Starting phenix.real_space_refine on Sat Apr 26 22:46:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zni_60272/04_2025/8zni_60272.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zni_60272/04_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_60272/04_2025/8zni_60272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zni_60272/04_2025/8zni_60272.map" model { file = "/net/cci-nas-00/data/ceres_data/8zni_60272/04_2025/8zni_60272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zni_60272/04_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-5669/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: 3.20, per 1000 atoms: 0.89 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: 0.89 Conformation dependent library (CDL) restraints added in 469.2 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: 0.39 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: 0.76 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: 1.680 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: 13.660 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.400 ------------------------------------------------------------------------------- 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 : 0.370 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: 0.1888 time to fit residues: 16.0452 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 : 0.368 ------------------------------------------------------------------------------- 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: 0.9980 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 0.0270 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 = 0.109109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.097579 restraints weight = 12961.120| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 4.91 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3666 Z= 0.153 Angle : 1.018 27.535 5044 Z= 0.429 Chirality : 0.072 1.294 614 Planarity : 0.005 0.048 652 Dihedral : 8.015 50.234 643 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.62 % Favored : 88.38 % Rotamer: Outliers : 6.05 % Allowed : 28.53 % 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: -2.58 (0.42), residues: 144 loop : -2.42 (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 0.011 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 0.00558 ( 3) link_NAG-ASN : angle 13.65123 ( 9) hydrogen bonds : bond 0.03667 ( 35) hydrogen bonds : angle 10.57222 ( 87) SS BOND : bond 0.00436 ( 1) SS BOND : angle 0.44705 ( 2) covalent geometry : bond 0.00332 ( 3662) covalent geometry : angle 0.84031 ( 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 67 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8694 (p0) cc_final: 0.8445 (p0) outliers start: 21 outliers final: 11 residues processed: 62 average time/residue: 0.1300 time to fit residues: 10.4858 Evaluate side-chains 54 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 47 ILE 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: 2.9990 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 2 optimal weight: 0.0870 overall best weight: 1.1562 ------------------------------------------------------------------------------- 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 = 0.4183 r_free = 0.4183 target = 0.102835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.091231 restraints weight = 13072.495| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 4.82 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3666 Z= 0.163 Angle : 0.837 22.330 5044 Z= 0.381 Chirality : 0.051 0.528 614 Planarity : 0.005 0.045 652 Dihedral : 7.239 51.196 643 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.52 % Favored : 85.48 % Rotamer: Outliers : 4.90 % Allowed : 29.11 % 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: -3.62 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -2.41 (0.42), residues: 149 loop : -2.55 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 162 HIS 0.002 0.001 HIS A 91 PHE 0.010 0.001 PHE B 132 TYR 0.020 0.002 TYR B 235 ARG 0.002 0.001 ARG B 387 Details of bonding type rmsd link_NAG-ASN : bond 0.01618 ( 3) link_NAG-ASN : angle 10.22139 ( 9) hydrogen bonds : bond 0.04049 ( 35) hydrogen bonds : angle 9.63507 ( 87) SS BOND : bond 0.00504 ( 1) SS BOND : angle 0.34916 ( 2) covalent geometry : bond 0.00358 ( 3662) covalent geometry : angle 0.71747 ( 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 58 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8528 (tp) cc_final: 0.8309 (pt) REVERT: A 116 ASN cc_start: 0.8628 (p0) cc_final: 0.8398 (p0) REVERT: B 175 ARG cc_start: 0.7018 (mmp-170) cc_final: 0.6816 (mmp-170) REVERT: B 269 ARG cc_start: 0.7682 (mmm-85) cc_final: 0.7077 (mmm-85) outliers start: 17 outliers final: 12 residues processed: 54 average time/residue: 0.1414 time to fit residues: 9.7188 Evaluate side-chains 48 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 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: 0.0670 chunk 2 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 26 optimal weight: 0.0770 chunk 11 optimal weight: 0.0470 chunk 33 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.105923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.095370 restraints weight = 13485.161| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 4.41 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3666 Z= 0.110 Angle : 0.786 20.867 5044 Z= 0.350 Chirality : 0.049 0.450 614 Planarity : 0.005 0.041 652 Dihedral : 6.131 34.187 643 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 5.48 % Allowed : 29.39 % 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: -3.55 (0.35), residues: 482 helix: None (None), residues: 0 sheet: -2.42 (0.42), residues: 144 loop : -2.47 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 352 HIS 0.002 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 269 Details of bonding type rmsd link_NAG-ASN : bond 0.01286 ( 3) link_NAG-ASN : angle 9.67658 ( 9) hydrogen bonds : bond 0.02828 ( 35) hydrogen bonds : angle 8.83002 ( 87) SS BOND : bond 0.00220 ( 1) SS BOND : angle 0.21671 ( 2) covalent geometry : bond 0.00241 ( 3662) covalent geometry : angle 0.67250 ( 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 57 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: B 132 PHE cc_start: 0.5754 (OUTLIER) cc_final: 0.4351 (t80) REVERT: B 213 MET cc_start: 0.5816 (ttp) cc_final: 0.5486 (ttt) REVERT: B 265 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7355 (tpt-90) REVERT: B 269 ARG cc_start: 0.7514 (mmm-85) cc_final: 0.7151 (mmm-85) outliers start: 19 outliers final: 10 residues processed: 52 average time/residue: 0.1484 time to fit residues: 9.7497 Evaluate side-chains 47 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 265 ARG Chi-restraints excluded: chain B residue 280 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 0.0770 chunk 4 optimal weight: 2.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.102314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.091521 restraints weight = 13700.680| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 4.45 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3666 Z= 0.157 Angle : 0.794 21.049 5044 Z= 0.367 Chirality : 0.051 0.483 614 Planarity : 0.005 0.042 652 Dihedral : 5.989 33.825 643 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.94 % Favored : 85.06 % Rotamer: Outliers : 6.05 % Allowed : 29.68 % 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: -3.53 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -2.24 (0.42), residues: 153 loop : -2.54 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 352 HIS 0.002 0.001 HIS A 91 PHE 0.010 0.001 PHE B 26 TYR 0.021 0.001 TYR B 235 ARG 0.003 0.000 ARG B 107 Details of bonding type rmsd link_NAG-ASN : bond 0.01286 ( 3) link_NAG-ASN : angle 9.04015 ( 9) hydrogen bonds : bond 0.03153 ( 35) hydrogen bonds : angle 8.77458 ( 87) SS BOND : bond 0.00526 ( 1) SS BOND : angle 0.46372 ( 2) covalent geometry : bond 0.00352 ( 3662) covalent geometry : angle 0.69655 ( 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 57 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 36 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: B 10 TYR cc_start: 0.3748 (OUTLIER) cc_final: 0.3508 (m-10) REVERT: B 132 PHE cc_start: 0.6303 (OUTLIER) cc_final: 0.4804 (t80) REVERT: B 213 MET cc_start: 0.6071 (ttp) cc_final: 0.5766 (ttt) REVERT: B 265 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7341 (tpt-90) REVERT: B 269 ARG cc_start: 0.7645 (mmm-85) cc_final: 0.7250 (mmm-85) REVERT: B 404 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7563 (pt) outliers start: 21 outliers final: 13 residues processed: 54 average time/residue: 0.1352 time to fit residues: 9.4266 Evaluate side-chains 50 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 33 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 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 235 TYR Chi-restraints excluded: chain B residue 265 ARG Chi-restraints excluded: chain B residue 280 ILE 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: 0.0030 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 19 optimal weight: 0.0040 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 overall best weight: 0.4804 ------------------------------------------------------------------------------- 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 = 0.4227 r_free = 0.4227 target = 0.104364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.093608 restraints weight = 13574.796| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 4.41 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3666 Z= 0.111 Angle : 0.742 20.343 5044 Z= 0.339 Chirality : 0.049 0.416 614 Planarity : 0.005 0.042 652 Dihedral : 5.439 33.452 643 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.41 % Favored : 88.59 % 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: -3.47 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -2.73 (0.42), residues: 142 loop : -2.22 (0.32), residues: 340 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 0.010 0.001 PHE B 33 TYR 0.022 0.001 TYR B 235 ARG 0.002 0.000 ARG B 107 Details of bonding type rmsd link_NAG-ASN : bond 0.01350 ( 3) link_NAG-ASN : angle 8.73940 ( 9) hydrogen bonds : bond 0.02532 ( 35) hydrogen bonds : angle 8.30048 ( 87) SS BOND : bond 0.00319 ( 1) SS BOND : angle 0.16362 ( 2) covalent geometry : bond 0.00242 ( 3662) covalent geometry : angle 0.64457 ( 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: 22 poor density : 37 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 TYR cc_start: 0.3566 (OUTLIER) cc_final: 0.3317 (m-10) REVERT: B 132 PHE cc_start: 0.5728 (OUTLIER) cc_final: 0.4241 (t80) REVERT: B 139 MET cc_start: 0.5630 (tpp) cc_final: 0.5065 (tpp) REVERT: B 213 MET cc_start: 0.6075 (ttp) cc_final: 0.5695 (ttt) REVERT: B 265 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7740 (ttt-90) outliers start: 22 outliers final: 18 residues processed: 55 average time/residue: 0.1576 time to fit residues: 10.8439 Evaluate side-chains 55 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 34 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 26 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 5 optimal weight: 0.0570 chunk 16 optimal weight: 4.9990 chunk 27 optimal weight: 0.0170 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 147 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 = 0.4206 r_free = 0.4206 target = 0.103298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.092348 restraints weight = 13544.050| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 4.39 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.4138 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= 0.124 Angle : 0.740 20.315 5044 Z= 0.342 Chirality : 0.050 0.452 614 Planarity : 0.005 0.040 652 Dihedral : 5.184 33.082 643 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.90 % Favored : 86.10 % Rotamer: Outliers : 5.48 % Allowed : 30.26 % 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: -3.53 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -2.68 (0.41), residues: 152 loop : -2.27 (0.33), residues: 330 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 0.010 0.001 PHE B 33 TYR 0.018 0.001 TYR B 235 ARG 0.005 0.001 ARG B 107 Details of bonding type rmsd link_NAG-ASN : bond 0.01375 ( 3) link_NAG-ASN : angle 8.45251 ( 9) hydrogen bonds : bond 0.02698 ( 35) hydrogen bonds : angle 8.01440 ( 87) SS BOND : bond 0.00402 ( 1) SS BOND : angle 0.38533 ( 2) covalent geometry : bond 0.00273 ( 3662) covalent geometry : angle 0.64930 ( 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 50 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 31 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 132 PHE cc_start: 0.5964 (OUTLIER) cc_final: 0.4533 (t80) REVERT: B 139 MET cc_start: 0.5670 (tpp) cc_final: 0.5139 (tpp) REVERT: B 213 MET cc_start: 0.6255 (ttp) cc_final: 0.5864 (ttt) outliers start: 19 outliers final: 17 residues processed: 47 average time/residue: 0.1241 time to fit residues: 7.7434 Evaluate side-chains 49 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 31 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 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 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 360 THR Chi-restraints excluded: chain B residue 402 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.0010 chunk 39 optimal weight: 0.0170 chunk 43 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.6426 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.103541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.092713 restraints weight = 13549.237| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 4.39 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.4292 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= 0.118 Angle : 0.734 20.073 5044 Z= 0.339 Chirality : 0.050 0.437 614 Planarity : 0.005 0.041 652 Dihedral : 5.041 32.680 643 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer: Outliers : 6.05 % Allowed : 29.68 % 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: -3.44 (0.37), residues: 482 helix: None (None), residues: 0 sheet: -2.39 (0.41), residues: 157 loop : -2.33 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 352 HIS 0.002 0.001 HIS B 143 PHE 0.010 0.001 PHE B 33 TYR 0.018 0.001 TYR B 235 ARG 0.004 0.001 ARG B 107 Details of bonding type rmsd link_NAG-ASN : bond 0.01363 ( 3) link_NAG-ASN : angle 8.33046 ( 9) hydrogen bonds : bond 0.02594 ( 35) hydrogen bonds : angle 7.80531 ( 87) SS BOND : bond 0.00375 ( 1) SS BOND : angle 0.32787 ( 2) covalent geometry : bond 0.00262 ( 3662) covalent geometry : angle 0.64458 ( 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: 21 poor density : 33 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 132 PHE cc_start: 0.6133 (OUTLIER) cc_final: 0.4797 (t80) REVERT: B 213 MET cc_start: 0.6295 (ttp) cc_final: 0.5873 (ttt) REVERT: B 265 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7751 (ttt-90) outliers start: 21 outliers final: 19 residues processed: 50 average time/residue: 0.1376 time to fit residues: 8.9189 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 : 0.371 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 1 optimal weight: 0.0030 chunk 36 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.101904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.091010 restraints weight = 13470.123| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 4.40 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3666 Z= 0.129 Angle : 0.739 20.005 5044 Z= 0.344 Chirality : 0.050 0.470 614 Planarity : 0.005 0.040 652 Dihedral : 4.962 31.734 643 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.11 % Favored : 85.89 % Rotamer: Outliers : 6.05 % Allowed : 29.97 % 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: -3.46 (0.37), residues: 482 helix: None (None), residues: 0 sheet: -2.37 (0.42), residues: 157 loop : -2.37 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 352 HIS 0.002 0.001 HIS A 91 PHE 0.010 0.001 PHE B 33 TYR 0.016 0.001 TYR B 235 ARG 0.003 0.001 ARG B 107 Details of bonding type rmsd link_NAG-ASN : bond 0.01335 ( 3) link_NAG-ASN : angle 8.11143 ( 9) hydrogen bonds : bond 0.02686 ( 35) hydrogen bonds : angle 7.71312 ( 87) SS BOND : bond 0.00443 ( 1) SS BOND : angle 0.52711 ( 2) covalent geometry : bond 0.00287 ( 3662) covalent geometry : angle 0.65586 ( 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 : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 132 PHE cc_start: 0.6237 (OUTLIER) cc_final: 0.4872 (t80) REVERT: B 265 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7814 (ttt-90) REVERT: B 269 ARG cc_start: 0.7541 (mmm-85) cc_final: 0.7145 (mmm-85) outliers start: 21 outliers final: 18 residues processed: 50 average time/residue: 0.1350 time to fit residues: 8.7627 Evaluate side-chains 52 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 32 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 402 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 0.0070 chunk 8 optimal weight: 0.0770 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.101158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.089364 restraints weight = 13251.819| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 4.79 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.4882 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= 0.139 Angle : 0.742 19.939 5044 Z= 0.347 Chirality : 0.050 0.476 614 Planarity : 0.005 0.042 652 Dihedral : 5.032 30.382 643 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % 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: -3.55 (0.37), residues: 482 helix: None (None), residues: 0 sheet: -2.33 (0.43), residues: 152 loop : -2.51 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 352 HIS 0.004 0.001 HIS A 91 PHE 0.010 0.002 PHE B 33 TYR 0.015 0.001 TYR B 235 ARG 0.003 0.001 ARG B 107 Details of bonding type rmsd link_NAG-ASN : bond 0.01265 ( 3) link_NAG-ASN : angle 8.07181 ( 9) hydrogen bonds : bond 0.02793 ( 35) hydrogen bonds : angle 7.73022 ( 87) SS BOND : bond 0.00468 ( 1) SS BOND : angle 0.49202 ( 2) covalent geometry : bond 0.00310 ( 3662) covalent geometry : angle 0.65971 ( 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 54 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 32 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 132 PHE cc_start: 0.6214 (OUTLIER) cc_final: 0.4649 (t80) REVERT: B 265 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7730 (ttt-90) REVERT: B 269 ARG cc_start: 0.7557 (mmm-85) cc_final: 0.7178 (mmm-85) REVERT: B 404 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7654 (pt) outliers start: 22 outliers final: 19 residues processed: 51 average time/residue: 0.1440 time to fit residues: 9.5768 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 : 0.414 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 404 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.101196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.089565 restraints weight = 13338.076| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 4.76 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3666 Z= 0.127 Angle : 0.736 19.783 5044 Z= 0.344 Chirality : 0.051 0.471 614 Planarity : 0.005 0.043 652 Dihedral : 4.966 30.887 643 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.69 % Favored : 86.31 % 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: -3.50 (0.37), residues: 482 helix: None (None), residues: 0 sheet: -2.22 (0.42), residues: 157 loop : -2.51 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 352 HIS 0.002 0.001 HIS A 91 PHE 0.010 0.001 PHE B 33 TYR 0.014 0.001 TYR B 235 ARG 0.003 0.000 ARG B 107 Details of bonding type rmsd link_NAG-ASN : bond 0.01310 ( 3) link_NAG-ASN : angle 7.99310 ( 9) hydrogen bonds : bond 0.02704 ( 35) hydrogen bonds : angle 7.70328 ( 87) SS BOND : bond 0.00389 ( 1) SS BOND : angle 0.42467 ( 2) covalent geometry : bond 0.00282 ( 3662) covalent geometry : angle 0.65487 ( 5033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2054.91 seconds wall clock time: 36 minutes 1.19 seconds (2161.19 seconds total)