Starting phenix.real_space_refine on Wed Jun 4 16:22:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qes_13939/06_2025/7qes_13939.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qes_13939/06_2025/7qes_13939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qes_13939/06_2025/7qes_13939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qes_13939/06_2025/7qes_13939.map" model { file = "/net/cci-nas-00/data/ceres_data/7qes_13939/06_2025/7qes_13939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qes_13939/06_2025/7qes_13939.cif" } resolution = 2.6 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= 0.002 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 29 5.16 5 C 2066 2.51 5 N 472 2.21 5 O 509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3076 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1494 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "B" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1483 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 175} Chain breaks: 1 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 2.85, per 1000 atoms: 0.93 Number of scatterers: 3076 At special positions: 0 Unit cell: (70.85, 66.49, 85.02, 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 29 16.00 O 509 8.00 N 472 7.00 C 2066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " 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 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 300.3 milliseconds 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 700 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 2 sheets defined 75.4% alpha, 3.8% 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 5 through 15 removed outlier: 3.766A pdb=" N ILE A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 39 removed outlier: 3.912A pdb=" N ILE A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 43 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 97 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 132 through 159 Processing helix chain 'A' and resid 184 through 217 Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.961A pdb=" N LYS B 15 " --> pdb=" O GLY B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 39 removed outlier: 4.336A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 removed outlier: 4.209A pdb=" N TRP B 44 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 45 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASP B 46 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 47 " --> pdb=" O TRP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 101 Proline residue: B 87 - end of helix removed outlier: 3.520A pdb=" N ALA B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 138 through 159 removed outlier: 3.582A pdb=" N ILE B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 215 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 206 hydrogen bonds defined for protein. 600 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: 0.65 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 872 1.34 - 1.46: 847 1.46 - 1.58: 1378 1.58 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 3139 Sorted by residual: bond pdb=" C1 LMT A 304 " pdb=" C2 LMT A 304 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.04e+00 bond pdb=" C1 LMT B 302 " pdb=" C2 LMT B 302 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" C7 LMT B 301 " pdb=" C8 LMT B 301 " ideal model delta sigma weight residual 1.529 1.567 -0.038 2.00e-02 2.50e+03 3.64e+00 bond pdb=" C7 LMT A 305 " pdb=" C8 LMT A 305 " ideal model delta sigma weight residual 1.529 1.567 -0.038 2.00e-02 2.50e+03 3.63e+00 bond pdb=" C7 LMT B 304 " pdb=" C8 LMT B 304 " ideal model delta sigma weight residual 1.529 1.567 -0.038 2.00e-02 2.50e+03 3.61e+00 ... (remaining 3134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 4085 1.60 - 3.20: 85 3.20 - 4.80: 28 4.80 - 6.39: 26 6.39 - 7.99: 15 Bond angle restraints: 4239 Sorted by residual: angle pdb=" C6 LMT B 302 " pdb=" C7 LMT B 302 " pdb=" C8 LMT B 302 " ideal model delta sigma weight residual 117.26 109.27 7.99 3.00e+00 1.11e-01 7.10e+00 angle pdb=" C6 LMT B 301 " pdb=" C7 LMT B 301 " pdb=" C8 LMT B 301 " ideal model delta sigma weight residual 117.26 109.49 7.77 3.00e+00 1.11e-01 6.71e+00 angle pdb=" C6 LMT A 301 " pdb=" C7 LMT A 301 " pdb=" C8 LMT A 301 " ideal model delta sigma weight residual 117.26 109.56 7.70 3.00e+00 1.11e-01 6.59e+00 angle pdb=" C6 LMT B 304 " pdb=" C7 LMT B 304 " pdb=" C8 LMT B 304 " ideal model delta sigma weight residual 117.26 109.68 7.58 3.00e+00 1.11e-01 6.39e+00 angle pdb=" C2 LMT B 304 " pdb=" C3 LMT B 304 " pdb=" C4 LMT B 304 " ideal model delta sigma weight residual 117.09 109.52 7.57 3.00e+00 1.11e-01 6.37e+00 ... (remaining 4234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.82: 1486 11.82 - 23.63: 223 23.63 - 35.45: 68 35.45 - 47.26: 26 47.26 - 59.08: 12 Dihedral angle restraints: 1815 sinusoidal: 735 harmonic: 1080 Sorted by residual: dihedral pdb=" CA PRO B 175 " pdb=" C PRO B 175 " pdb=" N ASN B 176 " pdb=" CA ASN B 176 " ideal model delta harmonic sigma weight residual -180.00 -159.26 -20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA PRO A 175 " pdb=" C PRO A 175 " pdb=" N ASN A 176 " pdb=" CA ASN A 176 " ideal model delta harmonic sigma weight residual -180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLU A 42 " pdb=" C GLU A 42 " pdb=" N VAL A 43 " pdb=" CA VAL A 43 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 1812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 291 0.032 - 0.064: 135 0.064 - 0.095: 39 0.095 - 0.127: 12 0.127 - 0.159: 2 Chirality restraints: 479 Sorted by residual: chirality pdb=" CA THR B 86 " pdb=" N THR B 86 " pdb=" C THR B 86 " pdb=" CB THR B 86 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA THR A 86 " pdb=" N THR A 86 " pdb=" C THR A 86 " pdb=" CB THR A 86 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CA PRO B 185 " pdb=" N PRO B 185 " pdb=" C PRO B 185 " pdb=" CB PRO B 185 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.27e-01 ... (remaining 476 not shown) Planarity restraints: 500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 174 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO A 175 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 86 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO B 87 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 57 " 0.012 5.00e-02 4.00e+02 1.83e-02 5.33e-01 pdb=" N PRO A 58 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " 0.010 5.00e-02 4.00e+02 ... (remaining 497 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 29 2.68 - 3.23: 2894 3.23 - 3.79: 4300 3.79 - 4.34: 5872 4.34 - 4.90: 9832 Nonbonded interactions: 22927 Sorted by model distance: nonbonded pdb=" O ILE B 71 " pdb=" OH TYR B 158 " model vdw 2.122 3.040 nonbonded pdb=" O ILE A 71 " pdb=" OH TYR A 158 " model vdw 2.154 3.040 nonbonded pdb=" OH TYR B 68 " pdb=" O LYS B 168 " model vdw 2.278 3.040 nonbonded pdb=" OH TYR A 68 " pdb=" O LYS A 168 " model vdw 2.296 3.040 nonbonded pdb=" OD1 ASP A 66 " pdb=" O HOH A 401 " model vdw 2.335 3.040 ... (remaining 22922 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 'A' and (resid 9 through 217 or resid 301 through 302 or (resid 304 and ( \ name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 )))) selection = (chain 'B' and (resid 9 through 97 or resid 131 through 217 or (resid 301 and (n \ ame C3 or name C4 or name C5 or name C6 or name C7 or name C8 )) or (resid 302 a \ nd (name C5 or name C6 or name C7 )) or resid 304)) } 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: 0.480 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.670 Find NCS groups from input model: 0.110 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:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 : 0.006 0.049 3145 Z= 0.264 Angle : 0.861 7.993 4251 Z= 0.375 Chirality : 0.041 0.159 479 Planarity : 0.003 0.036 500 Dihedral : 13.928 59.078 1097 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -0.99 (0.41), residues: 358 helix: -0.23 (0.31), residues: 238 sheet: 0.44 (0.95), residues: 28 loop : -1.85 (0.62), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 134 HIS 0.002 0.001 HIS A 73 PHE 0.010 0.001 PHE A 181 TYR 0.009 0.001 TYR B 65 ARG 0.005 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.27712 ( 206) hydrogen bonds : angle 7.29412 ( 600) SS BOND : bond 0.00172 ( 6) SS BOND : angle 0.92524 ( 12) covalent geometry : bond 0.00586 ( 3139) covalent geometry : angle 0.86047 ( 4239) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.355 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 1.2982 time to fit residues: 40.2113 Evaluate side-chains 24 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 40.0000 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.088530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.060385 restraints weight = 7958.057| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.41 r_work: 0.2877 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3145 Z= 0.157 Angle : 0.615 6.509 4251 Z= 0.336 Chirality : 0.042 0.157 479 Planarity : 0.004 0.035 500 Dihedral : 9.782 59.204 443 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.30 % Allowed : 7.32 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.22 (0.44), residues: 358 helix: 1.77 (0.33), residues: 239 sheet: 1.38 (1.09), residues: 22 loop : -1.86 (0.60), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 133 HIS 0.002 0.001 HIS A 94 PHE 0.011 0.001 PHE A 31 TYR 0.010 0.002 TYR B 212 ARG 0.002 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.07652 ( 206) hydrogen bonds : angle 3.96920 ( 600) SS BOND : bond 0.00232 ( 6) SS BOND : angle 0.95703 ( 12) covalent geometry : bond 0.00309 ( 3139) covalent geometry : angle 0.61349 ( 4239) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.350 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 1.2142 time to fit residues: 40.1958 Evaluate side-chains 27 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.089962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.061920 restraints weight = 7767.499| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.37 r_work: 0.2909 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3145 Z= 0.131 Angle : 0.542 6.361 4251 Z= 0.295 Chirality : 0.041 0.161 479 Planarity : 0.004 0.032 500 Dihedral : 8.814 57.961 443 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.52 % Allowed : 10.37 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.98 (0.45), residues: 358 helix: 2.55 (0.33), residues: 239 sheet: 1.43 (1.09), residues: 22 loop : -2.10 (0.58), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 133 HIS 0.002 0.001 HIS B 16 PHE 0.013 0.001 PHE B 161 TYR 0.012 0.001 TYR B 158 ARG 0.001 0.000 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.05617 ( 206) hydrogen bonds : angle 3.60998 ( 600) SS BOND : bond 0.00155 ( 6) SS BOND : angle 0.78070 ( 12) covalent geometry : bond 0.00274 ( 3139) covalent geometry : angle 0.54107 ( 4239) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.368 Fit side-chains REVERT: A 209 GLU cc_start: 0.8083 (tp30) cc_final: 0.7881 (tp30) REVERT: A 212 TYR cc_start: 0.6648 (OUTLIER) cc_final: 0.6009 (t80) REVERT: B 97 TYR cc_start: 0.5107 (t80) cc_final: 0.4751 (t80) outliers start: 5 outliers final: 0 residues processed: 32 average time/residue: 1.2282 time to fit residues: 40.5888 Evaluate side-chains 28 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.089929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.061677 restraints weight = 7872.001| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.37 r_work: 0.2900 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3145 Z= 0.137 Angle : 0.574 8.521 4251 Z= 0.308 Chirality : 0.041 0.170 479 Planarity : 0.004 0.033 500 Dihedral : 8.360 57.668 443 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.83 % Allowed : 10.98 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.25 (0.45), residues: 358 helix: 2.80 (0.32), residues: 239 sheet: 1.39 (1.09), residues: 22 loop : -2.12 (0.58), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 133 HIS 0.002 0.001 HIS A 73 PHE 0.010 0.001 PHE A 31 TYR 0.008 0.001 TYR B 65 ARG 0.002 0.000 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.05322 ( 206) hydrogen bonds : angle 3.43796 ( 600) SS BOND : bond 0.00159 ( 6) SS BOND : angle 0.75558 ( 12) covalent geometry : bond 0.00305 ( 3139) covalent geometry : angle 0.57380 ( 4239) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.330 Fit side-chains REVERT: A 136 TYR cc_start: 0.6824 (OUTLIER) cc_final: 0.6452 (m-80) REVERT: A 212 TYR cc_start: 0.6638 (OUTLIER) cc_final: 0.5986 (t80) REVERT: B 97 TYR cc_start: 0.4969 (t80) cc_final: 0.4723 (t80) REVERT: B 101 GLU cc_start: 0.5030 (OUTLIER) cc_final: 0.4662 (pt0) outliers start: 6 outliers final: 0 residues processed: 30 average time/residue: 1.2614 time to fit residues: 39.1525 Evaluate side-chains 28 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 101 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 1 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.089890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.061482 restraints weight = 7752.233| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.36 r_work: 0.2896 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3145 Z= 0.142 Angle : 0.559 6.420 4251 Z= 0.302 Chirality : 0.041 0.171 479 Planarity : 0.004 0.033 500 Dihedral : 8.069 57.597 443 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.52 % Allowed : 13.11 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.38 (0.45), residues: 358 helix: 2.92 (0.32), residues: 239 sheet: 1.38 (1.10), residues: 22 loop : -2.10 (0.57), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 133 HIS 0.003 0.001 HIS B 16 PHE 0.010 0.001 PHE A 31 TYR 0.009 0.001 TYR B 158 ARG 0.002 0.000 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.05141 ( 206) hydrogen bonds : angle 3.40422 ( 600) SS BOND : bond 0.00170 ( 6) SS BOND : angle 0.75519 ( 12) covalent geometry : bond 0.00328 ( 3139) covalent geometry : angle 0.55825 ( 4239) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.342 Fit side-chains REVERT: A 136 TYR cc_start: 0.6899 (OUTLIER) cc_final: 0.6546 (m-80) REVERT: A 212 TYR cc_start: 0.6506 (OUTLIER) cc_final: 0.5890 (t80) REVERT: B 97 TYR cc_start: 0.5014 (t80) cc_final: 0.4811 (t80) outliers start: 5 outliers final: 0 residues processed: 29 average time/residue: 1.2618 time to fit residues: 37.8638 Evaluate side-chains 28 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 212 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 5 optimal weight: 0.0770 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 6 optimal weight: 0.5980 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.090419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.062068 restraints weight = 7908.980| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.35 r_work: 0.2915 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3145 Z= 0.132 Angle : 0.588 9.888 4251 Z= 0.311 Chirality : 0.040 0.170 479 Planarity : 0.004 0.033 500 Dihedral : 7.751 57.070 443 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.13 % Allowed : 14.63 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.50 (0.45), residues: 358 helix: 3.04 (0.32), residues: 239 sheet: 1.35 (1.09), residues: 22 loop : -2.11 (0.57), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 133 HIS 0.013 0.001 HIS B 16 PHE 0.008 0.001 PHE A 31 TYR 0.008 0.001 TYR B 158 ARG 0.002 0.000 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 206) hydrogen bonds : angle 3.34622 ( 600) SS BOND : bond 0.00144 ( 6) SS BOND : angle 0.69087 ( 12) covalent geometry : bond 0.00295 ( 3139) covalent geometry : angle 0.58765 ( 4239) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.458 Fit side-chains REVERT: A 136 TYR cc_start: 0.7020 (OUTLIER) cc_final: 0.6702 (m-80) REVERT: A 212 TYR cc_start: 0.6479 (OUTLIER) cc_final: 0.5884 (t80) REVERT: B 97 TYR cc_start: 0.5118 (OUTLIER) cc_final: 0.4867 (t80) REVERT: B 101 GLU cc_start: 0.4741 (OUTLIER) cc_final: 0.4342 (pt0) outliers start: 7 outliers final: 0 residues processed: 32 average time/residue: 1.3163 time to fit residues: 43.5737 Evaluate side-chains 29 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 101 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.091052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.062799 restraints weight = 7782.575| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.35 r_work: 0.2934 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3145 Z= 0.123 Angle : 0.554 7.018 4251 Z= 0.298 Chirality : 0.040 0.169 479 Planarity : 0.004 0.032 500 Dihedral : 7.333 56.112 443 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.44 % Allowed : 15.24 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.60 (0.45), residues: 358 helix: 3.13 (0.32), residues: 239 sheet: 1.36 (1.10), residues: 22 loop : -2.11 (0.57), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 133 HIS 0.002 0.001 HIS B 16 PHE 0.009 0.001 PHE A 31 TYR 0.008 0.001 TYR B 158 ARG 0.001 0.000 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.04562 ( 206) hydrogen bonds : angle 3.30092 ( 600) SS BOND : bond 0.00144 ( 6) SS BOND : angle 0.65728 ( 12) covalent geometry : bond 0.00271 ( 3139) covalent geometry : angle 0.55320 ( 4239) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.334 Fit side-chains REVERT: A 136 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.6709 (m-80) REVERT: A 212 TYR cc_start: 0.6334 (OUTLIER) cc_final: 0.5705 (t80) REVERT: B 97 TYR cc_start: 0.5589 (OUTLIER) cc_final: 0.5364 (t80) REVERT: B 101 GLU cc_start: 0.4728 (OUTLIER) cc_final: 0.4210 (pt0) outliers start: 8 outliers final: 0 residues processed: 34 average time/residue: 1.2098 time to fit residues: 42.5043 Evaluate side-chains 29 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 101 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.090359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.062000 restraints weight = 7938.729| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.41 r_work: 0.2923 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3145 Z= 0.139 Angle : 0.616 12.423 4251 Z= 0.320 Chirality : 0.041 0.170 479 Planarity : 0.004 0.033 500 Dihedral : 7.300 56.195 443 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.52 % Allowed : 16.77 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.65 (0.45), residues: 358 helix: 3.12 (0.32), residues: 240 sheet: 1.34 (1.09), residues: 22 loop : -1.98 (0.59), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 133 HIS 0.002 0.001 HIS A 73 PHE 0.008 0.001 PHE A 31 TYR 0.008 0.001 TYR B 158 ARG 0.002 0.000 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.04732 ( 206) hydrogen bonds : angle 3.33376 ( 600) SS BOND : bond 0.00142 ( 6) SS BOND : angle 0.68206 ( 12) covalent geometry : bond 0.00322 ( 3139) covalent geometry : angle 0.61562 ( 4239) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.363 Fit side-chains REVERT: A 136 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.6716 (m-80) REVERT: A 212 TYR cc_start: 0.6338 (OUTLIER) cc_final: 0.5712 (t80) REVERT: B 101 GLU cc_start: 0.4609 (OUTLIER) cc_final: 0.4174 (pt0) outliers start: 5 outliers final: 0 residues processed: 29 average time/residue: 1.2412 time to fit residues: 37.2660 Evaluate side-chains 28 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 101 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.089799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.061549 restraints weight = 7883.082| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.39 r_work: 0.2909 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3145 Z= 0.153 Angle : 0.603 7.892 4251 Z= 0.323 Chirality : 0.041 0.170 479 Planarity : 0.004 0.033 500 Dihedral : 7.388 56.542 443 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.22 % Allowed : 17.38 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.62 (0.45), residues: 358 helix: 3.08 (0.32), residues: 240 sheet: 1.30 (1.09), residues: 22 loop : -1.96 (0.59), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 133 HIS 0.002 0.001 HIS B 16 PHE 0.009 0.001 PHE A 31 TYR 0.023 0.002 TYR B 97 ARG 0.002 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.04905 ( 206) hydrogen bonds : angle 3.37010 ( 600) SS BOND : bond 0.00160 ( 6) SS BOND : angle 0.72237 ( 12) covalent geometry : bond 0.00361 ( 3139) covalent geometry : angle 0.60219 ( 4239) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.334 Fit side-chains REVERT: A 136 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.6757 (m-80) REVERT: A 212 TYR cc_start: 0.6337 (OUTLIER) cc_final: 0.5700 (t80) REVERT: B 101 GLU cc_start: 0.4762 (OUTLIER) cc_final: 0.4501 (pt0) outliers start: 4 outliers final: 0 residues processed: 30 average time/residue: 1.2418 time to fit residues: 38.4854 Evaluate side-chains 27 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 101 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 5 optimal weight: 0.0020 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.090994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.062959 restraints weight = 7835.886| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.40 r_work: 0.2943 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3145 Z= 0.126 Angle : 0.624 12.866 4251 Z= 0.323 Chirality : 0.040 0.167 479 Planarity : 0.004 0.033 500 Dihedral : 7.059 55.405 443 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.83 % Allowed : 16.77 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.70 (0.45), residues: 358 helix: 3.15 (0.32), residues: 240 sheet: 1.38 (1.09), residues: 22 loop : -1.94 (0.60), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 133 HIS 0.002 0.000 HIS B 16 PHE 0.008 0.001 PHE A 31 TYR 0.025 0.001 TYR B 97 ARG 0.002 0.000 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 206) hydrogen bonds : angle 3.29763 ( 600) SS BOND : bond 0.00145 ( 6) SS BOND : angle 0.64969 ( 12) covalent geometry : bond 0.00282 ( 3139) covalent geometry : angle 0.62413 ( 4239) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.368 Fit side-chains REVERT: A 136 TYR cc_start: 0.7045 (OUTLIER) cc_final: 0.6765 (m-80) REVERT: A 212 TYR cc_start: 0.6262 (OUTLIER) cc_final: 0.5653 (t80) REVERT: B 101 GLU cc_start: 0.4670 (OUTLIER) cc_final: 0.4464 (pt0) REVERT: B 212 TYR cc_start: 0.6388 (t80) cc_final: 0.6018 (t80) outliers start: 6 outliers final: 1 residues processed: 30 average time/residue: 1.1682 time to fit residues: 36.3447 Evaluate side-chains 29 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 101 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 12 optimal weight: 0.0010 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.090345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.062142 restraints weight = 7831.893| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.39 r_work: 0.2929 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3145 Z= 0.143 Angle : 0.600 8.302 4251 Z= 0.320 Chirality : 0.041 0.170 479 Planarity : 0.004 0.032 500 Dihedral : 7.097 55.746 443 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.22 % Allowed : 17.38 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.62 (0.45), residues: 358 helix: 3.10 (0.32), residues: 241 sheet: 1.31 (1.08), residues: 22 loop : -2.07 (0.59), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 133 HIS 0.001 0.001 HIS B 16 PHE 0.009 0.001 PHE A 31 TYR 0.025 0.002 TYR B 97 ARG 0.002 0.000 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 206) hydrogen bonds : angle 3.32639 ( 600) SS BOND : bond 0.00148 ( 6) SS BOND : angle 0.68685 ( 12) covalent geometry : bond 0.00335 ( 3139) covalent geometry : angle 0.59929 ( 4239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2893.32 seconds wall clock time: 50 minutes 5.58 seconds (3005.58 seconds total)