Starting phenix.real_space_refine on Wed Mar 5 21:17:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zni_60272/03_2025/8zni_60272.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zni_60272/03_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_60272/03_2025/8zni_60272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zni_60272/03_2025/8zni_60272.map" model { file = "/net/cci-nas-00/data/ceres_data/8zni_60272/03_2025/8zni_60272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zni_60272/03_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-5624/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: 2.84, per 1000 atoms: 0.79 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: 0.82 Conformation dependent library (CDL) restraints added in 467.8 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: 0.39 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: 0.78 Time building geometry restraints manager: 1.00 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: 1.120 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.240 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5896 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3662 Z= 0.272 Angle : 0.713 7.418 5033 Z= 0.370 Chirality : 0.205 4.138 614 Planarity : 0.005 0.061 652 Dihedral : 14.834 81.893 1307 Min Nonbonded Distance : 1.220 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 0.00 % Allowed : 31.70 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -2.02 (0.49), residues: 121 loop : -2.65 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 112 HIS 0.002 0.001 HIS A 91 PHE 0.021 0.002 PHE B 33 TYR 0.021 0.001 TYR B 235 ARG 0.005 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.414 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: 0.1903 time to fit residues: 16.3661 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 : 0.356 ------------------------------------------------------------------------------- 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 3662 Z= 0.222 Angle : 0.840 16.602 5033 Z= 0.384 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 *********************** 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 : 0.374 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: 0.1353 time to fit residues: 10.9346 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 : 0.440 ------------------------------------------------------------------------------- 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: 0.8980 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 2 optimal weight: 0.0870 overall best weight: 1.1360 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4211 r_free = 0.4211 target = 0.103451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.092845 restraints weight = 13220.215| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 4.36 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3662 Z= 0.254 Angle : 0.728 11.213 5033 Z= 0.358 Chirality : 0.051 0.480 614 Planarity : 0.005 0.046 652 Dihedral : 7.269 52.382 643 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.32 % Favored : 85.68 % 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: -3.63 (0.35), residues: 482 helix: None (None), residues: 0 sheet: -2.42 (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 A 56 HIS 0.003 0.001 HIS A 91 PHE 0.011 0.002 PHE B 132 TYR 0.026 0.002 TYR B 235 ARG 0.004 0.001 ARG B 175 *********************** 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 : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8455 (p0) cc_final: 0.8247 (p0) REVERT: B 132 PHE cc_start: 0.6300 (OUTLIER) cc_final: 0.4725 (t80) REVERT: B 202 MET cc_start: 0.7117 (pmm) cc_final: 0.6915 (pmm) REVERT: B 269 ARG cc_start: 0.7668 (mmm-85) cc_final: 0.7129 (mmm-85) outliers start: 17 outliers final: 11 residues processed: 54 average time/residue: 0.1551 time to fit residues: 10.7482 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 : 0.397 ------------------------------------------------------------------------------- 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 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 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: 0.0870 chunk 18 optimal weight: 0.2980 chunk 2 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 26 optimal weight: 0.0170 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 27 optimal weight: 0.0570 chunk 10 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 overall best weight: 0.2514 ------------------------------------------------------------------------------- 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 226 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 = 0.4247 r_free = 0.4247 target = 0.105663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.095165 restraints weight = 13483.590| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 4.40 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3662 Z= 0.167 Angle : 0.682 9.715 5033 Z= 0.325 Chirality : 0.049 0.454 614 Planarity : 0.005 0.044 652 Dihedral : 6.260 37.126 643 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % 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: -3.55 (0.35), residues: 482 helix: None (None), residues: 0 sheet: -2.43 (0.42), residues: 144 loop : -2.46 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 352 HIS 0.002 0.000 HIS B 417 PHE 0.009 0.001 PHE B 33 TYR 0.019 0.001 TYR B 235 ARG 0.002 0.000 ARG B 269 *********************** 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 58 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: B 213 MET cc_start: 0.5806 (ttp) cc_final: 0.5498 (ttt) REVERT: B 265 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7368 (tpt-90) REVERT: B 269 ARG cc_start: 0.7521 (mmm-85) cc_final: 0.7280 (mmm-85) outliers start: 20 outliers final: 11 residues processed: 53 average time/residue: 0.1518 time to fit residues: 10.1454 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 : 0.357 ------------------------------------------------------------------------------- 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 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 135 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 265 ARG Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 346 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.099422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.088359 restraints weight = 13885.437| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 4.56 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3662 Z= 0.341 Angle : 0.763 10.022 5033 Z= 0.388 Chirality : 0.053 0.537 614 Planarity : 0.005 0.046 652 Dihedral : 6.476 31.720 643 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.01 % Favored : 82.99 % Rotamer: Outliers : 7.78 % Allowed : 26.51 % 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: -3.85 (0.36), residues: 482 helix: None (None), residues: 0 sheet: -2.37 (0.41), residues: 163 loop : -2.80 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 162 HIS 0.004 0.001 HIS A 91 PHE 0.011 0.002 PHE B 33 TYR 0.013 0.002 TYR B 235 ARG 0.003 0.001 ARG A 14 *********************** 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 61 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 34 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 TYR cc_start: 0.3681 (OUTLIER) cc_final: 0.3418 (m-10) REVERT: B 132 PHE cc_start: 0.6570 (OUTLIER) cc_final: 0.5188 (t80) REVERT: B 139 MET cc_start: 0.5913 (tpp) cc_final: 0.5307 (tpp) REVERT: B 213 MET cc_start: 0.6382 (ttp) cc_final: 0.5978 (ttt) REVERT: B 404 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7576 (pt) outliers start: 27 outliers final: 20 residues processed: 56 average time/residue: 0.1198 time to fit residues: 8.9479 Evaluate side-chains 53 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 30 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 10 TYR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 132 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 405 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.095715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.084051 restraints weight = 14013.484| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 4.85 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3662 Z= 0.401 Angle : 0.821 8.304 5033 Z= 0.423 Chirality : 0.056 0.576 614 Planarity : 0.006 0.050 652 Dihedral : 6.958 36.705 643 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.50 % Favored : 80.50 % Rotamer: Outliers : 9.51 % Allowed : 26.22 % 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: -4.23 (0.35), residues: 482 helix: None (None), residues: 0 sheet: -2.62 (0.43), residues: 145 loop : -3.10 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 162 HIS 0.009 0.002 HIS A 91 PHE 0.013 0.002 PHE B 33 TYR 0.015 0.002 TYR B 235 ARG 0.004 0.001 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 31 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: B 131 TYR cc_start: 0.6898 (OUTLIER) cc_final: 0.6687 (m-80) REVERT: B 132 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.5283 (t80) REVERT: B 139 MET cc_start: 0.6244 (tpp) cc_final: 0.5723 (tpp) REVERT: B 265 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7667 (tmt-80) REVERT: B 345 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7886 (m-40) REVERT: B 404 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7471 (pt) outliers start: 33 outliers final: 22 residues processed: 62 average time/residue: 0.1590 time to fit residues: 12.6235 Evaluate side-chains 52 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 25 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 94 SER 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 275 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 345 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 27 optimal weight: 6.9990 chunk 18 optimal weight: 0.0870 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.099861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.088335 restraints weight = 13195.854| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 4.76 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3662 Z= 0.195 Angle : 0.711 7.809 5033 Z= 0.356 Chirality : 0.051 0.437 614 Planarity : 0.005 0.051 652 Dihedral : 6.161 32.347 643 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 5.48 % Allowed : 30.55 % 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: -3.99 (0.35), residues: 482 helix: None (None), residues: 0 sheet: -2.53 (0.43), residues: 141 loop : -2.90 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 352 HIS 0.003 0.001 HIS A 91 PHE 0.012 0.002 PHE B 274 TYR 0.019 0.001 TYR B 235 ARG 0.004 0.001 ARG B 269 *********************** 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 : 0.416 Fit side-chains REVERT: B 132 PHE cc_start: 0.6254 (OUTLIER) cc_final: 0.4672 (t80) REVERT: B 265 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7698 (tmt-80) outliers start: 19 outliers final: 16 residues processed: 48 average time/residue: 0.1456 time to fit residues: 9.0709 Evaluate side-chains 47 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 29 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 chunk 43 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.098686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.087122 restraints weight = 13610.164| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 4.78 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3662 Z= 0.235 Angle : 0.716 9.940 5033 Z= 0.356 Chirality : 0.051 0.481 614 Planarity : 0.005 0.049 652 Dihedral : 5.925 32.307 643 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.77 % Favored : 84.23 % Rotamer: Outliers : 6.05 % Allowed : 30.55 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.35), residues: 482 helix: None (None), residues: 0 sheet: -2.49 (0.43), residues: 146 loop : -2.88 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 56 HIS 0.004 0.001 HIS A 91 PHE 0.011 0.001 PHE B 33 TYR 0.017 0.001 TYR B 235 ARG 0.005 0.001 ARG B 175 *********************** 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 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: B 131 TYR cc_start: 0.6773 (OUTLIER) cc_final: 0.6470 (m-80) REVERT: B 132 PHE cc_start: 0.6420 (OUTLIER) cc_final: 0.4849 (t80) REVERT: B 265 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7684 (tmt-80) REVERT: B 404 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7633 (pt) outliers start: 21 outliers final: 17 residues processed: 49 average time/residue: 0.1500 time to fit residues: 9.4699 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 : 0.381 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 0.0670 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.100730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.089303 restraints weight = 13117.913| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 4.71 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3662 Z= 0.179 Angle : 0.683 9.264 5033 Z= 0.335 Chirality : 0.049 0.429 614 Planarity : 0.005 0.047 652 Dihedral : 5.569 33.776 643 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 6.05 % Allowed : 30.84 % Favored : 63.11 % 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 (0.35), residues: 482 helix: None (None), residues: 0 sheet: -2.47 (0.43), residues: 139 loop : -2.75 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 352 HIS 0.002 0.001 HIS B 143 PHE 0.011 0.001 PHE B 33 TYR 0.015 0.001 TYR B 235 ARG 0.004 0.001 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 31 time to evaluate : 0.429 Fit side-chains REVERT: B 132 PHE cc_start: 0.6027 (OUTLIER) cc_final: 0.4406 (t80) REVERT: B 265 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7668 (tmt-80) outliers start: 21 outliers final: 16 residues processed: 47 average time/residue: 0.1465 time to fit residues: 8.9219 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 : 0.376 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- 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: 4.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.099128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.087782 restraints weight = 13113.315| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 4.65 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3662 Z= 0.237 Angle : 0.700 9.119 5033 Z= 0.347 Chirality : 0.051 0.469 614 Planarity : 0.005 0.047 652 Dihedral : 5.581 32.494 643 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % Rotamer: Outliers : 5.48 % Allowed : 31.70 % Favored : 62.82 % 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: -3.92 (0.35), residues: 482 helix: None (None), residues: 0 sheet: -2.41 (0.43), residues: 149 loop : -2.88 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 352 HIS 0.003 0.001 HIS A 91 PHE 0.015 0.002 PHE B 33 TYR 0.016 0.001 TYR B 235 ARG 0.004 0.001 ARG B 269 ********************** 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 50 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 31 time to evaluate : 0.402 Fit side-chains REVERT: B 132 PHE cc_start: 0.6194 (OUTLIER) cc_final: 0.4584 (t80) REVERT: B 213 MET cc_start: 0.6426 (ttt) cc_final: 0.5866 (ttt) REVERT: B 265 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7679 (tmt-80) outliers start: 19 outliers final: 16 residues processed: 46 average time/residue: 0.1532 time to fit residues: 9.0042 Evaluate side-chains 48 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 30 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 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 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 27 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.0370 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.101295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.089951 restraints weight = 13143.647| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 4.66 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3662 Z= 0.182 Angle : 0.682 9.145 5033 Z= 0.334 Chirality : 0.049 0.424 614 Planarity : 0.005 0.048 652 Dihedral : 5.327 33.735 643 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 4.61 % Allowed : 32.56 % Favored : 62.82 % 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: -2.44 (0.41), residues: 157 loop : -2.75 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 162 HIS 0.002 0.001 HIS B 143 PHE 0.013 0.001 PHE B 33 TYR 0.016 0.001 TYR B 235 ARG 0.005 0.001 ARG B 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1995.31 seconds wall clock time: 35 minutes 7.43 seconds (2107.43 seconds total)