Starting phenix.real_space_refine on Wed Jul 23 07:39:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9db1_46710/07_2025/9db1_46710.cif Found real_map, /net/cci-nas-00/data/ceres_data/9db1_46710/07_2025/9db1_46710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9db1_46710/07_2025/9db1_46710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9db1_46710/07_2025/9db1_46710.map" model { file = "/net/cci-nas-00/data/ceres_data/9db1_46710/07_2025/9db1_46710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9db1_46710/07_2025/9db1_46710.cif" } resolution = 3.2 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= 0.036 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 9 5.16 5 C 1315 2.51 5 N 325 2.21 5 O 390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 2039 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1875 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 241} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 8, 'GLU:plan': 7, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.36, per 1000 atoms: 1.65 Number of scatterers: 2039 At special positions: 0 Unit cell: (64.4864, 56.4256, 76.5776, 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 9 16.00 O 390 8.00 N 325 7.00 C 1315 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 68 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 260 " 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1501 " - " ASN A 176 " " NAG A1502 " - " ASN A 236 " " NAG A1503 " - " ASN A 29 " " NAG B 1 " - " ASN A 243 " " NAG C 1 " - " ASN A 67 " " NAG D 1 " - " ASN A 210 " " NAG E 1 " - " ASN A 95 " Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 260.6 milliseconds 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 466 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 11.2% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 256 through 264 removed outlier: 4.241A pdb=" N GLY A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 58 Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 81 removed outlier: 6.927A pdb=" N ALA A 76 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR A 215 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N HIS A 110 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN A 210 " --> pdb=" O HIS A 108 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N HIS A 108 " --> pdb=" O ASN A 210 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR A 212 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU A 106 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 197 through 201 75 hydrogen bonds defined for protein. 183 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: 0.47 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 606 1.34 - 1.46: 569 1.46 - 1.58: 909 1.58 - 1.70: 0 1.70 - 1.81: 12 Bond restraints: 2096 Sorted by residual: bond pdb=" CA GLY A 162 " pdb=" C GLY A 162 " ideal model delta sigma weight residual 1.515 1.530 -0.015 1.65e-02 3.67e+03 8.34e-01 bond pdb=" N GLY A 162 " pdb=" CA GLY A 162 " ideal model delta sigma weight residual 1.454 1.464 -0.010 1.25e-02 6.40e+03 6.77e-01 bond pdb=" CA VAL A 171 " pdb=" C VAL A 171 " ideal model delta sigma weight residual 1.526 1.519 0.007 1.19e-02 7.06e+03 3.36e-01 bond pdb=" CA ILE A 172 " pdb=" C ILE A 172 " ideal model delta sigma weight residual 1.528 1.524 0.004 7.70e-03 1.69e+04 2.89e-01 bond pdb=" C TYR A 59 " pdb=" N TYR A 60 " ideal model delta sigma weight residual 1.339 1.310 0.029 5.57e-02 3.22e+02 2.74e-01 ... (remaining 2091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.85: 2610 0.85 - 1.71: 215 1.71 - 2.56: 36 2.56 - 3.42: 9 3.42 - 4.27: 3 Bond angle restraints: 2873 Sorted by residual: angle pdb=" N VAL A 171 " pdb=" CA VAL A 171 " pdb=" C VAL A 171 " ideal model delta sigma weight residual 110.21 105.94 4.27 1.13e+00 7.83e-01 1.43e+01 angle pdb=" C VAL A 171 " pdb=" N ILE A 172 " pdb=" CA ILE A 172 " ideal model delta sigma weight residual 122.60 120.12 2.48 6.80e-01 2.16e+00 1.33e+01 angle pdb=" N GLY A 182 " pdb=" CA GLY A 182 " pdb=" C GLY A 182 " ideal model delta sigma weight residual 110.56 114.30 -3.74 1.66e+00 3.63e-01 5.08e+00 angle pdb=" N ILE A 172 " pdb=" CA ILE A 172 " pdb=" C ILE A 172 " ideal model delta sigma weight residual 107.56 109.31 -1.75 9.10e-01 1.21e+00 3.72e+00 angle pdb=" CA VAL A 171 " pdb=" C VAL A 171 " pdb=" N ILE A 172 " ideal model delta sigma weight residual 115.26 117.39 -2.13 1.11e+00 8.12e-01 3.68e+00 ... (remaining 2868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.30: 1203 11.30 - 22.59: 96 22.59 - 33.89: 31 33.89 - 45.18: 6 45.18 - 56.48: 1 Dihedral angle restraints: 1337 sinusoidal: 602 harmonic: 735 Sorted by residual: dihedral pdb=" CA ILE A 19 " pdb=" C ILE A 19 " pdb=" N LYS A 20 " pdb=" CA LYS A 20 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" N TYR A 231 " pdb=" CA TYR A 231 " pdb=" CB TYR A 231 " pdb=" CG TYR A 231 " ideal model delta sinusoidal sigma weight residual 60.00 3.52 56.48 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CA ILE A 140 " pdb=" C ILE A 140 " pdb=" N THR A 141 " pdb=" CA THR A 141 " ideal model delta harmonic sigma weight residual -180.00 -166.47 -13.53 0 5.00e+00 4.00e-02 7.32e+00 ... (remaining 1334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 227 0.036 - 0.071: 77 0.071 - 0.106: 32 0.106 - 0.142: 9 0.142 - 0.177: 2 Chirality restraints: 347 Sorted by residual: chirality pdb=" C1 NAG A1501 " pdb=" ND2 ASN A 176 " pdb=" C2 NAG A1501 " pdb=" O5 NAG A1501 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 67 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.64e-01 chirality pdb=" CA ILE A 140 " pdb=" N ILE A 140 " pdb=" C ILE A 140 " pdb=" CB ILE A 140 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 344 not shown) Planarity restraints: 359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 103 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO A 104 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 167 " 0.015 5.00e-02 4.00e+02 2.27e-02 8.24e-01 pdb=" N PRO A 168 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 167 " -0.004 2.00e-02 2.50e+03 8.79e-03 7.73e-01 pdb=" C VAL A 167 " 0.015 2.00e-02 2.50e+03 pdb=" O VAL A 167 " -0.006 2.00e-02 2.50e+03 pdb=" N PRO A 168 " -0.005 2.00e-02 2.50e+03 ... (remaining 356 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 704 2.85 - 3.36: 1488 3.36 - 3.88: 3170 3.88 - 4.39: 3506 4.39 - 4.90: 6486 Nonbonded interactions: 15354 Sorted by model distance: nonbonded pdb=" NH2 ARG A 101 " pdb=" OD2 ASP A 126 " model vdw 2.340 3.120 nonbonded pdb=" O TYR A 59 " pdb=" OH TYR A 87 " model vdw 2.365 3.040 nonbonded pdb=" NZ LYS A 70 " pdb=" O THR A 74 " model vdw 2.368 3.120 nonbonded pdb=" OH TYR A 119 " pdb=" OG1 THR A 222 " model vdw 2.486 3.040 nonbonded pdb=" O ASP A 175 " pdb=" OG1 THR A 178 " model vdw 2.508 3.040 ... (remaining 15349 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 5.480 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.970 Find NCS groups from input model: 0.020 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 0.029 2111 Z= 0.140 Angle : 0.576 4.269 2915 Z= 0.327 Chirality : 0.045 0.177 347 Planarity : 0.003 0.027 352 Dihedral : 9.167 56.480 862 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.20 % Allowed : 5.39 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.54 (0.55), residues: 247 helix: -3.36 (0.62), residues: 24 sheet: 0.70 (0.51), residues: 108 loop : -0.66 (0.62), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 65 HIS 0.002 0.001 HIS A 135 PHE 0.014 0.002 PHE A 107 TYR 0.007 0.001 TYR A 259 ARG 0.001 0.000 ARG A 130 Details of bonding type rmsd link_NAG-ASN : bond 0.00207 ( 7) link_NAG-ASN : angle 1.40467 ( 21) link_BETA1-4 : bond 0.00416 ( 4) link_BETA1-4 : angle 2.16478 ( 12) hydrogen bonds : bond 0.15437 ( 75) hydrogen bonds : angle 7.59837 ( 183) link_BETA1-6 : bond 0.00356 ( 1) link_BETA1-6 : angle 1.29736 ( 3) SS BOND : bond 0.00227 ( 3) SS BOND : angle 0.73384 ( 6) covalent geometry : bond 0.00296 ( 2096) covalent geometry : angle 0.54719 ( 2873) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.201 Fit side-chains REVERT: A 101 ARG cc_start: 0.8011 (mtp85) cc_final: 0.7809 (mtp85) REVERT: A 172 ILE cc_start: 0.8529 (mm) cc_final: 0.8126 (mm) outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 0.1552 time to fit residues: 6.1688 Evaluate side-chains 29 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.0070 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 129 HIS A 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.141181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112144 restraints weight = 2558.927| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.54 r_work: 0.3060 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 2111 Z= 0.176 Angle : 0.561 4.693 2915 Z= 0.283 Chirality : 0.046 0.176 347 Planarity : 0.004 0.027 352 Dihedral : 5.751 55.122 523 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.20 % Allowed : 7.19 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.48 (0.55), residues: 247 helix: -3.07 (0.71), residues: 23 sheet: 0.79 (0.51), residues: 108 loop : -0.77 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 65 HIS 0.001 0.000 HIS A 135 PHE 0.015 0.002 PHE A 107 TYR 0.010 0.001 TYR A 181 ARG 0.002 0.000 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 7) link_NAG-ASN : angle 1.33789 ( 21) link_BETA1-4 : bond 0.00456 ( 4) link_BETA1-4 : angle 2.18375 ( 12) hydrogen bonds : bond 0.03595 ( 75) hydrogen bonds : angle 6.01949 ( 183) link_BETA1-6 : bond 0.00262 ( 1) link_BETA1-6 : angle 1.28081 ( 3) SS BOND : bond 0.00230 ( 3) SS BOND : angle 1.58091 ( 6) covalent geometry : bond 0.00432 ( 2096) covalent geometry : angle 0.52899 ( 2873) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.216 Fit side-chains REVERT: A 172 ILE cc_start: 0.8609 (mm) cc_final: 0.8232 (mm) outliers start: 2 outliers final: 2 residues processed: 27 average time/residue: 0.1591 time to fit residues: 5.1111 Evaluate side-chains 28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 231 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 0.0470 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 0.2980 chunk 2 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.142070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.113237 restraints weight = 2503.857| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.53 r_work: 0.3080 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2111 Z= 0.117 Angle : 0.510 4.317 2915 Z= 0.257 Chirality : 0.044 0.166 347 Planarity : 0.003 0.026 352 Dihedral : 5.485 53.985 523 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.80 % Allowed : 9.58 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.24 (0.55), residues: 247 helix: -2.82 (0.74), residues: 23 sheet: 0.92 (0.51), residues: 108 loop : -0.60 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 65 HIS 0.001 0.000 HIS A 135 PHE 0.015 0.002 PHE A 107 TYR 0.007 0.001 TYR A 181 ARG 0.002 0.001 ARG A 130 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 7) link_NAG-ASN : angle 1.27841 ( 21) link_BETA1-4 : bond 0.00424 ( 4) link_BETA1-4 : angle 2.09826 ( 12) hydrogen bonds : bond 0.02981 ( 75) hydrogen bonds : angle 5.67334 ( 183) link_BETA1-6 : bond 0.00405 ( 1) link_BETA1-6 : angle 1.25084 ( 3) SS BOND : bond 0.00232 ( 3) SS BOND : angle 1.10589 ( 6) covalent geometry : bond 0.00280 ( 2096) covalent geometry : angle 0.47927 ( 2873) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.217 Fit side-chains REVERT: A 172 ILE cc_start: 0.8606 (mm) cc_final: 0.8240 (mm) outliers start: 3 outliers final: 2 residues processed: 28 average time/residue: 0.1274 time to fit residues: 4.4959 Evaluate side-chains 27 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 231 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.0980 chunk 18 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.142202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.113626 restraints weight = 2467.962| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.49 r_work: 0.3085 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2111 Z= 0.139 Angle : 0.519 4.312 2915 Z= 0.262 Chirality : 0.045 0.166 347 Planarity : 0.003 0.027 352 Dihedral : 5.413 53.801 523 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.80 % Allowed : 10.18 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.26 (0.55), residues: 247 helix: -2.75 (0.75), residues: 23 sheet: 0.91 (0.51), residues: 108 loop : -0.62 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 185 HIS 0.001 0.000 HIS A 135 PHE 0.015 0.002 PHE A 107 TYR 0.008 0.001 TYR A 259 ARG 0.001 0.000 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 7) link_NAG-ASN : angle 1.31134 ( 21) link_BETA1-4 : bond 0.00443 ( 4) link_BETA1-4 : angle 2.05275 ( 12) hydrogen bonds : bond 0.02957 ( 75) hydrogen bonds : angle 5.60663 ( 183) link_BETA1-6 : bond 0.00325 ( 1) link_BETA1-6 : angle 1.26812 ( 3) SS BOND : bond 0.00185 ( 3) SS BOND : angle 1.09499 ( 6) covalent geometry : bond 0.00340 ( 2096) covalent geometry : angle 0.48902 ( 2873) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.195 Fit side-chains REVERT: A 172 ILE cc_start: 0.8649 (mm) cc_final: 0.8292 (mm) outliers start: 3 outliers final: 3 residues processed: 27 average time/residue: 0.1147 time to fit residues: 3.8704 Evaluate side-chains 27 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 254 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 0.0270 chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.112226 restraints weight = 2556.803| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.54 r_work: 0.3062 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 2111 Z= 0.163 Angle : 0.538 4.505 2915 Z= 0.271 Chirality : 0.045 0.169 347 Planarity : 0.003 0.027 352 Dihedral : 5.487 54.385 523 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.40 % Allowed : 10.18 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.28 (0.55), residues: 247 helix: -2.61 (0.78), residues: 23 sheet: 0.85 (0.50), residues: 108 loop : -0.63 (0.62), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 185 HIS 0.001 0.000 HIS A 135 PHE 0.015 0.002 PHE A 107 TYR 0.009 0.001 TYR A 181 ARG 0.002 0.001 ARG A 130 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 7) link_NAG-ASN : angle 1.36453 ( 21) link_BETA1-4 : bond 0.00434 ( 4) link_BETA1-4 : angle 2.07745 ( 12) hydrogen bonds : bond 0.03020 ( 75) hydrogen bonds : angle 5.60103 ( 183) link_BETA1-6 : bond 0.00313 ( 1) link_BETA1-6 : angle 1.30820 ( 3) SS BOND : bond 0.00181 ( 3) SS BOND : angle 1.14919 ( 6) covalent geometry : bond 0.00400 ( 2096) covalent geometry : angle 0.50770 ( 2873) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.220 Fit side-chains REVERT: A 172 ILE cc_start: 0.8744 (mm) cc_final: 0.8424 (mm) outliers start: 4 outliers final: 3 residues processed: 28 average time/residue: 0.1531 time to fit residues: 5.0823 Evaluate side-chains 28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 254 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 2 optimal weight: 0.0170 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.141897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112460 restraints weight = 2513.967| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.58 r_work: 0.3071 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2111 Z= 0.136 Angle : 0.515 4.375 2915 Z= 0.261 Chirality : 0.045 0.164 347 Planarity : 0.003 0.027 352 Dihedral : 5.384 53.538 523 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.40 % Allowed : 10.78 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.23 (0.55), residues: 247 helix: -2.49 (0.82), residues: 23 sheet: 0.91 (0.50), residues: 108 loop : -0.64 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 201 HIS 0.001 0.000 HIS A 135 PHE 0.016 0.002 PHE A 107 TYR 0.007 0.001 TYR A 259 ARG 0.001 0.000 ARG A 130 Details of bonding type rmsd link_NAG-ASN : bond 0.00174 ( 7) link_NAG-ASN : angle 1.32200 ( 21) link_BETA1-4 : bond 0.00419 ( 4) link_BETA1-4 : angle 2.05933 ( 12) hydrogen bonds : bond 0.02912 ( 75) hydrogen bonds : angle 5.52631 ( 183) link_BETA1-6 : bond 0.00348 ( 1) link_BETA1-6 : angle 1.27686 ( 3) SS BOND : bond 0.00184 ( 3) SS BOND : angle 0.99513 ( 6) covalent geometry : bond 0.00332 ( 2096) covalent geometry : angle 0.48449 ( 2873) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.229 Fit side-chains REVERT: A 172 ILE cc_start: 0.8712 (mm) cc_final: 0.8383 (mm) outliers start: 4 outliers final: 4 residues processed: 28 average time/residue: 0.1190 time to fit residues: 4.1980 Evaluate side-chains 28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 254 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.4980 chunk 2 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.0470 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.0050 chunk 11 optimal weight: 0.0470 overall best weight: 0.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.144597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.114405 restraints weight = 2508.355| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.67 r_work: 0.3088 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 2111 Z= 0.079 Angle : 0.469 3.945 2915 Z= 0.240 Chirality : 0.043 0.151 347 Planarity : 0.003 0.029 352 Dihedral : 5.049 51.190 523 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.20 % Allowed : 11.98 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.04 (0.55), residues: 247 helix: -2.19 (0.87), residues: 23 sheet: 0.97 (0.50), residues: 108 loop : -0.49 (0.62), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 201 HIS 0.001 0.000 HIS A 108 PHE 0.015 0.001 PHE A 107 TYR 0.005 0.001 TYR A 259 ARG 0.001 0.000 ARG A 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00181 ( 7) link_NAG-ASN : angle 1.16117 ( 21) link_BETA1-4 : bond 0.00433 ( 4) link_BETA1-4 : angle 1.97318 ( 12) hydrogen bonds : bond 0.02524 ( 75) hydrogen bonds : angle 5.26858 ( 183) link_BETA1-6 : bond 0.00486 ( 1) link_BETA1-6 : angle 1.17321 ( 3) SS BOND : bond 0.00182 ( 3) SS BOND : angle 0.68480 ( 6) covalent geometry : bond 0.00184 ( 2096) covalent geometry : angle 0.44170 ( 2873) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.229 Fit side-chains REVERT: A 172 ILE cc_start: 0.8733 (mm) cc_final: 0.8412 (mm) outliers start: 2 outliers final: 2 residues processed: 30 average time/residue: 0.1160 time to fit residues: 4.3460 Evaluate side-chains 28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 254 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 0.0870 chunk 3 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.144241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.114151 restraints weight = 2582.820| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.66 r_work: 0.3067 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2111 Z= 0.136 Angle : 0.503 4.183 2915 Z= 0.255 Chirality : 0.045 0.164 347 Planarity : 0.003 0.028 352 Dihedral : 5.157 52.452 523 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.80 % Allowed : 11.38 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.03 (0.55), residues: 247 helix: -2.21 (0.87), residues: 23 sheet: 1.05 (0.50), residues: 108 loop : -0.55 (0.62), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 201 HIS 0.001 0.000 HIS A 135 PHE 0.015 0.002 PHE A 107 TYR 0.008 0.001 TYR A 259 ARG 0.001 0.000 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 7) link_NAG-ASN : angle 1.25292 ( 21) link_BETA1-4 : bond 0.00436 ( 4) link_BETA1-4 : angle 1.95675 ( 12) hydrogen bonds : bond 0.02842 ( 75) hydrogen bonds : angle 5.34510 ( 183) link_BETA1-6 : bond 0.00347 ( 1) link_BETA1-6 : angle 1.27042 ( 3) SS BOND : bond 0.00183 ( 3) SS BOND : angle 0.99419 ( 6) covalent geometry : bond 0.00335 ( 2096) covalent geometry : angle 0.47484 ( 2873) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.222 Fit side-chains REVERT: A 172 ILE cc_start: 0.8747 (mm) cc_final: 0.8417 (mm) outliers start: 3 outliers final: 3 residues processed: 28 average time/residue: 0.1181 time to fit residues: 4.1374 Evaluate side-chains 28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 254 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.111716 restraints weight = 2616.727| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.68 r_work: 0.3052 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 2111 Z= 0.161 Angle : 0.529 4.459 2915 Z= 0.267 Chirality : 0.045 0.168 347 Planarity : 0.003 0.028 352 Dihedral : 5.337 53.191 523 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.80 % Allowed : 11.38 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.07 (0.55), residues: 247 helix: -2.32 (0.86), residues: 23 sheet: 1.03 (0.50), residues: 108 loop : -0.56 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 201 HIS 0.001 0.000 HIS A 135 PHE 0.015 0.002 PHE A 107 TYR 0.008 0.001 TYR A 259 ARG 0.001 0.000 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 7) link_NAG-ASN : angle 1.34294 ( 21) link_BETA1-4 : bond 0.00418 ( 4) link_BETA1-4 : angle 2.01128 ( 12) hydrogen bonds : bond 0.02967 ( 75) hydrogen bonds : angle 5.44160 ( 183) link_BETA1-6 : bond 0.00296 ( 1) link_BETA1-6 : angle 1.31207 ( 3) SS BOND : bond 0.00196 ( 3) SS BOND : angle 1.08985 ( 6) covalent geometry : bond 0.00395 ( 2096) covalent geometry : angle 0.50002 ( 2873) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.223 Fit side-chains REVERT: A 172 ILE cc_start: 0.8785 (mm) cc_final: 0.8446 (mm) outliers start: 3 outliers final: 3 residues processed: 27 average time/residue: 0.1246 time to fit residues: 4.1829 Evaluate side-chains 26 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 254 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.0370 chunk 6 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.0170 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.144280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.114106 restraints weight = 2504.387| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.66 r_work: 0.3060 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2111 Z= 0.107 Angle : 0.488 4.146 2915 Z= 0.249 Chirality : 0.044 0.159 347 Planarity : 0.003 0.029 352 Dihedral : 5.147 51.677 523 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.20 % Allowed : 11.98 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.03 (0.55), residues: 247 helix: -2.26 (0.86), residues: 23 sheet: 1.01 (0.50), residues: 108 loop : -0.49 (0.62), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 201 HIS 0.001 0.000 HIS A 135 PHE 0.016 0.002 PHE A 107 TYR 0.007 0.001 TYR A 259 ARG 0.001 0.000 ARG A 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 7) link_NAG-ASN : angle 1.21290 ( 21) link_BETA1-4 : bond 0.00410 ( 4) link_BETA1-4 : angle 1.97681 ( 12) hydrogen bonds : bond 0.02714 ( 75) hydrogen bonds : angle 5.30241 ( 183) link_BETA1-6 : bond 0.00398 ( 1) link_BETA1-6 : angle 1.23657 ( 3) SS BOND : bond 0.00183 ( 3) SS BOND : angle 0.82680 ( 6) covalent geometry : bond 0.00260 ( 2096) covalent geometry : angle 0.46005 ( 2873) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.213 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 27 average time/residue: 0.1251 time to fit residues: 4.1869 Evaluate side-chains 27 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 254 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 2 optimal weight: 0.0980 chunk 17 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.0050 chunk 20 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.144030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.113576 restraints weight = 2552.349| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.70 r_work: 0.3073 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2111 Z= 0.105 Angle : 0.480 4.105 2915 Z= 0.245 Chirality : 0.044 0.159 347 Planarity : 0.003 0.030 352 Dihedral : 5.042 51.042 523 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.20 % Allowed : 11.98 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.05 (0.55), residues: 247 helix: -2.18 (0.86), residues: 23 sheet: 1.06 (0.50), residues: 108 loop : -0.44 (0.62), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 201 HIS 0.001 0.000 HIS A 135 PHE 0.015 0.002 PHE A 107 TYR 0.007 0.001 TYR A 259 ARG 0.001 0.000 ARG A 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 7) link_NAG-ASN : angle 1.20323 ( 21) link_BETA1-4 : bond 0.00414 ( 4) link_BETA1-4 : angle 1.92151 ( 12) hydrogen bonds : bond 0.02663 ( 75) hydrogen bonds : angle 5.24562 ( 183) link_BETA1-6 : bond 0.00394 ( 1) link_BETA1-6 : angle 1.22151 ( 3) SS BOND : bond 0.00172 ( 3) SS BOND : angle 0.81952 ( 6) covalent geometry : bond 0.00256 ( 2096) covalent geometry : angle 0.45284 ( 2873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1838.10 seconds wall clock time: 32 minutes 20.36 seconds (1940.36 seconds total)