Starting phenix.real_space_refine on Fri May 9 20:13:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zni_60272/05_2025/8zni_60272.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zni_60272/05_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_60272/05_2025/8zni_60272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zni_60272/05_2025/8zni_60272.map" model { file = "/net/cci-nas-00/data/ceres_data/8zni_60272/05_2025/8zni_60272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zni_60272/05_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-5687/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: 2.95, per 1000 atoms: 0.82 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: 0.86 Conformation dependent library (CDL) restraints added in 457.8 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: 0.37 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: 0.73 Time building geometry restraints manager: 1.01 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.800 Find NCS groups from input model: 0.030 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.810 ------------------------------------------------------------------------------- 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 : 0.015 0.769 3666 Z= 0.779 Angle : 1.649 65.639 5044 Z= 0.618 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 Details of bonding type rmsd link_NAG-ASN : bond 0.51946 ( 3) link_NAG-ASN : angle 35.19294 ( 9) hydrogen bonds : bond 0.28184 ( 35) hydrogen bonds : angle 14.10424 ( 87) SS BOND : bond 0.00801 ( 1) SS BOND : angle 1.48545 ( 2) covalent geometry : bond 0.00401 ( 3662) covalent geometry : angle 0.71345 ( 5033) *********************** 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 : 0.433 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: 0.1895 time to fit residues: 16.1318 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 : 0.373 ------------------------------------------------------------------------------- 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 3666 Z= 0.151 Angle : 1.019 27.481 5044 Z= 0.429 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 3) link_NAG-ASN : angle 13.73813 ( 9) hydrogen bonds : bond 0.03530 ( 35) hydrogen bonds : angle 10.58641 ( 87) SS BOND : bond 0.00425 ( 1) SS BOND : angle 0.42282 ( 2) covalent geometry : bond 0.00326 ( 3662) covalent geometry : angle 0.83821 ( 5033) *********************** 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 : 0.392 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: 0.1317 time to fit residues: 10.3301 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 : 0.398 ------------------------------------------------------------------------------- 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: 0.8980 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4202 r_free = 0.4202 target = 0.104014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.092473 restraints weight = 13175.500| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 4.80 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3666 Z= 0.149 Angle : 0.829 21.896 5044 Z= 0.374 Chirality : 0.050 0.519 614 Planarity : 0.005 0.045 652 Dihedral : 7.195 52.677 643 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 4.32 % Allowed : 29.97 % Favored : 65.71 % 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: -3.65 (0.35), residues: 482 helix: None (None), residues: 0 sheet: -2.64 (0.42), residues: 140 loop : -2.47 (0.31), residues: 342 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 0.021 0.001 TYR B 235 ARG 0.003 0.000 ARG B 387 Details of bonding type rmsd link_NAG-ASN : bond 0.01883 ( 3) link_NAG-ASN : angle 10.13550 ( 9) hydrogen bonds : bond 0.04052 ( 35) hydrogen bonds : angle 9.64135 ( 87) SS BOND : bond 0.00664 ( 1) SS BOND : angle 0.62715 ( 2) covalent geometry : bond 0.00325 ( 3662) covalent geometry : angle 0.71009 ( 5033) *********************** 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 57 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8524 (tp) cc_final: 0.8307 (pt) REVERT: A 116 ASN cc_start: 0.8620 (p0) cc_final: 0.8391 (p0) REVERT: B 175 ARG cc_start: 0.6989 (mmp-170) cc_final: 0.6785 (mmp-170) REVERT: B 269 ARG cc_start: 0.7635 (mmm-85) cc_final: 0.7061 (mmm-85) outliers start: 15 outliers final: 11 residues processed: 53 average time/residue: 0.1497 time to fit residues: 10.0868 Evaluate side-chains 47 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 46 CYS 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 235 TYR Chi-restraints excluded: chain B residue 237 SER 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: 6.9990 chunk 18 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 33 optimal weight: 9.9990 chunk 27 optimal weight: 0.0000 chunk 10 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 overall best weight: 0.7546 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.104099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.093495 restraints weight = 13582.351| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 4.41 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3666 Z= 0.125 Angle : 0.789 21.162 5044 Z= 0.354 Chirality : 0.050 0.498 614 Planarity : 0.005 0.043 652 Dihedral : 6.270 35.242 643 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.45 % Favored : 87.55 % Rotamer: Outliers : 6.92 % Allowed : 27.67 % 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: -3.61 (0.35), residues: 482 helix: None (None), residues: 0 sheet: -2.52 (0.43), residues: 139 loop : -2.50 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 352 HIS 0.001 0.001 HIS B 417 PHE 0.009 0.001 PHE B 33 TYR 0.018 0.001 TYR B 235 ARG 0.002 0.001 ARG B 107 Details of bonding type rmsd link_NAG-ASN : bond 0.01210 ( 3) link_NAG-ASN : angle 9.71684 ( 9) hydrogen bonds : bond 0.03060 ( 35) hydrogen bonds : angle 8.95539 ( 87) SS BOND : bond 0.00338 ( 1) SS BOND : angle 0.18583 ( 2) covalent geometry : bond 0.00276 ( 3662) covalent geometry : angle 0.67456 ( 5033) *********************** 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 62 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 38 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: B 132 PHE cc_start: 0.6036 (OUTLIER) cc_final: 0.4543 (t80) REVERT: B 213 MET cc_start: 0.5897 (ttp) cc_final: 0.5586 (ttt) REVERT: B 269 ARG cc_start: 0.7594 (mmm-85) cc_final: 0.7357 (mmm-85) REVERT: B 404 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7490 (pt) outliers start: 24 outliers final: 12 residues processed: 57 average time/residue: 0.1341 time to fit residues: 9.9577 Evaluate side-chains 49 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 47 ILE 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 280 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 404 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 0.1980 chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 0.0370 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 overall best weight: 0.3858 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.105378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.094890 restraints weight = 13594.075| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 4.39 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3666 Z= 0.112 Angle : 0.764 20.612 5044 Z= 0.346 Chirality : 0.049 0.429 614 Planarity : 0.005 0.040 652 Dihedral : 5.758 35.409 643 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 5.76 % Allowed : 29.11 % Favored : 65.13 % 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 (0.35), residues: 482 helix: None (None), residues: 0 sheet: -2.63 (0.42), residues: 142 loop : -2.32 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 352 HIS 0.001 0.000 HIS B 417 PHE 0.009 0.001 PHE B 26 TYR 0.025 0.001 TYR B 235 ARG 0.002 0.000 ARG B 269 Details of bonding type rmsd link_NAG-ASN : bond 0.01474 ( 3) link_NAG-ASN : angle 8.99005 ( 9) hydrogen bonds : bond 0.02940 ( 35) hydrogen bonds : angle 8.49505 ( 87) SS BOND : bond 0.00302 ( 1) SS BOND : angle 0.23055 ( 2) covalent geometry : bond 0.00245 ( 3662) covalent geometry : angle 0.66378 ( 5033) *********************** 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 58 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: B 10 TYR cc_start: 0.3811 (OUTLIER) cc_final: 0.3304 (m-10) REVERT: B 132 PHE cc_start: 0.5694 (OUTLIER) cc_final: 0.4311 (t80) REVERT: B 139 MET cc_start: 0.5486 (tpp) cc_final: 0.4885 (tpp) REVERT: B 213 MET cc_start: 0.5965 (ttp) cc_final: 0.5588 (ttt) REVERT: B 265 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7376 (tpt-90) outliers start: 20 outliers final: 14 residues processed: 53 average time/residue: 0.1551 time to fit residues: 10.3815 Evaluate side-chains 51 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 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 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 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 360 THR Chi-restraints excluded: chain B residue 402 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 9 optimal weight: 0.3980 chunk 27 optimal weight: 0.0010 chunk 3 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 overall best weight: 1.4590 ------------------------------------------------------------------------------- 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 87 ASN ** B 313 GLN ** 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 = 0.4150 r_free = 0.4150 target = 0.100068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.088976 restraints weight = 13796.448| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 4.47 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3666 Z= 0.184 Angle : 0.799 21.055 5044 Z= 0.378 Chirality : 0.052 0.516 614 Planarity : 0.005 0.046 652 Dihedral : 5.925 29.884 643 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.18 % Favored : 83.82 % Rotamer: Outliers : 7.49 % Allowed : 28.53 % 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: -3.71 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -2.28 (0.41), residues: 163 loop : -2.70 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 162 HIS 0.003 0.001 HIS A 91 PHE 0.010 0.002 PHE B 33 TYR 0.017 0.002 TYR B 235 ARG 0.003 0.001 ARG A 14 Details of bonding type rmsd link_NAG-ASN : bond 0.01213 ( 3) link_NAG-ASN : angle 8.81138 ( 9) hydrogen bonds : bond 0.03330 ( 35) hydrogen bonds : angle 8.67075 ( 87) SS BOND : bond 0.00678 ( 1) SS BOND : angle 0.89688 ( 2) covalent geometry : bond 0.00404 ( 3662) covalent geometry : angle 0.70743 ( 5033) *********************** 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 59 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 33 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: B 132 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.5119 (t80) REVERT: B 139 MET cc_start: 0.6030 (tpp) cc_final: 0.5499 (tpp) REVERT: B 213 MET cc_start: 0.6384 (ttp) cc_final: 0.5983 (ttt) REVERT: B 265 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7770 (ttt-90) REVERT: B 269 ARG cc_start: 0.7734 (mmm-85) cc_final: 0.7323 (mmm-85) REVERT: B 404 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7583 (pt) outliers start: 26 outliers final: 20 residues processed: 56 average time/residue: 0.1469 time to fit residues: 10.7962 Evaluate side-chains 54 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 31 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE 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 111 VAL Chi-restraints excluded: chain A residue 116 ASN 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 265 ARG Chi-restraints excluded: chain B residue 280 ILE 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=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: 0.9980 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.099064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.087397 restraints weight = 13529.876| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 4.79 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3666 Z= 0.183 Angle : 0.802 20.837 5044 Z= 0.382 Chirality : 0.053 0.489 614 Planarity : 0.005 0.045 652 Dihedral : 5.943 30.501 643 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.18 % Favored : 83.82 % Rotamer: Outliers : 7.78 % Allowed : 28.24 % 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: -3.83 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -2.31 (0.42), residues: 157 loop : -2.83 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 352 HIS 0.006 0.001 HIS A 91 PHE 0.012 0.002 PHE B 33 TYR 0.019 0.002 TYR B 235 ARG 0.005 0.001 ARG B 175 Details of bonding type rmsd link_NAG-ASN : bond 0.01157 ( 3) link_NAG-ASN : angle 8.64608 ( 9) hydrogen bonds : bond 0.03271 ( 35) hydrogen bonds : angle 8.65473 ( 87) SS BOND : bond 0.00586 ( 1) SS BOND : angle 0.57979 ( 2) covalent geometry : bond 0.00399 ( 3662) covalent geometry : angle 0.71429 ( 5033) *********************** 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: 27 poor density : 30 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: B 132 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.5016 (t80) REVERT: B 265 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7783 (ttt-90) REVERT: B 404 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7647 (pt) outliers start: 27 outliers final: 21 residues processed: 54 average time/residue: 0.1428 time to fit residues: 9.9302 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 : 0.408 ------------------------------------------------------------------------------- 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 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 265 ARG 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.100423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.088806 restraints weight = 13176.820| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 4.75 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3666 Z= 0.135 Angle : 0.760 20.593 5044 Z= 0.356 Chirality : 0.051 0.460 614 Planarity : 0.005 0.049 652 Dihedral : 5.528 32.446 643 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.73 % Favored : 85.27 % Rotamer: Outliers : 6.34 % Allowed : 29.68 % 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: -3.80 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -2.36 (0.41), residues: 158 loop : -2.76 (0.32), residues: 324 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 0.011 0.001 PHE B 33 TYR 0.018 0.001 TYR B 235 ARG 0.003 0.001 ARG B 175 Details of bonding type rmsd link_NAG-ASN : bond 0.01308 ( 3) link_NAG-ASN : angle 8.52112 ( 9) hydrogen bonds : bond 0.02850 ( 35) hydrogen bonds : angle 8.33056 ( 87) SS BOND : bond 0.00825 ( 1) SS BOND : angle 0.53009 ( 2) covalent geometry : bond 0.00299 ( 3662) covalent geometry : angle 0.66952 ( 5033) *********************** 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 54 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 32 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: B 132 PHE cc_start: 0.6407 (OUTLIER) cc_final: 0.4806 (t80) REVERT: B 265 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7759 (ttt-90) outliers start: 22 outliers final: 19 residues processed: 51 average time/residue: 0.1442 time to fit residues: 9.4767 Evaluate side-chains 53 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 32 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 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 265 ARG Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 402 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.098709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.087308 restraints weight = 13379.289| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 4.68 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3666 Z= 0.162 Angle : 0.780 20.573 5044 Z= 0.370 Chirality : 0.051 0.496 614 Planarity : 0.005 0.049 652 Dihedral : 5.623 31.142 643 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.18 % Favored : 83.82 % Rotamer: Outliers : 6.05 % Allowed : 30.26 % Favored : 63.69 % 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: -2.39 (0.42), residues: 159 loop : -2.86 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 352 HIS 0.003 0.001 HIS A 91 PHE 0.011 0.002 PHE B 33 TYR 0.014 0.001 TYR B 235 ARG 0.003 0.001 ARG B 107 Details of bonding type rmsd link_NAG-ASN : bond 0.01255 ( 3) link_NAG-ASN : angle 8.40088 ( 9) hydrogen bonds : bond 0.03378 ( 35) hydrogen bonds : angle 8.30969 ( 87) SS BOND : bond 0.00626 ( 1) SS BOND : angle 0.42781 ( 2) covalent geometry : bond 0.00360 ( 3662) covalent geometry : angle 0.69477 ( 5033) *********************** 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 53 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 32 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: B 132 PHE cc_start: 0.6472 (OUTLIER) cc_final: 0.4947 (t80) REVERT: B 265 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7667 (tmt-80) REVERT: B 269 ARG cc_start: 0.7647 (mmm-85) cc_final: 0.7236 (mmm-85) outliers start: 21 outliers final: 19 residues processed: 50 average time/residue: 0.1456 time to fit residues: 9.3022 Evaluate side-chains 52 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 31 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 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 265 ARG 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 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: 0.9980 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 32)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.088075 restraints weight = 13077.591| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 4.76 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3666 Z= 0.137 Angle : 0.757 20.310 5044 Z= 0.358 Chirality : 0.051 0.469 614 Planarity : 0.005 0.050 652 Dihedral : 5.409 31.950 643 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.69 % Favored : 86.31 % Rotamer: Outliers : 6.63 % Allowed : 29.68 % Favored : 63.69 % 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: -3.93 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -2.54 (0.41), residues: 159 loop : -2.79 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 352 HIS 0.002 0.001 HIS B 143 PHE 0.011 0.001 PHE B 33 TYR 0.013 0.001 TYR B 235 ARG 0.003 0.000 ARG B 107 Details of bonding type rmsd link_NAG-ASN : bond 0.01297 ( 3) link_NAG-ASN : angle 8.30786 ( 9) hydrogen bonds : bond 0.03022 ( 35) hydrogen bonds : angle 8.15079 ( 87) SS BOND : bond 0.00437 ( 1) SS BOND : angle 0.11091 ( 2) covalent geometry : bond 0.00300 ( 3662) covalent geometry : angle 0.67193 ( 5033) ********************** 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 56 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 33 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: B 131 TYR cc_start: 0.6649 (OUTLIER) cc_final: 0.6375 (m-80) REVERT: B 132 PHE cc_start: 0.6215 (OUTLIER) cc_final: 0.4604 (t80) REVERT: B 265 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7727 (ttt-90) REVERT: B 269 ARG cc_start: 0.7553 (mmm-85) cc_final: 0.7134 (mmm-85) outliers start: 23 outliers final: 20 residues processed: 51 average time/residue: 0.1381 time to fit residues: 9.1111 Evaluate side-chains 55 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 32 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 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 131 TYR 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 265 ARG 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 0.0050 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 26 optimal weight: 0.0670 chunk 39 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.4332 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.101711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.090159 restraints weight = 13245.257| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 4.79 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3666 Z= 0.112 Angle : 0.731 19.911 5044 Z= 0.342 Chirality : 0.050 0.441 614 Planarity : 0.005 0.049 652 Dihedral : 5.049 33.700 643 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.45 % Favored : 87.55 % Rotamer: Outliers : 5.76 % Allowed : 30.26 % 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: -3.80 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -2.39 (0.41), residues: 157 loop : -2.74 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 162 HIS 0.002 0.000 HIS B 143 PHE 0.010 0.001 PHE B 33 TYR 0.014 0.001 TYR B 235 ARG 0.003 0.001 ARG B 107 Details of bonding type rmsd link_NAG-ASN : bond 0.01414 ( 3) link_NAG-ASN : angle 8.14881 ( 9) hydrogen bonds : bond 0.02796 ( 35) hydrogen bonds : angle 7.68462 ( 87) SS BOND : bond 0.00316 ( 1) SS BOND : angle 0.13775 ( 2) covalent geometry : bond 0.00244 ( 3662) covalent geometry : angle 0.64613 ( 5033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1992.16 seconds wall clock time: 35 minutes 20.65 seconds (2120.65 seconds total)