Starting phenix.real_space_refine on Wed Jun 4 17:27:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qev_13942/06_2025/7qev_13942.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qev_13942/06_2025/7qev_13942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qev_13942/06_2025/7qev_13942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qev_13942/06_2025/7qev_13942.map" model { file = "/net/cci-nas-00/data/ceres_data/7qev_13942/06_2025/7qev_13942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qev_13942/06_2025/7qev_13942.cif" } resolution = 2.9 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 30 5.16 5 C 2141 2.51 5 N 504 2.21 5 O 529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 3204 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1577 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 186} Chain breaks: 1 Chain: "B" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1548 Classifications: {'peptide': 190} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 183} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Unusual residues: {'LMT': 3, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {'LMT': 3, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 2.88, per 1000 atoms: 0.90 Number of scatterers: 3204 At special positions: 0 Unit cell: (71.94, 64.31, 92.65, 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 30 16.00 O 529 8.00 N 504 7.00 C 2141 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: 0.87 Conformation dependent library (CDL) restraints added in 370.6 milliseconds 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 730 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 75.5% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 removed outlier: 4.411A pdb=" N LYS A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 39 removed outlier: 3.548A pdb=" N ILE A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N THR A 26 " --> pdb=" O LYS A 22 " (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 95 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.959A pdb=" N LYS A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 159 removed outlier: 3.816A pdb=" N TRP A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 145 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 155 " --> pdb=" O MET A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 216 removed outlier: 3.614A pdb=" N GLU A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 15 removed outlier: 3.855A pdb=" N LYS B 15 " --> pdb=" O GLY B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 39 removed outlier: 4.263A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 removed outlier: 4.084A pdb=" N TRP B 44 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B 45 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP B 46 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.688A 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 84 Processing helix chain 'B' and resid 85 through 101 removed outlier: 3.564A pdb=" N VAL B 91 " --> pdb=" O PRO B 87 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU B 101 " --> pdb=" O TYR B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 159 removed outlier: 3.585A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 217 removed outlier: 4.012A pdb=" N ARG B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) 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 53 210 hydrogen bonds defined for protein. 612 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: 0.76 Time building geometry restraints manager: 1.02 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: 927 1.34 - 1.46: 689 1.46 - 1.57: 1618 1.57 - 1.69: 0 1.69 - 1.80: 44 Bond restraints: 3278 Sorted by residual: bond pdb=" C1 LMT A 301 " pdb=" C2 LMT A 301 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 5.94e+00 bond pdb=" C1 LMT B 302 " pdb=" C2 LMT B 302 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.00e-02 2.50e+03 5.83e+00 bond pdb=" C7 LMT A 303 " pdb=" C8 LMT A 303 " ideal model delta sigma weight residual 1.529 1.568 -0.039 2.00e-02 2.50e+03 3.90e+00 bond pdb=" C7 LMT A 302 " pdb=" C8 LMT A 302 " ideal model delta sigma weight residual 1.529 1.567 -0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" C7 LMT B 302 " pdb=" C8 LMT B 302 " ideal model delta sigma weight residual 1.529 1.566 -0.037 2.00e-02 2.50e+03 3.42e+00 ... (remaining 3273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 4248 1.63 - 3.27: 114 3.27 - 4.90: 32 4.90 - 6.53: 26 6.53 - 8.16: 9 Bond angle restraints: 4429 Sorted by residual: angle pdb=" C6 LMT A 303 " pdb=" C7 LMT A 303 " pdb=" C8 LMT A 303 " ideal model delta sigma weight residual 117.26 109.10 8.16 3.00e+00 1.11e-01 7.41e+00 angle pdb=" C6 LMT A 301 " pdb=" C7 LMT A 301 " pdb=" C8 LMT A 301 " ideal model delta sigma weight residual 117.26 109.62 7.64 3.00e+00 1.11e-01 6.48e+00 angle pdb=" C6 LMT A 302 " pdb=" C7 LMT A 302 " pdb=" C8 LMT A 302 " ideal model delta sigma weight residual 117.26 109.64 7.62 3.00e+00 1.11e-01 6.45e+00 angle pdb=" C2 LMT A 301 " pdb=" C3 LMT A 301 " pdb=" C4 LMT A 301 " ideal model delta sigma weight residual 117.09 109.67 7.42 3.00e+00 1.11e-01 6.12e+00 angle pdb=" C6 LMT B 302 " pdb=" C7 LMT B 302 " pdb=" C8 LMT B 302 " ideal model delta sigma weight residual 117.26 110.14 7.12 3.00e+00 1.11e-01 5.64e+00 ... (remaining 4424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 1707 17.88 - 35.76: 164 35.76 - 53.64: 24 53.64 - 71.52: 3 71.52 - 89.40: 1 Dihedral angle restraints: 1899 sinusoidal: 772 harmonic: 1127 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 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ILE B 23 " pdb=" C ILE B 23 " pdb=" N TRP B 24 " pdb=" CA TRP B 24 " ideal model delta harmonic sigma weight residual -180.00 -158.55 -21.45 0 5.00e+00 4.00e-02 1.84e+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 -159.14 -20.86 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 1896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 209 0.029 - 0.058: 203 0.058 - 0.088: 58 0.088 - 0.117: 20 0.117 - 0.146: 7 Chirality restraints: 497 Sorted by residual: 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 2.38 0.15 2.00e-01 2.50e+01 5.32e-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 2.58 0.14 2.00e-01 2.50e+01 4.59e-01 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 2.40 0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 494 not shown) Planarity restraints: 526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 174 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 175 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" CG ASN A 176 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 86 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO A 87 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 87 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 87 " 0.015 5.00e-02 4.00e+02 ... (remaining 523 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 124 2.71 - 3.26: 3328 3.26 - 3.81: 4894 3.81 - 4.35: 5842 4.35 - 4.90: 9936 Nonbonded interactions: 24124 Sorted by model distance: nonbonded pdb=" O ILE B 71 " pdb=" OH TYR B 158 " model vdw 2.164 3.040 nonbonded pdb=" O ILE A 71 " pdb=" OH TYR A 158 " model vdw 2.167 3.040 nonbonded pdb=" O TYR B 152 " pdb=" O HOH B 401 " model vdw 2.211 3.040 nonbonded pdb=" O SER A 17 " pdb=" NZ LYS A 22 " model vdw 2.260 3.120 nonbonded pdb=" OH TYR B 68 " pdb=" O LYS B 168 " model vdw 2.284 3.040 ... (remaining 24119 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 1 through 101 or resid 129 through 217 or (resid 301 and ( \ name C4 or name C5 or name C6 or name C7 )) or resid 302 through 304)) selection = (chain 'B' and (resid 1 through 217 or resid 301 or (resid 302 and (name C2 or n \ ame C3 or name C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 th \ rough 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: 0.530 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.710 Find NCS groups from input model: 0.120 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:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 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 : 0.009 0.054 3284 Z= 0.383 Angle : 0.864 8.164 4441 Z= 0.405 Chirality : 0.046 0.146 497 Planarity : 0.003 0.029 526 Dihedral : 13.679 89.401 1151 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % 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: -0.15 (0.42), residues: 375 helix: 0.22 (0.31), residues: 247 sheet: 0.19 (0.90), residues: 34 loop : -0.70 (0.66), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 24 HIS 0.002 0.001 HIS A 73 PHE 0.012 0.002 PHE A 31 TYR 0.012 0.002 TYR B 65 ARG 0.003 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.27523 ( 210) hydrogen bonds : angle 7.64735 ( 612) SS BOND : bond 0.00200 ( 6) SS BOND : angle 1.26770 ( 12) covalent geometry : bond 0.00873 ( 3278) covalent geometry : angle 0.86306 ( 4429) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: B 41 LYS cc_start: 0.9261 (tttt) cc_final: 0.9016 (tttt) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 1.2955 time to fit residues: 79.7961 Evaluate side-chains 46 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.082393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.058115 restraints weight = 8926.374| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.56 r_work: 0.2738 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3284 Z= 0.194 Angle : 0.681 8.492 4441 Z= 0.367 Chirality : 0.042 0.135 497 Planarity : 0.004 0.027 526 Dihedral : 7.224 58.588 455 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.46 % Allowed : 10.20 % Favored : 88.34 % 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: 1.26 (0.43), residues: 375 helix: 1.58 (0.32), residues: 251 sheet: 0.69 (1.01), residues: 28 loop : -1.09 (0.64), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 133 HIS 0.003 0.001 HIS B 94 PHE 0.021 0.002 PHE A 29 TYR 0.012 0.002 TYR B 65 ARG 0.003 0.001 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.08512 ( 210) hydrogen bonds : angle 4.62544 ( 612) SS BOND : bond 0.00198 ( 6) SS BOND : angle 1.03900 ( 12) covalent geometry : bond 0.00356 ( 3278) covalent geometry : angle 0.68006 ( 4429) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.404 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 57 average time/residue: 1.1378 time to fit residues: 66.9492 Evaluate side-chains 47 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 211 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 30.0000 chunk 34 optimal weight: 0.0670 chunk 26 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.084878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.060480 restraints weight = 8787.105| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.57 r_work: 0.2805 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3284 Z= 0.137 Angle : 0.589 7.453 4441 Z= 0.310 Chirality : 0.041 0.140 497 Planarity : 0.003 0.023 526 Dihedral : 5.844 53.245 455 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.21 % Allowed : 13.70 % Favored : 83.09 % 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: 1.75 (0.43), residues: 375 helix: 2.06 (0.33), residues: 251 sheet: 1.43 (1.12), residues: 22 loop : -1.25 (0.57), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 133 HIS 0.003 0.001 HIS B 16 PHE 0.028 0.001 PHE A 29 TYR 0.011 0.001 TYR B 152 ARG 0.005 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.05927 ( 210) hydrogen bonds : angle 4.09305 ( 612) SS BOND : bond 0.00173 ( 6) SS BOND : angle 0.83383 ( 12) covalent geometry : bond 0.00264 ( 3278) covalent geometry : angle 0.58802 ( 4429) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8780 (p0) cc_final: 0.8564 (p0) REVERT: A 93 MET cc_start: 0.8565 (ppp) cc_final: 0.8363 (ppp) REVERT: A 212 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.8174 (m-10) outliers start: 11 outliers final: 2 residues processed: 66 average time/residue: 1.0553 time to fit residues: 71.9038 Evaluate side-chains 54 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 97 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 26 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 30.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.084838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.060828 restraints weight = 8865.324| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.55 r_work: 0.2816 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3284 Z= 0.129 Angle : 0.607 8.639 4441 Z= 0.311 Chirality : 0.041 0.162 497 Planarity : 0.003 0.025 526 Dihedral : 5.406 48.382 455 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.46 % Allowed : 18.08 % Favored : 80.47 % 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: 2.00 (0.44), residues: 375 helix: 2.18 (0.32), residues: 258 sheet: 1.44 (1.12), residues: 22 loop : -1.17 (0.60), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 133 HIS 0.002 0.001 HIS B 73 PHE 0.021 0.001 PHE A 29 TYR 0.009 0.001 TYR A 97 ARG 0.004 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.05398 ( 210) hydrogen bonds : angle 3.98203 ( 612) SS BOND : bond 0.00141 ( 6) SS BOND : angle 0.78571 ( 12) covalent geometry : bond 0.00264 ( 3278) covalent geometry : angle 0.60594 ( 4429) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8762 (mttp) cc_final: 0.8228 (mttm) REVERT: A 46 ASP cc_start: 0.8808 (p0) cc_final: 0.8505 (p0) REVERT: A 141 PHE cc_start: 0.8664 (t80) cc_final: 0.8424 (t80) REVERT: A 212 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.8175 (m-10) outliers start: 5 outliers final: 2 residues processed: 59 average time/residue: 1.2119 time to fit residues: 73.6057 Evaluate side-chains 55 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 97 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.084426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.060450 restraints weight = 8922.407| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.51 r_work: 0.2794 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3284 Z= 0.134 Angle : 0.614 8.147 4441 Z= 0.311 Chirality : 0.041 0.157 497 Planarity : 0.003 0.026 526 Dihedral : 5.155 43.222 455 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.04 % Allowed : 19.24 % Favored : 78.72 % 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: 2.13 (0.44), residues: 375 helix: 2.29 (0.32), residues: 257 sheet: 1.37 (1.10), residues: 22 loop : -1.08 (0.60), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 133 HIS 0.002 0.001 HIS B 73 PHE 0.009 0.001 PHE A 31 TYR 0.010 0.001 TYR B 136 ARG 0.003 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.05287 ( 210) hydrogen bonds : angle 3.91216 ( 612) SS BOND : bond 0.00151 ( 6) SS BOND : angle 0.77836 ( 12) covalent geometry : bond 0.00295 ( 3278) covalent geometry : angle 0.61349 ( 4429) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8752 (mttp) cc_final: 0.8247 (mttp) REVERT: A 46 ASP cc_start: 0.8862 (p0) cc_final: 0.8611 (p0) REVERT: A 141 PHE cc_start: 0.8617 (t80) cc_final: 0.8395 (t80) REVERT: A 212 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.8158 (m-10) outliers start: 7 outliers final: 2 residues processed: 59 average time/residue: 1.1821 time to fit residues: 71.8871 Evaluate side-chains 54 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 97 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 0.0870 chunk 31 optimal weight: 4.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.082484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.058008 restraints weight = 9168.527| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.64 r_work: 0.2730 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3284 Z= 0.217 Angle : 0.666 8.285 4441 Z= 0.343 Chirality : 0.045 0.158 497 Planarity : 0.004 0.029 526 Dihedral : 5.444 40.129 455 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.92 % Allowed : 18.95 % Favored : 78.13 % 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: 1.93 (0.44), residues: 375 helix: 2.17 (0.32), residues: 253 sheet: 1.15 (1.09), residues: 22 loop : -1.08 (0.62), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 24 HIS 0.003 0.001 HIS A 73 PHE 0.011 0.001 PHE A 31 TYR 0.014 0.002 TYR B 65 ARG 0.002 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.06051 ( 210) hydrogen bonds : angle 4.10308 ( 612) SS BOND : bond 0.00185 ( 6) SS BOND : angle 0.96150 ( 12) covalent geometry : bond 0.00512 ( 3278) covalent geometry : angle 0.66495 ( 4429) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8795 (mttp) cc_final: 0.8557 (mttp) REVERT: A 141 PHE cc_start: 0.8674 (t80) cc_final: 0.8452 (t80) REVERT: A 212 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.8115 (m-10) REVERT: B 41 LYS cc_start: 0.9237 (tttt) cc_final: 0.8511 (tmmt) outliers start: 10 outliers final: 4 residues processed: 59 average time/residue: 1.1588 time to fit residues: 70.4949 Evaluate side-chains 55 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 97 TYR Chi-restraints excluded: chain B residue 211 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.0170 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 overall best weight: 0.8018 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.084265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.060297 restraints weight = 8934.567| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.54 r_work: 0.2796 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3284 Z= 0.126 Angle : 0.604 8.564 4441 Z= 0.307 Chirality : 0.042 0.160 497 Planarity : 0.003 0.028 526 Dihedral : 5.057 35.587 455 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.62 % Allowed : 20.99 % Favored : 76.38 % 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: 1.95 (0.44), residues: 375 helix: 2.25 (0.32), residues: 254 sheet: 1.35 (1.10), residues: 22 loop : -1.37 (0.60), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 133 HIS 0.002 0.001 HIS A 73 PHE 0.032 0.001 PHE A 29 TYR 0.010 0.001 TYR A 97 ARG 0.003 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.05256 ( 210) hydrogen bonds : angle 3.88938 ( 612) SS BOND : bond 0.00156 ( 6) SS BOND : angle 0.78270 ( 12) covalent geometry : bond 0.00266 ( 3278) covalent geometry : angle 0.60305 ( 4429) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 PHE cc_start: 0.8642 (t80) cc_final: 0.8412 (t80) REVERT: A 212 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8035 (m-10) REVERT: B 41 LYS cc_start: 0.9212 (tttt) cc_final: 0.8516 (tmmt) outliers start: 9 outliers final: 4 residues processed: 61 average time/residue: 1.0846 time to fit residues: 68.2905 Evaluate side-chains 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 97 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 31 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.084457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.060205 restraints weight = 8868.600| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.61 r_work: 0.2800 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3284 Z= 0.128 Angle : 0.636 10.185 4441 Z= 0.317 Chirality : 0.042 0.158 497 Planarity : 0.003 0.027 526 Dihedral : 4.764 29.701 455 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.75 % Allowed : 21.57 % Favored : 76.68 % 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 (0.44), residues: 375 helix: 2.28 (0.32), residues: 254 sheet: 1.42 (1.10), residues: 22 loop : -1.40 (0.60), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 44 HIS 0.002 0.001 HIS A 73 PHE 0.010 0.001 PHE A 31 TYR 0.009 0.001 TYR A 97 ARG 0.002 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.05012 ( 210) hydrogen bonds : angle 3.84078 ( 612) SS BOND : bond 0.00151 ( 6) SS BOND : angle 0.74049 ( 12) covalent geometry : bond 0.00276 ( 3278) covalent geometry : angle 0.63522 ( 4429) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 PHE cc_start: 0.9081 (t80) cc_final: 0.8837 (t80) REVERT: A 141 PHE cc_start: 0.8661 (t80) cc_final: 0.8447 (t80) REVERT: A 212 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.8057 (m-10) REVERT: B 41 LYS cc_start: 0.9177 (tttt) cc_final: 0.8442 (tmmt) REVERT: B 50 ASP cc_start: 0.8787 (m-30) cc_final: 0.8541 (m-30) outliers start: 6 outliers final: 4 residues processed: 56 average time/residue: 1.1684 time to fit residues: 67.5003 Evaluate side-chains 56 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 97 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 0.0170 chunk 34 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 0.0570 chunk 19 optimal weight: 3.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.086261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.062761 restraints weight = 8900.262| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.60 r_work: 0.2858 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3284 Z= 0.116 Angle : 0.626 10.173 4441 Z= 0.307 Chirality : 0.041 0.156 497 Planarity : 0.003 0.029 526 Dihedral : 4.488 21.007 455 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.17 % Allowed : 21.87 % Favored : 76.97 % 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: 2.11 (0.44), residues: 375 helix: 2.33 (0.32), residues: 259 sheet: 1.51 (1.11), residues: 22 loop : -1.42 (0.61), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 133 HIS 0.001 0.000 HIS A 73 PHE 0.008 0.001 PHE A 31 TYR 0.011 0.001 TYR A 97 ARG 0.002 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 210) hydrogen bonds : angle 3.68522 ( 612) SS BOND : bond 0.00132 ( 6) SS BOND : angle 0.69328 ( 12) covalent geometry : bond 0.00233 ( 3278) covalent geometry : angle 0.62550 ( 4429) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8684 (mttp) cc_final: 0.8475 (mttp) REVERT: A 46 ASP cc_start: 0.8704 (p0) cc_final: 0.8485 (p0) REVERT: A 212 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.8213 (m-10) REVERT: B 46 ASP cc_start: 0.9136 (p0) cc_final: 0.8782 (p0) REVERT: B 50 ASP cc_start: 0.8729 (m-30) cc_final: 0.8411 (m-30) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 1.3220 time to fit residues: 86.8453 Evaluate side-chains 55 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 97 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 29 optimal weight: 4.9990 chunk 14 optimal weight: 0.0770 chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.084831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.061118 restraints weight = 8853.424| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.51 r_work: 0.2821 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3284 Z= 0.134 Angle : 0.679 10.234 4441 Z= 0.340 Chirality : 0.043 0.208 497 Planarity : 0.003 0.028 526 Dihedral : 4.311 19.691 455 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.87 % Allowed : 25.07 % Favored : 74.05 % 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: 2.14 (0.44), residues: 375 helix: 2.41 (0.32), residues: 254 sheet: 1.51 (1.10), residues: 22 loop : -1.38 (0.61), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 44 HIS 0.002 0.001 HIS A 73 PHE 0.019 0.001 PHE A 141 TYR 0.010 0.001 TYR A 97 ARG 0.003 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04519 ( 210) hydrogen bonds : angle 3.79112 ( 612) SS BOND : bond 0.00140 ( 6) SS BOND : angle 0.69204 ( 12) covalent geometry : bond 0.00303 ( 3278) covalent geometry : angle 0.67909 ( 4429) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8703 (p0) cc_final: 0.8379 (p0) REVERT: A 50 ASP cc_start: 0.8803 (m-30) cc_final: 0.8562 (m-30) REVERT: B 46 ASP cc_start: 0.9134 (p0) cc_final: 0.8891 (p0) outliers start: 3 outliers final: 3 residues processed: 57 average time/residue: 1.0850 time to fit residues: 63.8323 Evaluate side-chains 54 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 97 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 0.3980 chunk 1 optimal weight: 8.9990 chunk 4 optimal weight: 0.0000 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.085543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.061943 restraints weight = 8865.816| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.51 r_work: 0.2844 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3284 Z= 0.125 Angle : 0.670 10.150 4441 Z= 0.334 Chirality : 0.043 0.176 497 Planarity : 0.003 0.029 526 Dihedral : 4.140 17.632 455 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.87 % Allowed : 25.66 % Favored : 73.47 % 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: 2.07 (0.43), residues: 375 helix: 2.38 (0.31), residues: 254 sheet: 1.50 (1.10), residues: 22 loop : -1.49 (0.59), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 44 HIS 0.002 0.000 HIS A 73 PHE 0.015 0.001 PHE A 141 TYR 0.011 0.001 TYR A 97 ARG 0.002 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 210) hydrogen bonds : angle 3.77675 ( 612) SS BOND : bond 0.00131 ( 6) SS BOND : angle 0.68232 ( 12) covalent geometry : bond 0.00275 ( 3278) covalent geometry : angle 0.67039 ( 4429) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2693.97 seconds wall clock time: 46 minutes 39.03 seconds (2799.03 seconds total)