Starting phenix.real_space_refine on Wed Sep 17 03:00:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9db1_46710/09_2025/9db1_46710.cif Found real_map, /net/cci-nas-00/data/ceres_data/9db1_46710/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9db1_46710/09_2025/9db1_46710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9db1_46710/09_2025/9db1_46710.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9db1_46710/09_2025/9db1_46710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9db1_46710/09_2025/9db1_46710.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASN:plan1': 8, 'ASP:plan': 6, 'ARG:plan': 4, 'GLU:plan': 7} 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: 0.85, per 1000 atoms: 0.42 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: 0.26 Conformation dependent library (CDL) restraints added in 84.9 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.08 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: 0.32 Time building geometry restraints manager: 0.31 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: 8.670 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.530 Find NCS groups from input model: 0.010 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.570 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG A 130 TYR 0.007 0.001 TYR A 259 PHE 0.014 0.002 PHE A 107 TRP 0.004 0.001 TRP A 65 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 2096) covalent geometry : angle 0.54719 ( 2873) SS BOND : bond 0.00227 ( 3) SS BOND : angle 0.73384 ( 6) hydrogen bonds : bond 0.15437 ( 75) hydrogen bonds : angle 7.59837 ( 183) link_BETA1-4 : bond 0.00416 ( 4) link_BETA1-4 : angle 2.16478 ( 12) link_BETA1-6 : bond 0.00356 ( 1) link_BETA1-6 : angle 1.29736 ( 3) link_NAG-ASN : bond 0.00207 ( 7) link_NAG-ASN : angle 1.40467 ( 21) *********************** 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 : 0.080 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: 0.0716 time to fit residues: 2.8492 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 : 0.076 ------------------------------------------------------------------------------- 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 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 chunk 4 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.142528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.113402 restraints weight = 2562.709| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.55 r_work: 0.3075 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 2111 Z= 0.142 Angle : 0.539 4.441 2915 Z= 0.273 Chirality : 0.045 0.171 347 Planarity : 0.003 0.026 352 Dihedral : 5.638 54.566 523 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.89 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.55), residues: 247 helix: -3.01 (0.72), residues: 23 sheet: 0.82 (0.51), residues: 108 loop : -0.72 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 101 TYR 0.008 0.001 TYR A 181 PHE 0.015 0.002 PHE A 107 TRP 0.003 0.001 TRP A 65 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 2096) covalent geometry : angle 0.50739 ( 2873) SS BOND : bond 0.00394 ( 3) SS BOND : angle 1.49260 ( 6) hydrogen bonds : bond 0.03475 ( 75) hydrogen bonds : angle 5.95172 ( 183) link_BETA1-4 : bond 0.00456 ( 4) link_BETA1-4 : angle 2.13302 ( 12) link_BETA1-6 : bond 0.00341 ( 1) link_BETA1-6 : angle 1.24936 ( 3) link_NAG-ASN : bond 0.00243 ( 7) link_NAG-ASN : angle 1.29848 ( 21) *********************** 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 29 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.079 Fit side-chains REVERT: A 101 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7944 (mtp85) REVERT: A 172 ILE cc_start: 0.8570 (mm) cc_final: 0.8153 (mm) outliers start: 2 outliers final: 2 residues processed: 28 average time/residue: 0.0755 time to fit residues: 2.4854 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 : 0.076 ------------------------------------------------------------------------------- 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 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.0030 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 0.0870 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 0.0970 chunk 21 optimal weight: 0.5980 overall best weight: 0.2966 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.143069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.114227 restraints weight = 2545.725| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.53 r_work: 0.3092 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2111 Z= 0.102 Angle : 0.491 4.151 2915 Z= 0.249 Chirality : 0.044 0.161 347 Planarity : 0.003 0.026 352 Dihedral : 5.330 52.780 523 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.20 % Allowed : 8.98 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.55), residues: 247 helix: -2.77 (0.75), residues: 23 sheet: 0.94 (0.51), residues: 108 loop : -0.60 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 101 TYR 0.006 0.001 TYR A 181 PHE 0.015 0.001 PHE A 107 TRP 0.002 0.000 TRP A 65 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 2096) covalent geometry : angle 0.46081 ( 2873) SS BOND : bond 0.00262 ( 3) SS BOND : angle 1.04804 ( 6) hydrogen bonds : bond 0.02904 ( 75) hydrogen bonds : angle 5.59435 ( 183) link_BETA1-4 : bond 0.00443 ( 4) link_BETA1-4 : angle 2.05585 ( 12) link_BETA1-6 : bond 0.00417 ( 1) link_BETA1-6 : angle 1.19540 ( 3) link_NAG-ASN : bond 0.00201 ( 7) link_NAG-ASN : angle 1.21681 ( 21) *********************** 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: 2 poor density : 27 time to evaluate : 0.081 Fit side-chains REVERT: A 172 ILE cc_start: 0.8602 (mm) cc_final: 0.8219 (mm) outliers start: 2 outliers final: 1 residues processed: 29 average time/residue: 0.0742 time to fit residues: 2.5216 Evaluate side-chains 28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 11 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 7 optimal weight: 0.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.142874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.112855 restraints weight = 2505.202| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.65 r_work: 0.3060 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2111 Z= 0.128 Angle : 0.504 4.224 2915 Z= 0.256 Chirality : 0.044 0.162 347 Planarity : 0.003 0.027 352 Dihedral : 5.305 53.245 523 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.55), residues: 247 helix: -2.67 (0.76), residues: 23 sheet: 1.00 (0.51), residues: 108 loop : -0.62 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.007 0.001 TYR A 259 PHE 0.014 0.002 PHE A 107 TRP 0.003 0.001 TRP A 185 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 2096) covalent geometry : angle 0.47530 ( 2873) SS BOND : bond 0.00180 ( 3) SS BOND : angle 1.03331 ( 6) hydrogen bonds : bond 0.02866 ( 75) hydrogen bonds : angle 5.55066 ( 183) link_BETA1-4 : bond 0.00442 ( 4) link_BETA1-4 : angle 2.01729 ( 12) link_BETA1-6 : bond 0.00381 ( 1) link_BETA1-6 : angle 1.24949 ( 3) link_NAG-ASN : bond 0.00186 ( 7) link_NAG-ASN : angle 1.24174 ( 21) *********************** 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 31 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.084 Fit side-chains REVERT: A 172 ILE cc_start: 0.8624 (mm) cc_final: 0.8259 (mm) outliers start: 3 outliers final: 3 residues processed: 30 average time/residue: 0.0474 time to fit residues: 1.7899 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 : 0.070 ------------------------------------------------------------------------------- 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 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 6 optimal weight: 0.0070 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.141653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112578 restraints weight = 2538.043| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.52 r_work: 0.3073 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 2111 Z= 0.142 Angle : 0.514 4.347 2915 Z= 0.261 Chirality : 0.045 0.166 347 Planarity : 0.003 0.027 352 Dihedral : 5.331 53.691 523 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.55), residues: 247 helix: -2.50 (0.81), residues: 23 sheet: 0.97 (0.50), residues: 108 loop : -0.58 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 130 TYR 0.008 0.001 TYR A 181 PHE 0.015 0.002 PHE A 107 TRP 0.003 0.001 TRP A 185 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 2096) covalent geometry : angle 0.48473 ( 2873) SS BOND : bond 0.00182 ( 3) SS BOND : angle 1.08039 ( 6) hydrogen bonds : bond 0.02936 ( 75) hydrogen bonds : angle 5.51996 ( 183) link_BETA1-4 : bond 0.00422 ( 4) link_BETA1-4 : angle 2.01768 ( 12) link_BETA1-6 : bond 0.00351 ( 1) link_BETA1-6 : angle 1.28396 ( 3) link_NAG-ASN : bond 0.00174 ( 7) link_NAG-ASN : angle 1.29886 ( 21) *********************** 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 27 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.079 Fit side-chains REVERT: A 172 ILE cc_start: 0.8677 (mm) cc_final: 0.8323 (mm) outliers start: 3 outliers final: 3 residues processed: 26 average time/residue: 0.0511 time to fit residues: 1.6498 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 : 0.076 ------------------------------------------------------------------------------- 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 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 11 optimal weight: 0.1980 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 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 = 0.3565 r_free = 0.3565 target = 0.142452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.113717 restraints weight = 2491.966| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.48 r_work: 0.3075 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2111 Z= 0.137 Angle : 0.511 4.315 2915 Z= 0.258 Chirality : 0.045 0.164 347 Planarity : 0.003 0.027 352 Dihedral : 5.304 53.367 523 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.40 % Allowed : 9.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.55), residues: 247 helix: -2.42 (0.82), residues: 23 sheet: 0.98 (0.50), residues: 108 loop : -0.63 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 130 TYR 0.008 0.001 TYR A 259 PHE 0.015 0.002 PHE A 107 TRP 0.004 0.001 TRP A 201 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 2096) covalent geometry : angle 0.48143 ( 2873) SS BOND : bond 0.00193 ( 3) SS BOND : angle 1.00668 ( 6) hydrogen bonds : bond 0.02868 ( 75) hydrogen bonds : angle 5.47990 ( 183) link_BETA1-4 : bond 0.00436 ( 4) link_BETA1-4 : angle 2.02194 ( 12) link_BETA1-6 : bond 0.00345 ( 1) link_BETA1-6 : angle 1.26281 ( 3) link_NAG-ASN : bond 0.00173 ( 7) link_NAG-ASN : angle 1.27675 ( 21) *********************** 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 : 0.075 Fit side-chains REVERT: A 172 ILE cc_start: 0.8695 (mm) cc_final: 0.8324 (mm) outliers start: 4 outliers final: 3 residues processed: 28 average time/residue: 0.0728 time to fit residues: 2.3895 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 : 0.067 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.141643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112225 restraints weight = 2557.669| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.58 r_work: 0.3062 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 2111 Z= 0.151 Angle : 0.520 4.468 2915 Z= 0.263 Chirality : 0.045 0.165 347 Planarity : 0.003 0.028 352 Dihedral : 5.356 53.486 523 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.55), residues: 247 helix: -2.37 (0.84), residues: 23 sheet: 1.01 (0.51), residues: 108 loop : -0.61 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.008 0.001 TYR A 181 PHE 0.015 0.002 PHE A 107 TRP 0.005 0.001 TRP A 201 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 2096) covalent geometry : angle 0.48978 ( 2873) SS BOND : bond 0.00194 ( 3) SS BOND : angle 1.07812 ( 6) hydrogen bonds : bond 0.02979 ( 75) hydrogen bonds : angle 5.47838 ( 183) link_BETA1-4 : bond 0.00429 ( 4) link_BETA1-4 : angle 2.02918 ( 12) link_BETA1-6 : bond 0.00315 ( 1) link_BETA1-6 : angle 1.28946 ( 3) link_NAG-ASN : bond 0.00173 ( 7) link_NAG-ASN : angle 1.31909 ( 21) *********************** 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 28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.074 Fit side-chains REVERT: A 172 ILE cc_start: 0.8742 (mm) cc_final: 0.8410 (mm) outliers start: 4 outliers final: 4 residues processed: 27 average time/residue: 0.0456 time to fit residues: 1.5556 Evaluate side-chains 27 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.074 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 19 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.142303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112414 restraints weight = 2542.205| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.64 r_work: 0.3074 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2111 Z= 0.127 Angle : 0.504 4.294 2915 Z= 0.256 Chirality : 0.044 0.162 347 Planarity : 0.003 0.029 352 Dihedral : 5.269 52.707 523 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.80 % Allowed : 10.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.55), residues: 247 helix: -2.33 (0.84), residues: 23 sheet: 1.01 (0.50), residues: 108 loop : -0.59 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 41 TYR 0.008 0.001 TYR A 259 PHE 0.015 0.002 PHE A 107 TRP 0.004 0.001 TRP A 201 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 2096) covalent geometry : angle 0.47560 ( 2873) SS BOND : bond 0.00192 ( 3) SS BOND : angle 0.93915 ( 6) hydrogen bonds : bond 0.02833 ( 75) hydrogen bonds : angle 5.42994 ( 183) link_BETA1-4 : bond 0.00418 ( 4) link_BETA1-4 : angle 2.01195 ( 12) link_BETA1-6 : bond 0.00360 ( 1) link_BETA1-6 : angle 1.26198 ( 3) link_NAG-ASN : bond 0.00174 ( 7) link_NAG-ASN : angle 1.25626 ( 21) *********************** 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 29 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.130 Fit side-chains REVERT: A 172 ILE cc_start: 0.8780 (mm) cc_final: 0.8441 (mm) outliers start: 3 outliers final: 3 residues processed: 28 average time/residue: 0.0512 time to fit residues: 1.8169 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 : 0.092 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 0.0020 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.0170 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 overall best weight: 0.5026 ------------------------------------------------------------------------------- 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 = 0.143739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.113964 restraints weight = 2547.627| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.64 r_work: 0.3058 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2111 Z= 0.147 Angle : 0.522 4.421 2915 Z= 0.263 Chirality : 0.045 0.166 347 Planarity : 0.003 0.028 352 Dihedral : 5.315 53.115 523 Min Nonbonded Distance : 2.607 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.55), residues: 247 helix: -2.33 (0.84), residues: 23 sheet: 1.01 (0.50), residues: 108 loop : -0.58 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 130 TYR 0.008 0.001 TYR A 259 PHE 0.015 0.002 PHE A 107 TRP 0.005 0.001 TRP A 201 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 2096) covalent geometry : angle 0.49273 ( 2873) SS BOND : bond 0.00182 ( 3) SS BOND : angle 1.01132 ( 6) hydrogen bonds : bond 0.02930 ( 75) hydrogen bonds : angle 5.44344 ( 183) link_BETA1-4 : bond 0.00424 ( 4) link_BETA1-4 : angle 2.01712 ( 12) link_BETA1-6 : bond 0.00327 ( 1) link_BETA1-6 : angle 1.29025 ( 3) link_NAG-ASN : bond 0.00171 ( 7) link_NAG-ASN : angle 1.29932 ( 21) *********************** 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 26 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.079 Fit side-chains REVERT: A 172 ILE cc_start: 0.8797 (mm) cc_final: 0.8474 (mm) outliers start: 4 outliers final: 4 residues processed: 26 average time/residue: 0.0551 time to fit residues: 1.7755 Evaluate side-chains 26 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.080 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.0870 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.142752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.111819 restraints weight = 2557.719| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.77 r_work: 0.3046 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 2111 Z= 0.156 Angle : 0.530 4.506 2915 Z= 0.267 Chirality : 0.045 0.167 347 Planarity : 0.003 0.030 352 Dihedral : 5.368 53.242 523 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.55), residues: 247 helix: -2.36 (0.84), residues: 23 sheet: 0.96 (0.50), residues: 108 loop : -0.56 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.008 0.001 TYR A 181 PHE 0.015 0.002 PHE A 107 TRP 0.006 0.001 TRP A 201 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 2096) covalent geometry : angle 0.50113 ( 2873) SS BOND : bond 0.00188 ( 3) SS BOND : angle 1.05854 ( 6) hydrogen bonds : bond 0.02964 ( 75) hydrogen bonds : angle 5.44773 ( 183) link_BETA1-4 : bond 0.00419 ( 4) link_BETA1-4 : angle 2.03469 ( 12) link_BETA1-6 : bond 0.00304 ( 1) link_BETA1-6 : angle 1.31008 ( 3) link_NAG-ASN : bond 0.00170 ( 7) link_NAG-ASN : angle 1.31907 ( 21) ********************** 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 26 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.059 Fit side-chains REVERT: A 172 ILE cc_start: 0.8803 (mm) cc_final: 0.8483 (mm) outliers start: 4 outliers final: 4 residues processed: 26 average time/residue: 0.0405 time to fit residues: 1.3395 Evaluate side-chains 26 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.141410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112314 restraints weight = 2590.792| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.54 r_work: 0.3054 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 2111 Z= 0.182 Angle : 0.557 4.697 2915 Z= 0.279 Chirality : 0.046 0.168 347 Planarity : 0.003 0.029 352 Dihedral : 5.540 53.813 523 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.54), residues: 247 helix: -2.43 (0.83), residues: 23 sheet: 0.92 (0.50), residues: 108 loop : -0.64 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 130 TYR 0.009 0.001 TYR A 259 PHE 0.015 0.002 PHE A 107 TRP 0.008 0.001 TRP A 201 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 2096) covalent geometry : angle 0.52686 ( 2873) SS BOND : bond 0.00206 ( 3) SS BOND : angle 1.18301 ( 6) hydrogen bonds : bond 0.03089 ( 75) hydrogen bonds : angle 5.51803 ( 183) link_BETA1-4 : bond 0.00414 ( 4) link_BETA1-4 : angle 2.08148 ( 12) link_BETA1-6 : bond 0.00256 ( 1) link_BETA1-6 : angle 1.35690 ( 3) link_NAG-ASN : bond 0.00180 ( 7) link_NAG-ASN : angle 1.39735 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 953.77 seconds wall clock time: 16 minutes 58.99 seconds (1018.99 seconds total)