 166 TYR 0.024 0.001 TYR D 53 PHE 0.011 0.001 PHE B 56 TRP 0.006 0.001 TRP A 165 HIS 0.002 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 4391) covalent geometry : angle 0.52396 / 0.27 ( 5989) SS BOND : bond 0.00075 / 0.04 ( 2) SS BOND : angle 0.48064 / 0.31 ( 4) hydrogen bonds : bond 0.04001 / 2.69 ( 240) hydrogen bonds : angle 4.56606 / 3.36 ( 705) ********************** 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 67 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.151 Fit side-chains REVERT: B 17 ARG cc_start: 0.7933 (mtp85) cc_final: 0.7397 (ttp-110) REVERT: B 21 LEU cc_start: 0.7866 (mt) cc_final: 0.7509 (mp) REVERT: B 182 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6873 (mp) REVERT: B 226 ASN cc_start: 0.8411 (m110) cc_final: 0.7660 (t0) REVERT: A 28 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6757 (tp) REVERT: A 36 LEU cc_start: 0.8013 (mt) cc_final: 0.7576 (tp) REVERT: A 203 MET cc_start: 0.9032 (mmp) cc_final: 0.8759 (mmm) REVERT: A 205 CYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7406 (m) REVERT: A 294 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7483 (mp) REVERT: A 305 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7287 (tt0) REVERT: D 108 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7943 (pt0) outliers start: 14 outliers final: 7 residues processed: 65 average time/residue: 0.3449 time to fit residues: 23.5582 Evaluate side-chains 65 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.088 ------------------------------------------------------------------------------- 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 28 LEU 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 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 Chi-restraints excluded: chain D residue 108 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3831 r_free = 0.3831 target = 0.168935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.126599 restraints weight = 4488.037| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.60 r_work: 0.3112 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4393 Z= 0.161 Angle : 0.545 6.117 5993 Z= 0.279 Chirality : 0.043 0.129 692 Planarity : 0.004 0.039 740 Dihedral : 7.501 71.361 621 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.26 % Allowed : 18.60 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.37), residues: 544 helix: 1.01 (0.32), residues: 279 sheet: -0.71 (0.54), residues: 97 loop : -1.23 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 166 TYR 0.026 0.002 TYR D 53 PHE 0.012 0.002 PHE A 94 TRP 0.009 0.001 TRP A 165 HIS 0.003 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 4391) covalent geometry : angle 0.54468 / 0.28 ( 5989) SS BOND : bond 0.00089 / 0.05 ( 2) SS BOND : angle 0.53214 / 0.35 ( 4) hydrogen bonds : bond 0.04199 / 2.83 ( 240) hydrogen bonds : angle 4.63655 / 3.41 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1455.31 seconds wall clock time: 25 minutes 29.74 seconds (1529.74 seconds total)