Starting phenix.real_space_refine on Thu Jun 5 03:01:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wo7_32641/06_2025/7wo7_32641.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wo7_32641/06_2025/7wo7_32641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wo7_32641/06_2025/7wo7_32641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wo7_32641/06_2025/7wo7_32641.map" model { file = "/net/cci-nas-00/data/ceres_data/7wo7_32641/06_2025/7wo7_32641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wo7_32641/06_2025/7wo7_32641.cif" } resolution = 3.8 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= 0.001 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 20 5.16 5 C 3069 2.51 5 N 816 2.21 5 O 965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4870 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "B" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.15, per 1000 atoms: 1.06 Number of scatterers: 4870 At special positions: 0 Unit cell: (74.9, 95.23, 107, 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 20 16.00 O 965 8.00 N 816 7.00 C 3069 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 91 " distance=2.03 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 556.1 milliseconds 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1168 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 13 sheets defined 5.4% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.625A pdb=" N LYS A 65 " --> pdb=" O ASP A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.520A pdb=" N THR A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.516A pdb=" N ASP B 85 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 86 " --> pdb=" O THR B 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 82 through 86' Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.876A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.709A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.222A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.797A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 5 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 7 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 20 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.986A pdb=" N GLY A 10 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET A 34 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 36 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 59 " --> pdb=" O ASN A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.986A pdb=" N GLY A 10 " --> pdb=" O THR A 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.654A pdb=" N SER A 186 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER A 185 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A 172 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 187 " --> pdb=" O HIS A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.127A pdb=" N VAL B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 107 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.127A pdb=" N VAL B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 107 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 102 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.743A pdb=" N ILE B 20 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 197 through 199 removed outlier: 3.586A pdb=" N CYS B 199 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS B 210 " --> pdb=" O CYS B 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.873A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.602A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.582A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) 73 hydrogen bonds defined for protein. 153 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: 1.23 Time building geometry restraints manager: 1.41 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: 1472 1.33 - 1.45: 883 1.45 - 1.57: 2618 1.57 - 1.70: 0 1.70 - 1.82: 23 Bond restraints: 4996 Sorted by residual: bond pdb=" C GLN B 114 " pdb=" N PRO B 115 " ideal model delta sigma weight residual 1.326 1.387 -0.061 1.44e-02 4.82e+03 1.79e+01 bond pdb=" CA GLN B 114 " pdb=" C GLN B 114 " ideal model delta sigma weight residual 1.523 1.558 -0.035 1.25e-02 6.40e+03 7.77e+00 bond pdb=" C GLU A 154 " pdb=" N PRO A 155 " ideal model delta sigma weight residual 1.333 1.351 -0.018 7.80e-03 1.64e+04 5.42e+00 bond pdb=" N ALA A 120 " pdb=" CA ALA A 120 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.27e+00 bond pdb=" C TYR B 146 " pdb=" N PRO B 147 " ideal model delta sigma weight residual 1.332 1.356 -0.025 1.30e-02 5.92e+03 3.56e+00 ... (remaining 4991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 6475 1.49 - 2.97: 297 2.97 - 4.46: 28 4.46 - 5.94: 7 5.94 - 7.43: 4 Bond angle restraints: 6811 Sorted by residual: angle pdb=" C GLN B 114 " pdb=" N PRO B 115 " pdb=" CA PRO B 115 " ideal model delta sigma weight residual 120.98 115.18 5.80 1.07e+00 8.73e-01 2.94e+01 angle pdb=" C PRO A 153 " pdb=" N GLU A 154 " pdb=" CA GLU A 154 " ideal model delta sigma weight residual 122.28 118.32 3.96 1.02e+00 9.61e-01 1.51e+01 angle pdb=" N THR A 197 " pdb=" CA THR A 197 " pdb=" C THR A 197 " ideal model delta sigma weight residual 112.68 107.71 4.97 1.33e+00 5.65e-01 1.40e+01 angle pdb=" N ALA A 120 " pdb=" CA ALA A 120 " pdb=" C ALA A 120 " ideal model delta sigma weight residual 110.80 118.23 -7.43 2.13e+00 2.20e-01 1.22e+01 angle pdb=" N LYS C 378 " pdb=" CA LYS C 378 " pdb=" C LYS C 378 " ideal model delta sigma weight residual 108.17 114.22 -6.05 1.85e+00 2.92e-01 1.07e+01 ... (remaining 6806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 2797 16.83 - 33.66: 130 33.66 - 50.49: 41 50.49 - 67.32: 10 67.32 - 84.15: 2 Dihedral angle restraints: 2980 sinusoidal: 1145 harmonic: 1835 Sorted by residual: dihedral pdb=" N ALA A 120 " pdb=" C ALA A 120 " pdb=" CA ALA A 120 " pdb=" CB ALA A 120 " ideal model delta harmonic sigma weight residual 122.90 132.46 -9.56 0 2.50e+00 1.60e-01 1.46e+01 dihedral pdb=" C ALA A 120 " pdb=" N ALA A 120 " pdb=" CA ALA A 120 " pdb=" CB ALA A 120 " ideal model delta harmonic sigma weight residual -122.60 -131.98 9.38 0 2.50e+00 1.60e-01 1.41e+01 dihedral pdb=" CB GLU B 189 " pdb=" CG GLU B 189 " pdb=" CD GLU B 189 " pdb=" OE1 GLU B 189 " ideal model delta sinusoidal sigma weight residual 0.00 -84.15 84.15 1 3.00e+01 1.11e-03 9.58e+00 ... (remaining 2977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 676 0.073 - 0.145: 71 0.145 - 0.218: 2 0.218 - 0.290: 0 0.290 - 0.363: 1 Chirality restraints: 750 Sorted by residual: chirality pdb=" CA ALA A 120 " pdb=" N ALA A 120 " pdb=" C ALA A 120 " pdb=" CB ALA A 120 " both_signs ideal model delta sigma weight residual False 2.48 2.12 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA LYS C 378 " pdb=" N LYS C 378 " pdb=" C LYS C 378 " pdb=" CB LYS C 378 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA TYR C 369 " pdb=" N TYR C 369 " pdb=" C TYR C 369 " pdb=" CB TYR C 369 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 747 not shown) Planarity restraints: 883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 190 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.80e+00 pdb=" N PRO A 191 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 191 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 191 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 27 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C GLY B 27 " 0.027 2.00e-02 2.50e+03 pdb=" O GLY B 27 " -0.010 2.00e-02 2.50e+03 pdb=" N SER B 28 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 125 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO B 126 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " -0.019 5.00e-02 4.00e+02 ... (remaining 880 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 207 2.71 - 3.26: 4598 3.26 - 3.81: 7752 3.81 - 4.35: 9274 4.35 - 4.90: 15771 Nonbonded interactions: 37602 Sorted by model distance: nonbonded pdb=" O LYS B 155 " pdb=" OG SER B 198 " model vdw 2.163 3.040 nonbonded pdb=" OG1 THR B 122 " pdb=" O LEU B 141 " model vdw 2.254 3.040 nonbonded pdb=" O ARG C 408 " pdb=" NE2 GLN C 414 " model vdw 2.266 3.120 nonbonded pdb=" O ALA B 163 " pdb=" OG SER B 185 " model vdw 2.277 3.040 nonbonded pdb=" O SER B 13 " pdb=" NZ LYS B 16 " model vdw 2.315 3.120 ... (remaining 37597 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 group one per residue 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: 9.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.740 Find NCS groups from input model: 0.060 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 : 0.003 0.061 5005 Z= 0.191 Angle : 0.705 7.428 6830 Z= 0.446 Chirality : 0.044 0.363 750 Planarity : 0.004 0.042 882 Dihedral : 11.244 84.155 1788 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 8.82 % Allowed : 7.17 % Favored : 84.01 % 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: -4.70 (0.28), residues: 628 helix: -4.77 (0.47), residues: 12 sheet: -2.88 (0.35), residues: 172 loop : -3.42 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 33 HIS 0.001 0.000 HIS A 206 PHE 0.009 0.001 PHE C 400 TYR 0.010 0.001 TYR C 369 ARG 0.001 0.000 ARG A 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00058 ( 1) link_NAG-ASN : angle 0.80955 ( 3) hydrogen bonds : bond 0.29587 ( 66) hydrogen bonds : angle 11.65844 ( 153) SS BOND : bond 0.00089 ( 8) SS BOND : angle 0.46736 ( 16) covalent geometry : bond 0.00293 ( 4996) covalent geometry : angle 0.70585 ( 6811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8329 (mt0) REVERT: A 184 LEU cc_start: 0.6631 (tp) cc_final: 0.6263 (tp) REVERT: A 212 LYS cc_start: 0.6387 (mmtt) cc_final: 0.5984 (mmtt) REVERT: B 29 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8955 (tt) REVERT: B 113 SER cc_start: 0.6507 (OUTLIER) cc_final: 0.6204 (p) REVERT: B 168 THR cc_start: 0.5662 (OUTLIER) cc_final: 0.5215 (p) REVERT: B 189 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.6904 (mm-30) REVERT: B 190 GLN cc_start: 0.6304 (OUTLIER) cc_final: 0.6037 (tt0) REVERT: B 192 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.5021 (mmmt) REVERT: B 194 HIS cc_start: 0.6438 (OUTLIER) cc_final: 0.6054 (m90) REVERT: B 195 ARG cc_start: 0.6583 (mmm160) cc_final: 0.5683 (mpp-170) REVERT: C 356 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7948 (tptp) REVERT: C 378 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8526 (mmmt) REVERT: C 394 ASN cc_start: 0.7748 (m-40) cc_final: 0.7288 (m-40) REVERT: C 452 LEU cc_start: 0.8394 (mt) cc_final: 0.8036 (mp) REVERT: C 516 GLU cc_start: 0.6658 (pt0) cc_final: 0.6439 (pt0) REVERT: C 517 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7591 (tm) outliers start: 48 outliers final: 15 residues processed: 177 average time/residue: 0.1973 time to fit residues: 42.8594 Evaluate side-chains 105 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 517 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 HIS B 92 GLN B 99 HIS B 100 ASN B 190 GLN ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 409 GLN C 439 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN C 493 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.149500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.124051 restraints weight = 11985.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.122756 restraints weight = 8439.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.124195 restraints weight = 6393.768| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5005 Z= 0.176 Angle : 0.623 7.011 6830 Z= 0.325 Chirality : 0.046 0.282 750 Planarity : 0.006 0.082 882 Dihedral : 9.666 83.111 767 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.06 % Favored : 86.94 % Rotamer: Outliers : 7.35 % Allowed : 11.95 % Favored : 80.70 % 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: -4.24 (0.29), residues: 628 helix: -4.46 (0.70), residues: 18 sheet: -2.32 (0.36), residues: 189 loop : -3.17 (0.26), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 36 HIS 0.002 0.001 HIS B 99 PHE 0.021 0.002 PHE C 400 TYR 0.015 0.002 TYR A 182 ARG 0.003 0.001 ARG B 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 1) link_NAG-ASN : angle 1.18841 ( 3) hydrogen bonds : bond 0.04252 ( 66) hydrogen bonds : angle 7.32618 ( 153) SS BOND : bond 0.00391 ( 8) SS BOND : angle 1.03567 ( 16) covalent geometry : bond 0.00407 ( 4996) covalent geometry : angle 0.62145 ( 6811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7179 (t0) cc_final: 0.6570 (t70) REVERT: A 102 TYR cc_start: 0.9212 (t80) cc_final: 0.8943 (t80) REVERT: A 147 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.5693 (mp) REVERT: A 184 LEU cc_start: 0.6824 (tp) cc_final: 0.6613 (tp) REVERT: A 203 ASN cc_start: 0.6109 (t0) cc_final: 0.5888 (m-40) REVERT: A 212 LYS cc_start: 0.6343 (mmtt) cc_final: 0.6107 (mmtt) REVERT: B 154 TRP cc_start: 0.6543 (m-90) cc_final: 0.6314 (m-90) REVERT: B 189 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7780 (mm-30) REVERT: B 194 HIS cc_start: 0.6618 (OUTLIER) cc_final: 0.6353 (m90) REVERT: B 195 ARG cc_start: 0.6499 (mmm160) cc_final: 0.5412 (mpp-170) REVERT: C 378 LYS cc_start: 0.9012 (mmtm) cc_final: 0.8308 (tptp) REVERT: C 406 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6573 (tt0) REVERT: C 452 LEU cc_start: 0.8679 (mt) cc_final: 0.8471 (mp) REVERT: C 517 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.7968 (tm) outliers start: 40 outliers final: 23 residues processed: 128 average time/residue: 0.2055 time to fit residues: 32.5936 Evaluate side-chains 99 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 LYS Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 0.0870 chunk 47 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 474 GLN C 501 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.151460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.122156 restraints weight = 12064.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.123051 restraints weight = 7197.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.124435 restraints weight = 5300.707| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5005 Z= 0.158 Angle : 0.619 6.689 6830 Z= 0.320 Chirality : 0.046 0.285 750 Planarity : 0.006 0.087 882 Dihedral : 8.310 83.605 745 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.17 % Favored : 85.83 % Rotamer: Outliers : 7.35 % Allowed : 15.07 % Favored : 77.57 % 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: -4.02 (0.30), residues: 628 helix: -4.42 (0.80), residues: 18 sheet: -2.19 (0.34), residues: 203 loop : -3.01 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 353 HIS 0.005 0.001 HIS B 203 PHE 0.020 0.002 PHE C 400 TYR 0.013 0.002 TYR A 151 ARG 0.002 0.001 ARG A 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 1) link_NAG-ASN : angle 1.19682 ( 3) hydrogen bonds : bond 0.03594 ( 66) hydrogen bonds : angle 6.77685 ( 153) SS BOND : bond 0.00419 ( 8) SS BOND : angle 1.15165 ( 16) covalent geometry : bond 0.00362 ( 4996) covalent geometry : angle 0.61688 ( 6811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 81 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7167 (t0) cc_final: 0.6612 (t70) REVERT: A 76 LYS cc_start: 0.8368 (pttp) cc_final: 0.8001 (pttm) REVERT: A 184 LEU cc_start: 0.6924 (tp) cc_final: 0.6723 (tp) REVERT: A 203 ASN cc_start: 0.5895 (t0) cc_final: 0.5685 (m-40) REVERT: A 212 LYS cc_start: 0.6631 (mmtt) cc_final: 0.6418 (mmtt) REVERT: B 154 TRP cc_start: 0.6528 (m-90) cc_final: 0.6325 (m-90) REVERT: B 176 ASN cc_start: 0.6165 (m-40) cc_final: 0.5846 (t0) REVERT: B 189 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7829 (mm-30) REVERT: B 195 ARG cc_start: 0.6452 (mmm160) cc_final: 0.5288 (mpp-170) REVERT: C 378 LYS cc_start: 0.8928 (mmtm) cc_final: 0.8566 (mmtm) REVERT: C 406 GLU cc_start: 0.6804 (tt0) cc_final: 0.6568 (tt0) REVERT: C 452 LEU cc_start: 0.8749 (mt) cc_final: 0.8549 (mp) REVERT: C 505 TYR cc_start: 0.7892 (m-10) cc_final: 0.7641 (m-10) REVERT: C 525 CYS cc_start: 0.4497 (t) cc_final: 0.3914 (t) outliers start: 40 outliers final: 26 residues processed: 111 average time/residue: 0.2024 time to fit residues: 28.1339 Evaluate side-chains 99 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 510 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 3 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 0.0570 chunk 38 optimal weight: 0.0070 chunk 56 optimal weight: 0.5980 chunk 54 optimal weight: 0.1980 chunk 55 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 HIS ** 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 = 0.4199 r_free = 0.4199 target = 0.152066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.125230 restraints weight = 12016.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.124420 restraints weight = 7608.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.125925 restraints weight = 5753.553| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5005 Z= 0.117 Angle : 0.580 6.702 6830 Z= 0.300 Chirality : 0.045 0.243 750 Planarity : 0.005 0.084 882 Dihedral : 7.959 83.529 740 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.85 % Favored : 86.15 % Rotamer: Outliers : 5.88 % Allowed : 18.01 % Favored : 76.10 % 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: -3.79 (0.30), residues: 628 helix: -4.51 (0.68), residues: 18 sheet: -1.81 (0.36), residues: 196 loop : -2.96 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.004 0.001 HIS B 203 PHE 0.017 0.001 PHE C 400 TYR 0.010 0.001 TYR B 50 ARG 0.002 0.000 ARG B 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00035 ( 1) link_NAG-ASN : angle 1.02353 ( 3) hydrogen bonds : bond 0.02968 ( 66) hydrogen bonds : angle 6.27392 ( 153) SS BOND : bond 0.00327 ( 8) SS BOND : angle 1.02856 ( 16) covalent geometry : bond 0.00269 ( 4996) covalent geometry : angle 0.57844 ( 6811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7237 (t0) cc_final: 0.6956 (t70) REVERT: A 184 LEU cc_start: 0.6649 (tp) cc_final: 0.6424 (tp) REVERT: B 114 GLN cc_start: 0.7229 (mp10) cc_final: 0.6985 (mp10) REVERT: B 176 ASN cc_start: 0.6188 (m-40) cc_final: 0.5791 (t0) REVERT: B 195 ARG cc_start: 0.6482 (mmm160) cc_final: 0.5271 (mpp-170) REVERT: C 378 LYS cc_start: 0.8903 (mmtm) cc_final: 0.8304 (tptp) REVERT: C 406 GLU cc_start: 0.6663 (tt0) cc_final: 0.6360 (tt0) REVERT: C 409 GLN cc_start: 0.8107 (mt0) cc_final: 0.7776 (mp10) REVERT: C 452 LEU cc_start: 0.8719 (mt) cc_final: 0.8506 (mp) REVERT: C 461 LEU cc_start: 0.6497 (tp) cc_final: 0.6243 (mp) outliers start: 32 outliers final: 20 residues processed: 105 average time/residue: 0.1975 time to fit residues: 26.7252 Evaluate side-chains 93 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 510 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 0.0570 chunk 13 optimal weight: 4.9990 chunk 43 optimal weight: 0.0570 chunk 22 optimal weight: 0.0770 chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 0.0270 overall best weight: 0.2032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 HIS ** 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 = 0.4215 r_free = 0.4215 target = 0.153361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.124408 restraints weight = 11884.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.124972 restraints weight = 8305.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.126161 restraints weight = 5845.146| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5005 Z= 0.107 Angle : 0.588 6.293 6830 Z= 0.302 Chirality : 0.046 0.205 750 Planarity : 0.005 0.089 882 Dihedral : 7.017 65.311 735 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.74 % Favored : 87.26 % Rotamer: Outliers : 4.41 % Allowed : 19.49 % Favored : 76.10 % 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: -3.57 (0.31), residues: 628 helix: -4.50 (0.66), residues: 18 sheet: -1.57 (0.38), residues: 197 loop : -2.86 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.003 0.001 HIS B 203 PHE 0.015 0.001 PHE B 145 TYR 0.009 0.001 TYR B 50 ARG 0.002 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00026 ( 1) link_NAG-ASN : angle 0.99766 ( 3) hydrogen bonds : bond 0.02844 ( 66) hydrogen bonds : angle 6.01934 ( 153) SS BOND : bond 0.00267 ( 8) SS BOND : angle 1.28680 ( 16) covalent geometry : bond 0.00251 ( 4996) covalent geometry : angle 0.58471 ( 6811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.6101 (tt) cc_final: 0.5496 (mp) REVERT: B 176 ASN cc_start: 0.6241 (m-40) cc_final: 0.5846 (t0) REVERT: B 195 ARG cc_start: 0.6381 (mmm160) cc_final: 0.5189 (mpp-170) REVERT: C 378 LYS cc_start: 0.8809 (mmtm) cc_final: 0.8282 (tptp) REVERT: C 406 GLU cc_start: 0.6517 (tt0) cc_final: 0.6268 (tt0) outliers start: 24 outliers final: 19 residues processed: 94 average time/residue: 0.1822 time to fit residues: 22.0433 Evaluate side-chains 83 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.0770 chunk 57 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 0.0170 chunk 20 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.146153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.121502 restraints weight = 11838.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.120514 restraints weight = 8470.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.121791 restraints weight = 7971.317| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5005 Z= 0.168 Angle : 0.646 7.453 6830 Z= 0.331 Chirality : 0.046 0.198 750 Planarity : 0.005 0.093 882 Dihedral : 7.437 67.210 735 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.29 % Favored : 84.71 % Rotamer: Outliers : 4.78 % Allowed : 19.12 % Favored : 76.10 % 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 (0.32), residues: 628 helix: -4.47 (0.67), residues: 18 sheet: -1.64 (0.37), residues: 203 loop : -2.79 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.005 0.001 HIS A 206 PHE 0.017 0.002 PHE C 400 TYR 0.019 0.002 TYR C 489 ARG 0.003 0.001 ARG B 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 1) link_NAG-ASN : angle 1.33571 ( 3) hydrogen bonds : bond 0.03471 ( 66) hydrogen bonds : angle 6.19777 ( 153) SS BOND : bond 0.00329 ( 8) SS BOND : angle 1.52473 ( 16) covalent geometry : bond 0.00399 ( 4996) covalent geometry : angle 0.64210 ( 6811) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.6215 (tt) cc_final: 0.5661 (mp) REVERT: B 116 LYS cc_start: 0.6645 (tmtt) cc_final: 0.6370 (tptt) REVERT: B 195 ARG cc_start: 0.6287 (mmm160) cc_final: 0.5115 (mpp-170) REVERT: C 378 LYS cc_start: 0.8911 (mmtm) cc_final: 0.8430 (tptp) outliers start: 26 outliers final: 20 residues processed: 92 average time/residue: 0.2289 time to fit residues: 27.0995 Evaluate side-chains 82 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.0870 chunk 61 optimal weight: 0.0040 chunk 59 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 0.0020 chunk 45 optimal weight: 0.4980 chunk 60 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 overall best weight: 0.1778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.149053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.123020 restraints weight = 11637.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.122552 restraints weight = 8564.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.123579 restraints weight = 6551.619| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5005 Z= 0.109 Angle : 0.623 8.852 6830 Z= 0.312 Chirality : 0.045 0.192 750 Planarity : 0.005 0.095 882 Dihedral : 7.069 65.669 734 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.85 % Favored : 86.15 % Rotamer: Outliers : 4.23 % Allowed : 19.85 % Favored : 75.92 % 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: -3.33 (0.32), residues: 628 helix: -4.55 (0.61), residues: 18 sheet: -1.33 (0.38), residues: 200 loop : -2.72 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.003 0.001 HIS B 203 PHE 0.018 0.001 PHE C 400 TYR 0.017 0.001 TYR C 489 ARG 0.002 0.000 ARG B 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00047 ( 1) link_NAG-ASN : angle 1.08262 ( 3) hydrogen bonds : bond 0.02839 ( 66) hydrogen bonds : angle 5.74039 ( 153) SS BOND : bond 0.00246 ( 8) SS BOND : angle 1.34836 ( 16) covalent geometry : bond 0.00263 ( 4996) covalent geometry : angle 0.61962 ( 6811) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: B 176 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.6925 (t0) REVERT: B 195 ARG cc_start: 0.6313 (mmm160) cc_final: 0.5193 (mpp-170) REVERT: C 378 LYS cc_start: 0.8850 (mmtm) cc_final: 0.8363 (tptp) REVERT: C 406 GLU cc_start: 0.6042 (OUTLIER) cc_final: 0.5671 (tt0) outliers start: 23 outliers final: 20 residues processed: 85 average time/residue: 0.2977 time to fit residues: 33.7392 Evaluate side-chains 82 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 27 optimal weight: 0.9990 chunk 60 optimal weight: 0.0980 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 43 optimal weight: 0.0980 chunk 59 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.145099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.121013 restraints weight = 11935.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.119927 restraints weight = 9561.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.121568 restraints weight = 7449.967| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5005 Z= 0.183 Angle : 0.693 8.522 6830 Z= 0.350 Chirality : 0.046 0.176 750 Planarity : 0.005 0.089 882 Dihedral : 7.447 68.222 734 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.45 % Favored : 84.55 % Rotamer: Outliers : 4.23 % Allowed : 20.77 % Favored : 75.00 % 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 (0.32), residues: 628 helix: -4.41 (0.70), residues: 18 sheet: -1.54 (0.37), residues: 203 loop : -2.82 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 47 HIS 0.005 0.001 HIS A 206 PHE 0.020 0.002 PHE C 400 TYR 0.013 0.002 TYR A 151 ARG 0.003 0.001 ARG A 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 1) link_NAG-ASN : angle 1.44988 ( 3) hydrogen bonds : bond 0.03570 ( 66) hydrogen bonds : angle 6.16884 ( 153) SS BOND : bond 0.00360 ( 8) SS BOND : angle 1.66817 ( 16) covalent geometry : bond 0.00437 ( 4996) covalent geometry : angle 0.68872 ( 6811) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: B 116 LYS cc_start: 0.6672 (tmtt) cc_final: 0.6457 (tptt) REVERT: B 176 ASN cc_start: 0.7512 (OUTLIER) cc_final: 0.7292 (t0) REVERT: B 195 ARG cc_start: 0.6510 (mmm160) cc_final: 0.5252 (mpp-170) REVERT: C 378 LYS cc_start: 0.8888 (mmtm) cc_final: 0.8328 (tptp) REVERT: C 452 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8167 (tp) REVERT: C 525 CYS cc_start: 0.4755 (t) cc_final: 0.4472 (t) outliers start: 23 outliers final: 20 residues processed: 83 average time/residue: 0.3871 time to fit residues: 42.0035 Evaluate side-chains 79 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 452 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 0.0270 chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 26 optimal weight: 0.0010 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 19 optimal weight: 0.0040 chunk 55 optimal weight: 0.9980 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.148097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.122623 restraints weight = 11678.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.122555 restraints weight = 8784.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.123927 restraints weight = 7056.920| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5005 Z= 0.122 Angle : 0.647 8.002 6830 Z= 0.325 Chirality : 0.046 0.198 750 Planarity : 0.005 0.097 882 Dihedral : 7.169 65.921 734 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.69 % Favored : 86.31 % Rotamer: Outliers : 4.23 % Allowed : 20.96 % Favored : 74.82 % 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: -3.33 (0.32), residues: 628 helix: -4.49 (0.65), residues: 18 sheet: -1.29 (0.38), residues: 201 loop : -2.76 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 154 HIS 0.003 0.001 HIS B 203 PHE 0.017 0.001 PHE C 400 TYR 0.011 0.001 TYR A 151 ARG 0.002 0.000 ARG C 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00012 ( 1) link_NAG-ASN : angle 1.20518 ( 3) hydrogen bonds : bond 0.02926 ( 66) hydrogen bonds : angle 5.73480 ( 153) SS BOND : bond 0.00264 ( 8) SS BOND : angle 1.33322 ( 16) covalent geometry : bond 0.00300 ( 4996) covalent geometry : angle 0.64435 ( 6811) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.7450 (mmmt) cc_final: 0.7237 (mmmt) REVERT: B 116 LYS cc_start: 0.6705 (tmtt) cc_final: 0.6455 (tptt) REVERT: B 195 ARG cc_start: 0.6588 (mmm160) cc_final: 0.5366 (mpp-170) REVERT: C 378 LYS cc_start: 0.8825 (mmtm) cc_final: 0.8353 (tptp) REVERT: C 452 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8045 (tp) REVERT: C 525 CYS cc_start: 0.4266 (t) cc_final: 0.4018 (t) outliers start: 23 outliers final: 21 residues processed: 84 average time/residue: 0.1904 time to fit residues: 20.2390 Evaluate side-chains 81 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 46 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.0470 chunk 44 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 47 optimal weight: 0.0670 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 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 = 0.4130 r_free = 0.4130 target = 0.148263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.123567 restraints weight = 11683.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.124042 restraints weight = 8412.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.125377 restraints weight = 6659.649| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5005 Z= 0.122 Angle : 0.649 7.793 6830 Z= 0.328 Chirality : 0.046 0.230 750 Planarity : 0.005 0.096 882 Dihedral : 7.011 65.221 734 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.49 % Favored : 85.51 % Rotamer: Outliers : 4.04 % Allowed : 21.14 % Favored : 74.82 % 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: -3.29 (0.32), residues: 628 helix: -4.46 (0.64), residues: 18 sheet: -1.30 (0.38), residues: 207 loop : -2.72 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 154 HIS 0.003 0.001 HIS A 206 PHE 0.016 0.001 PHE C 400 TYR 0.010 0.001 TYR A 151 ARG 0.002 0.000 ARG B 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00017 ( 1) link_NAG-ASN : angle 1.22679 ( 3) hydrogen bonds : bond 0.02818 ( 66) hydrogen bonds : angle 5.68080 ( 153) SS BOND : bond 0.00245 ( 8) SS BOND : angle 1.24487 ( 16) covalent geometry : bond 0.00301 ( 4996) covalent geometry : angle 0.64688 ( 6811) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.7504 (mmmt) cc_final: 0.7292 (mmmt) REVERT: B 116 LYS cc_start: 0.6661 (tmtt) cc_final: 0.6427 (tptt) REVERT: B 176 ASN cc_start: 0.7347 (OUTLIER) cc_final: 0.6885 (t0) REVERT: C 378 LYS cc_start: 0.8858 (mmtm) cc_final: 0.8391 (tptp) REVERT: C 406 GLU cc_start: 0.6011 (tt0) cc_final: 0.5570 (tt0) REVERT: C 452 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8097 (tp) outliers start: 22 outliers final: 20 residues processed: 79 average time/residue: 0.2102 time to fit residues: 21.3849 Evaluate side-chains 82 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 0.0870 chunk 27 optimal weight: 0.0020 chunk 40 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.0980 chunk 31 optimal weight: 0.6980 overall best weight: 0.2366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.149726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.125145 restraints weight = 11678.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.125577 restraints weight = 8215.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.126996 restraints weight = 6842.491| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5005 Z= 0.116 Angle : 0.627 7.650 6830 Z= 0.319 Chirality : 0.045 0.219 750 Planarity : 0.005 0.094 882 Dihedral : 6.875 63.776 734 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer: Outliers : 4.04 % Allowed : 21.32 % Favored : 74.63 % 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: -3.13 (0.32), residues: 628 helix: -4.54 (0.61), residues: 18 sheet: -1.21 (0.39), residues: 195 loop : -2.55 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 191 HIS 0.003 0.001 HIS B 203 PHE 0.015 0.001 PHE C 400 TYR 0.008 0.001 TYR A 151 ARG 0.002 0.000 ARG B 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00005 ( 1) link_NAG-ASN : angle 1.19682 ( 3) hydrogen bonds : bond 0.02721 ( 66) hydrogen bonds : angle 5.52767 ( 153) SS BOND : bond 0.00228 ( 8) SS BOND : angle 0.97494 ( 16) covalent geometry : bond 0.00280 ( 4996) covalent geometry : angle 0.62560 ( 6811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3218.31 seconds wall clock time: 58 minutes 7.30 seconds (3487.30 seconds total)