Starting phenix.real_space_refine on Tue Feb 11 02:13:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zni_60272/02_2025/8zni_60272.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zni_60272/02_2025/8zni_60272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zni_60272/02_2025/8zni_60272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zni_60272/02_2025/8zni_60272.map" model { file = "/net/cci-nas-00/data/ceres_data/8zni_60272/02_2025/8zni_60272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zni_60272/02_2025/8zni_60272.cif" } resolution = 3.29 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= 0.000 sd= 0.009 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 15 5.16 5 C 2239 2.51 5 N 599 2.21 5 O 732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3585 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 832 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 12, 'TRANS': 107} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2669 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 22, 'TRANS': 353} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 5, 'PHE:plan': 7, 'GLU:plan': 8, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 150 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 3.13, per 1000 atoms: 0.87 Number of scatterers: 3585 At special positions: 0 Unit cell: (58.1, 72.21, 106.24, 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 15 16.00 O 732 8.00 N 599 7.00 C 2239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 46 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM 3527 O5 NAG B 902 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3513 O5 NAG B 901 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 901 " - " ASN B 411 " " NAG B 902 " - " ASN B 386 " " NAG B 905 " - " ASN B 328 " Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 538.1 milliseconds 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 920 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 3.630A pdb=" N LYS A 62 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 15 through 16 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.735A pdb=" N PHE B 65 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 48 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 67 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 165 through 174 removed outlier: 6.976A pdb=" N CYS B 298 " --> pdb=" O ASN B 166 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR B 168 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLN B 300 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE B 170 " --> pdb=" O GLN B 300 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 304 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 174 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B 297 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE B 209 " --> pdb=" O MET B 202 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 228 through 229 Processing sheet with id=AA7, first strand: chain 'B' and resid 321 through 323 removed outlier: 6.942A pdb=" N ILE B 322 " --> pdb=" O SER B 422 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 330 through 332 Processing sheet with id=AA9, first strand: chain 'B' and resid 348 through 351 removed outlier: 4.216A pdb=" N THR B 349 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B 406 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 405 " --> pdb=" O HIS B 417 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 415 " --> pdb=" O ARG B 407 " (cutoff:3.500A) 35 hydrogen bonds defined for protein. 87 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: 0.77 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1007 1.33 - 1.45: 630 1.45 - 1.57: 2005 1.57 - 1.69: 0 1.69 - 1.82: 20 Bond restraints: 3662 Sorted by residual: bond pdb=" N CYS A 72 " pdb=" CA CYS A 72 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.46e+01 bond pdb=" N SER A 43 " pdb=" CA SER A 43 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.32e-02 5.74e+03 7.30e+00 bond pdb=" N LYS A 42 " pdb=" CA LYS A 42 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.92e+00 bond pdb=" N LEU A 45 " pdb=" CA LEU A 45 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.25e-02 6.40e+03 6.46e+00 bond pdb=" N LEU A 44 " pdb=" CA LEU A 44 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.45e+00 ... (remaining 3657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 4796 1.48 - 2.97: 181 2.97 - 4.45: 39 4.45 - 5.93: 16 5.93 - 7.42: 1 Bond angle restraints: 5033 Sorted by residual: angle pdb=" N LEU B 96 " pdb=" CA LEU B 96 " pdb=" C LEU B 96 " ideal model delta sigma weight residual 114.56 109.82 4.74 1.27e+00 6.20e-01 1.39e+01 angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" O GLY A 40 " ideal model delta sigma weight residual 122.39 118.01 4.38 1.25e+00 6.40e-01 1.23e+01 angle pdb=" CA SER A 43 " pdb=" C SER A 43 " pdb=" O SER A 43 " ideal model delta sigma weight residual 121.87 118.14 3.73 1.10e+00 8.26e-01 1.15e+01 angle pdb=" CA CYS A 46 " pdb=" C CYS A 46 " pdb=" O CYS A 46 " ideal model delta sigma weight residual 120.98 118.01 2.97 1.08e+00 8.57e-01 7.58e+00 angle pdb=" CA PRO A 73 " pdb=" C PRO A 73 " pdb=" O PRO A 73 " ideal model delta sigma weight residual 121.56 118.40 3.16 1.16e+00 7.43e-01 7.40e+00 ... (remaining 5028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 1961 16.38 - 32.76: 198 32.76 - 49.14: 54 49.14 - 65.51: 15 65.51 - 81.89: 2 Dihedral angle restraints: 2230 sinusoidal: 804 harmonic: 1426 Sorted by residual: dihedral pdb=" CA PHE B 92 " pdb=" C PHE B 92 " pdb=" N LEU B 93 " pdb=" CA LEU B 93 " ideal model delta harmonic sigma weight residual 180.00 161.42 18.58 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ASP B 215 " pdb=" CB ASP B 215 " pdb=" CG ASP B 215 " pdb=" OD1 ASP B 215 " ideal model delta sinusoidal sigma weight residual -30.00 -88.98 58.98 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ILE B 404 " pdb=" CB ILE B 404 " pdb=" CG1 ILE B 404 " pdb=" CD1 ILE B 404 " ideal model delta sinusoidal sigma weight residual 180.00 122.15 57.85 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 2227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.828: 612 0.828 - 1.655: 0 1.655 - 2.483: 0 2.483 - 3.311: 1 3.311 - 4.138: 1 Chirality restraints: 614 Sorted by residual: chirality pdb=" C1 NAG B 902 " pdb=" ND2 ASN B 386 " pdb=" C2 NAG B 902 " pdb=" O5 NAG B 902 " both_signs ideal model delta sigma weight residual False -2.40 1.74 -4.14 2.00e-01 2.50e+01 4.28e+02 chirality pdb=" C1 NAG B 905 " pdb=" ND2 ASN B 328 " pdb=" C2 NAG B 905 " pdb=" O5 NAG B 905 " both_signs ideal model delta sigma weight residual False -2.40 0.26 -2.66 2.00e-01 2.50e+01 1.77e+02 chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 411 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-01 2.50e+01 8.79e-01 ... (remaining 611 not shown) Planarity restraints: 655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 328 " -0.134 2.00e-02 2.50e+03 4.85e-01 2.94e+03 pdb=" CG ASN B 328 " 0.104 2.00e-02 2.50e+03 pdb=" OD1 ASN B 328 " -0.410 2.00e-02 2.50e+03 pdb=" ND2 ASN B 328 " 0.884 2.00e-02 2.50e+03 pdb=" C1 NAG B 905 " -0.444 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 386 " -0.004 2.00e-02 2.50e+03 1.60e-01 3.21e+02 pdb=" CG ASN B 386 " 0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN B 386 " -0.104 2.00e-02 2.50e+03 pdb=" ND2 ASN B 386 " 0.267 2.00e-02 2.50e+03 pdb=" C1 NAG B 902 " -0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 411 " -0.026 2.00e-02 2.50e+03 4.82e-02 2.90e+01 pdb=" CG ASN B 411 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN B 411 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN B 411 " 0.086 2.00e-02 2.50e+03 pdb=" C1 NAG B 901 " -0.054 2.00e-02 2.50e+03 ... (remaining 652 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.96: 2 1.96 - 2.69: 168 2.69 - 3.43: 5166 3.43 - 4.16: 8097 4.16 - 4.90: 13473 Nonbonded interactions: 26906 Sorted by model distance: nonbonded pdb=" ND2 ASN B 328 " pdb=" C4 NAG B 905 " model vdw 1.220 3.550 nonbonded pdb=" ND2 ASN B 328 " pdb=" C3 NAG B 905 " model vdw 1.469 2.840 nonbonded pdb=" ND2 ASN B 328 " pdb=" C5 NAG B 905 " model vdw 1.956 2.840 nonbonded pdb=" ND2 ASN B 229 " pdb=" C2 NAG B 904 " model vdw 2.130 3.550 nonbonded pdb=" ND2 ASN B 277 " pdb=" C1 NAG B 906 " model vdw 2.159 3.550 ... (remaining 26901 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: 1.270 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.200 Find NCS groups from input model: 0.030 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5896 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 : 0.004 0.039 3662 Z= 0.272 Angle : 0.713 7.418 5033 Z= 0.370 Chirality : 0.205 4.138 614 Planarity : 0.005 0.061 652 Dihedral : 14.834 81.893 1307 Min Nonbonded Distance : 1.220 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 0.00 % Allowed : 31.70 % Favored : 68.30 % 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: -3.51 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -2.02 (0.49), residues: 121 loop : -2.65 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 112 HIS 0.002 0.001 HIS A 91 PHE 0.021 0.002 PHE B 33 TYR 0.021 0.001 TYR B 235 ARG 0.005 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8404 (p0) cc_final: 0.8195 (p0) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1981 time to fit residues: 16.7666 Evaluate side-chains 45 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 20 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 0.0270 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN B 300 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.109135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.097616 restraints weight = 12959.565| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 4.91 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3662 Z= 0.218 Angle : 0.838 16.471 5033 Z= 0.384 Chirality : 0.072 1.290 614 Planarity : 0.005 0.048 652 Dihedral : 7.967 49.247 643 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 5.76 % Allowed : 28.82 % Favored : 65.42 % 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: -3.58 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -2.57 (0.42), residues: 144 loop : -2.43 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 56 HIS 0.002 0.001 HIS A 91 PHE 0.010 0.001 PHE B 284 TYR 0.020 0.001 TYR B 235 ARG 0.004 0.001 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8696 (p0) cc_final: 0.8447 (p0) outliers start: 20 outliers final: 10 residues processed: 61 average time/residue: 0.1373 time to fit residues: 10.9159 Evaluate side-chains 53 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 346 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 226 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.104325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.092786 restraints weight = 13081.028| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 4.80 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3662 Z= 0.221 Angle : 0.706 11.043 5033 Z= 0.343 Chirality : 0.049 0.483 614 Planarity : 0.005 0.045 652 Dihedral : 7.105 51.781 643 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer: Outliers : 3.75 % Allowed : 30.26 % Favored : 65.99 % 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: -3.61 (0.35), residues: 482 helix: None (None), residues: 0 sheet: -2.63 (0.41), residues: 144 loop : -2.42 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 352 HIS 0.002 0.001 HIS A 91 PHE 0.009 0.001 PHE B 132 TYR 0.020 0.001 TYR B 235 ARG 0.004 0.001 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8519 (tp) cc_final: 0.8302 (pt) REVERT: A 116 ASN cc_start: 0.8619 (p0) cc_final: 0.8388 (p0) REVERT: B 269 ARG cc_start: 0.7622 (mmm-85) cc_final: 0.7054 (mmm-85) outliers start: 13 outliers final: 9 residues processed: 51 average time/residue: 0.1588 time to fit residues: 10.3044 Evaluate side-chains 46 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 360 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.0030 chunk 2 optimal weight: 7.9990 chunk 25 optimal weight: 0.1980 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 10 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** 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 = 0.4179 r_free = 0.4179 target = 0.101765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.091091 restraints weight = 13727.452| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 4.40 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3662 Z= 0.256 Angle : 0.708 9.950 5033 Z= 0.349 Chirality : 0.051 0.549 614 Planarity : 0.005 0.045 652 Dihedral : 6.441 31.748 643 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % Rotamer: Outliers : 8.93 % Allowed : 26.80 % Favored : 64.27 % 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: -3.72 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -2.36 (0.43), residues: 144 loop : -2.69 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 352 HIS 0.002 0.001 HIS B 71 PHE 0.009 0.002 PHE B 33 TYR 0.024 0.002 TYR B 235 ARG 0.002 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 37 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 132 PHE cc_start: 0.6415 (OUTLIER) cc_final: 0.4904 (t80) REVERT: B 213 MET cc_start: 0.6067 (ttp) cc_final: 0.5764 (ttt) REVERT: B 265 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7327 (tpt-90) REVERT: B 404 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7554 (pt) outliers start: 31 outliers final: 19 residues processed: 62 average time/residue: 0.1379 time to fit residues: 11.0667 Evaluate side-chains 57 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 35 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 265 ARG Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 405 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 38 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 0.0980 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** 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 = 0.4094 r_free = 0.4094 target = 0.097958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.086404 restraints weight = 13683.056| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 4.82 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 3662 Z= 0.332 Angle : 0.777 9.047 5033 Z= 0.393 Chirality : 0.053 0.526 614 Planarity : 0.005 0.049 652 Dihedral : 6.590 33.162 643 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.63 % Favored : 82.37 % Rotamer: Outliers : 8.93 % Allowed : 26.22 % Favored : 64.84 % 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: -4.00 (0.35), residues: 482 helix: None (None), residues: 0 sheet: -2.42 (0.41), residues: 163 loop : -2.94 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 162 HIS 0.006 0.001 HIS A 91 PHE 0.012 0.002 PHE B 33 TYR 0.017 0.002 TYR B 235 ARG 0.002 0.000 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 31 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 TYR cc_start: 0.3606 (OUTLIER) cc_final: 0.3331 (m-10) REVERT: B 132 PHE cc_start: 0.6556 (OUTLIER) cc_final: 0.5082 (t80) REVERT: B 139 MET cc_start: 0.6059 (tpp) cc_final: 0.5410 (tpp) REVERT: B 237 SER cc_start: 0.7016 (OUTLIER) cc_final: 0.6223 (p) REVERT: B 404 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7534 (pt) outliers start: 31 outliers final: 20 residues processed: 59 average time/residue: 0.1319 time to fit residues: 9.9848 Evaluate side-chains 55 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 31 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 405 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** 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 = 0.4093 r_free = 0.4093 target = 0.098036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.086440 restraints weight = 13758.259| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 4.80 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3662 Z= 0.297 Angle : 0.738 7.508 5033 Z= 0.375 Chirality : 0.053 0.516 614 Planarity : 0.005 0.051 652 Dihedral : 6.445 32.269 643 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.18 % Favored : 83.82 % Rotamer: Outliers : 6.92 % Allowed : 28.24 % Favored : 64.84 % 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: -3.97 (0.35), residues: 482 helix: None (None), residues: 0 sheet: -2.41 (0.44), residues: 139 loop : -2.93 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 352 HIS 0.005 0.001 HIS A 91 PHE 0.012 0.002 PHE B 33 TYR 0.018 0.001 TYR B 235 ARG 0.003 0.001 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 31 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 132 PHE cc_start: 0.6507 (OUTLIER) cc_final: 0.4942 (t80) REVERT: B 139 MET cc_start: 0.6151 (tpp) cc_final: 0.5513 (tpp) REVERT: B 237 SER cc_start: 0.7384 (OUTLIER) cc_final: 0.6605 (p) REVERT: B 404 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7488 (pt) outliers start: 24 outliers final: 19 residues processed: 52 average time/residue: 0.1276 time to fit residues: 8.8361 Evaluate side-chains 51 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 29 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 405 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 0.0050 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** 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 = 0.4106 r_free = 0.4106 target = 0.098674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.087369 restraints weight = 13320.896| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 4.65 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3662 Z= 0.235 Angle : 0.711 7.507 5033 Z= 0.357 Chirality : 0.052 0.472 614 Planarity : 0.005 0.053 652 Dihedral : 6.043 31.957 643 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.60 % Favored : 83.40 % Rotamer: Outliers : 7.20 % Allowed : 28.24 % Favored : 64.55 % 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: -3.91 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -2.40 (0.43), residues: 145 loop : -2.88 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 352 HIS 0.002 0.001 HIS A 91 PHE 0.011 0.001 PHE B 33 TYR 0.017 0.001 TYR B 235 ARG 0.004 0.001 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 32 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: B 132 PHE cc_start: 0.6461 (OUTLIER) cc_final: 0.4924 (t80) REVERT: B 404 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7653 (pt) outliers start: 25 outliers final: 21 residues processed: 53 average time/residue: 0.1412 time to fit residues: 9.7422 Evaluate side-chains 53 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 30 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 405 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.0770 chunk 39 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** 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 = 0.4109 r_free = 0.4109 target = 0.098844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.087432 restraints weight = 13611.667| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 4.70 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3662 Z= 0.227 Angle : 0.697 7.465 5033 Z= 0.352 Chirality : 0.051 0.472 614 Planarity : 0.005 0.052 652 Dihedral : 5.826 31.991 643 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.94 % Favored : 85.06 % Rotamer: Outliers : 7.20 % Allowed : 28.82 % Favored : 63.98 % 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: -3.91 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -2.35 (0.44), residues: 141 loop : -2.90 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 352 HIS 0.002 0.001 HIS A 91 PHE 0.011 0.001 PHE B 33 TYR 0.015 0.001 TYR B 235 ARG 0.004 0.001 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 30 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: B 132 PHE cc_start: 0.6338 (OUTLIER) cc_final: 0.4753 (t80) REVERT: B 213 MET cc_start: 0.6285 (ttt) cc_final: 0.5682 (ttt) REVERT: B 404 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7647 (pt) outliers start: 25 outliers final: 20 residues processed: 49 average time/residue: 0.1241 time to fit residues: 8.1177 Evaluate side-chains 52 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 30 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 405 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** 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 = 0.4115 r_free = 0.4115 target = 0.099117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.087740 restraints weight = 13241.867| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 4.70 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3662 Z= 0.216 Angle : 0.697 10.659 5033 Z= 0.346 Chirality : 0.051 0.464 614 Planarity : 0.005 0.051 652 Dihedral : 5.615 32.390 643 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.11 % Favored : 85.89 % Rotamer: Outliers : 7.20 % Allowed : 28.82 % Favored : 63.98 % 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: -3.97 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -2.61 (0.42), residues: 147 loop : -2.82 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 352 HIS 0.003 0.001 HIS A 91 PHE 0.018 0.002 PHE B 33 TYR 0.013 0.001 TYR B 235 ARG 0.004 0.001 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 31 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: B 132 PHE cc_start: 0.6201 (OUTLIER) cc_final: 0.4580 (t80) REVERT: B 213 MET cc_start: 0.6447 (ttt) cc_final: 0.5826 (ttt) REVERT: B 404 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7593 (pt) outliers start: 25 outliers final: 22 residues processed: 51 average time/residue: 0.1214 time to fit residues: 8.1939 Evaluate side-chains 55 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 31 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 405 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** 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 = 0.4086 r_free = 0.4086 target = 0.097560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.086491 restraints weight = 13256.913| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 4.59 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3662 Z= 0.289 Angle : 0.736 9.350 5033 Z= 0.371 Chirality : 0.054 0.503 614 Planarity : 0.005 0.052 652 Dihedral : 5.785 31.093 643 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.01 % Favored : 82.99 % Rotamer: Outliers : 6.92 % Allowed : 28.53 % Favored : 64.55 % 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: -4.09 (0.35), residues: 482 helix: None (None), residues: 0 sheet: -2.68 (0.42), residues: 147 loop : -2.91 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 162 HIS 0.003 0.001 HIS A 91 PHE 0.013 0.002 PHE B 33 TYR 0.016 0.002 TYR B 10 ARG 0.004 0.001 ARG B 265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 33 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: B 132 PHE cc_start: 0.6552 (OUTLIER) cc_final: 0.5058 (t80) REVERT: B 213 MET cc_start: 0.6502 (ttt) cc_final: 0.6090 (ttt) REVERT: B 404 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7551 (pt) outliers start: 24 outliers final: 22 residues processed: 52 average time/residue: 0.1312 time to fit residues: 9.0863 Evaluate side-chains 55 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 31 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 405 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 0.0870 chunk 11 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 35 optimal weight: 2.9990 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** 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 = 0.4123 r_free = 0.4123 target = 0.099691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.088587 restraints weight = 13563.352| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 4.63 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3662 Z= 0.198 Angle : 0.701 9.442 5033 Z= 0.349 Chirality : 0.051 0.457 614 Planarity : 0.005 0.053 652 Dihedral : 5.589 32.534 643 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer: Outliers : 6.34 % Allowed : 29.39 % Favored : 64.27 % 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: -3.96 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -2.59 (0.43), residues: 145 loop : -2.82 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 140 HIS 0.002 0.001 HIS B 143 PHE 0.014 0.002 PHE B 33 TYR 0.013 0.001 TYR B 235 ARG 0.005 0.001 ARG B 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2001.16 seconds wall clock time: 36 minutes 18.69 seconds (2178.69 seconds total)