Starting phenix.real_space_refine on Sun Apr 27 03:10:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uc3_42114/04_2025/8uc3_42114.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uc3_42114/04_2025/8uc3_42114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uc3_42114/04_2025/8uc3_42114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uc3_42114/04_2025/8uc3_42114.map" model { file = "/net/cci-nas-00/data/ceres_data/8uc3_42114/04_2025/8uc3_42114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uc3_42114/04_2025/8uc3_42114.cif" } resolution = 2.78 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= 0.039 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 28 5.16 5 C 2700 2.51 5 N 766 2.21 5 O 808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4304 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1365 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 13, 'TRANS': 166} Chain: "C" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 756 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: D, B Time building chain proxies: 4.08, per 1000 atoms: 0.95 Number of scatterers: 4304 At special positions: 0 Unit cell: (84.87, 75.5343, 78.9291, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 2 15.00 O 808 8.00 N 766 7.00 C 2700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 549.7 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 58.3% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.801A pdb=" N ARG A 71 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 101 through 130 removed outlier: 3.733A pdb=" N THR A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 150 removed outlier: 3.503A pdb=" N VAL A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.855A pdb=" N VAL A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 181' Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 37 through 55 removed outlier: 3.505A pdb=" N GLU D 55 " --> pdb=" O GLN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 76 removed outlier: 3.732A pdb=" N ARG D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 99 Processing helix chain 'D' and resid 100 through 103 Processing helix chain 'C' and resid 9 through 29 Processing helix chain 'C' and resid 37 through 55 removed outlier: 3.505A pdb=" N GLU C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 76 removed outlier: 3.733A pdb=" N ARG C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 99 Processing helix chain 'C' and resid 100 through 103 Processing helix chain 'B' and resid 16 through 24 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 66 through 76 removed outlier: 3.801A pdb=" N ARG B 71 " --> pdb=" O PRO B 67 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 101 through 130 removed outlier: 3.733A pdb=" N THR B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 119 " --> pdb=" O CYS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 150 removed outlier: 3.504A pdb=" N VAL B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.855A pdb=" N VAL B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 181' Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.078A pdb=" N VAL A 92 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 184 removed outlier: 6.903A pdb=" N ASN A 183 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL B 92 " --> pdb=" O PRO B 157 " (cutoff:3.500A) 234 hydrogen bonds defined for protein. 672 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1176 1.33 - 1.45: 646 1.45 - 1.57: 2514 1.57 - 1.69: 2 1.69 - 1.81: 46 Bond restraints: 4384 Sorted by residual: bond pdb=" C4 FMN B 301 " pdb=" C4A FMN B 301 " ideal model delta sigma weight residual 1.485 1.387 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C4 FMN A 301 " pdb=" C4A FMN A 301 " ideal model delta sigma weight residual 1.485 1.388 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C4A FMN A 301 " pdb=" N5 FMN A 301 " ideal model delta sigma weight residual 1.300 1.377 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C4A FMN B 301 " pdb=" N5 FMN B 301 " ideal model delta sigma weight residual 1.300 1.377 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" N VAL B 182 " pdb=" CA VAL B 182 " ideal model delta sigma weight residual 1.458 1.500 -0.041 1.19e-02 7.06e+03 1.21e+01 ... (remaining 4379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 5515 1.59 - 3.18: 372 3.18 - 4.77: 57 4.77 - 6.36: 16 6.36 - 7.95: 10 Bond angle restraints: 5970 Sorted by residual: angle pdb=" N THR B 23 " pdb=" CA THR B 23 " pdb=" C THR B 23 " ideal model delta sigma weight residual 112.54 118.53 -5.99 1.22e+00 6.72e-01 2.41e+01 angle pdb=" N THR A 23 " pdb=" CA THR A 23 " pdb=" C THR A 23 " ideal model delta sigma weight residual 112.54 118.49 -5.95 1.22e+00 6.72e-01 2.38e+01 angle pdb=" N ARG B 66 " pdb=" CA ARG B 66 " pdb=" C ARG B 66 " ideal model delta sigma weight residual 109.64 103.67 5.97 1.27e+00 6.20e-01 2.21e+01 angle pdb=" N ARG A 66 " pdb=" CA ARG A 66 " pdb=" C ARG A 66 " ideal model delta sigma weight residual 109.64 103.68 5.96 1.27e+00 6.20e-01 2.20e+01 angle pdb=" CA GLU A 180 " pdb=" C GLU A 180 " pdb=" O GLU A 180 " ideal model delta sigma weight residual 120.55 116.93 3.62 1.06e+00 8.90e-01 1.17e+01 ... (remaining 5965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 2347 16.90 - 33.79: 227 33.79 - 50.69: 94 50.69 - 67.58: 12 67.58 - 84.48: 8 Dihedral angle restraints: 2688 sinusoidal: 1080 harmonic: 1608 Sorted by residual: dihedral pdb=" CG ARG A 74 " pdb=" CD ARG A 74 " pdb=" NE ARG A 74 " pdb=" CZ ARG A 74 " ideal model delta sinusoidal sigma weight residual -180.00 -135.17 -44.83 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG B 74 " pdb=" CD ARG B 74 " pdb=" NE ARG B 74 " pdb=" CZ ARG B 74 " ideal model delta sinusoidal sigma weight residual 180.00 -135.19 -44.81 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA ARG A 56 " pdb=" CB ARG A 56 " pdb=" CG ARG A 56 " pdb=" CD ARG A 56 " ideal model delta sinusoidal sigma weight residual -180.00 -125.98 -54.02 3 1.50e+01 4.44e-03 9.25e+00 ... (remaining 2685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 536 0.050 - 0.100: 105 0.100 - 0.149: 45 0.149 - 0.199: 0 0.199 - 0.249: 2 Chirality restraints: 688 Sorted by residual: chirality pdb=" CA VAL A 64 " pdb=" N VAL A 64 " pdb=" C VAL A 64 " pdb=" CB VAL A 64 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA VAL B 64 " pdb=" N VAL B 64 " pdb=" C VAL B 64 " pdb=" CB VAL B 64 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CG LEU A 100 " pdb=" CB LEU A 100 " pdb=" CD1 LEU A 100 " pdb=" CD2 LEU A 100 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 685 not shown) Planarity restraints: 774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 179 " -0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C ASN A 179 " 0.064 2.00e-02 2.50e+03 pdb=" O ASN A 179 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU A 180 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 179 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C ASN B 179 " -0.064 2.00e-02 2.50e+03 pdb=" O ASN B 179 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU B 180 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 161 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO B 162 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " 0.030 5.00e-02 4.00e+02 ... (remaining 771 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 74 2.67 - 3.23: 4019 3.23 - 3.79: 6215 3.79 - 4.34: 8917 4.34 - 4.90: 14548 Nonbonded interactions: 33773 Sorted by model distance: nonbonded pdb=" OE2 GLU D 32 " pdb=" NH2 ARG B 141 " model vdw 2.115 3.120 nonbonded pdb=" OD1 ASP C 44 " pdb=" NH1 ARG C 47 " model vdw 2.321 3.120 nonbonded pdb=" OD1 ASP D 44 " pdb=" NH1 ARG D 47 " model vdw 2.321 3.120 nonbonded pdb=" NH2 ARG C 62 " pdb=" OE2 GLU C 101 " model vdw 2.343 3.120 nonbonded pdb=" NH2 ARG D 62 " pdb=" OE2 GLU D 101 " model vdw 2.343 3.120 ... (remaining 33768 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: 0.02 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'B' } 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: 3.130 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.030 Find NCS groups from input model: 0.080 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:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 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 0.098 4386 Z= 0.374 Angle : 0.919 7.947 5970 Z= 0.560 Chirality : 0.049 0.249 688 Planarity : 0.006 0.054 774 Dihedral : 16.352 84.478 1644 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.78 % Allowed : 22.67 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.36), residues: 548 helix: 0.58 (0.32), residues: 272 sheet: 2.34 (0.74), residues: 44 loop : -0.48 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 187 HIS 0.002 0.001 HIS B 154 PHE 0.005 0.001 PHE B 86 TYR 0.009 0.001 TYR B 109 ARG 0.004 0.001 ARG C 69 Details of bonding type rmsd hydrogen bonds : bond 0.27114 ( 234) hydrogen bonds : angle 6.93495 ( 672) covalent geometry : bond 0.00614 ( 4384) covalent geometry : angle 0.91874 ( 5970) Misc. bond : bond 0.00104 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.426 Fit side-chains REVERT: C 62 ARG cc_start: 0.6692 (ttm170) cc_final: 0.6217 (mtp180) REVERT: C 94 GLN cc_start: 0.7342 (mt0) cc_final: 0.7056 (mt0) REVERT: B 118 MET cc_start: 0.7280 (mtt) cc_final: 0.6907 (mtt) outliers start: 8 outliers final: 2 residues processed: 89 average time/residue: 1.2972 time to fit residues: 119.2479 Evaluate side-chains 70 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 183 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.0030 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.190970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.152227 restraints weight = 4815.579| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.06 r_work: 0.3800 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4386 Z= 0.148 Angle : 0.615 6.473 5970 Z= 0.320 Chirality : 0.042 0.137 688 Planarity : 0.006 0.053 774 Dihedral : 6.294 56.500 633 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 6.44 % Allowed : 19.78 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.37), residues: 548 helix: 1.08 (0.30), residues: 294 sheet: 2.07 (0.76), residues: 54 loop : -0.39 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 18 HIS 0.003 0.001 HIS A 154 PHE 0.007 0.001 PHE A 86 TYR 0.013 0.002 TYR D 22 ARG 0.003 0.001 ARG C 62 Details of bonding type rmsd hydrogen bonds : bond 0.05618 ( 234) hydrogen bonds : angle 4.18180 ( 672) covalent geometry : bond 0.00318 ( 4384) covalent geometry : angle 0.61465 ( 5970) Misc. bond : bond 0.00146 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.488 Fit side-chains REVERT: D 33 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: D 97 ASP cc_start: 0.7432 (m-30) cc_final: 0.7163 (m-30) REVERT: C 33 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7184 (mt-10) REVERT: C 40 TYR cc_start: 0.7204 (m-80) cc_final: 0.6966 (m-80) REVERT: C 97 ASP cc_start: 0.7310 (m-30) cc_final: 0.6679 (t0) REVERT: B 108 ILE cc_start: 0.7882 (pt) cc_final: 0.7644 (pp) REVERT: B 174 GLN cc_start: 0.7292 (tp40) cc_final: 0.7062 (tp40) outliers start: 29 outliers final: 11 residues processed: 81 average time/residue: 1.2388 time to fit residues: 104.6335 Evaluate side-chains 76 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.182940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.142043 restraints weight = 4679.809| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.09 r_work: 0.3661 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4386 Z= 0.149 Angle : 0.607 10.272 5970 Z= 0.308 Chirality : 0.042 0.136 688 Planarity : 0.006 0.058 774 Dihedral : 5.993 55.803 633 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.78 % Allowed : 21.78 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.37), residues: 548 helix: 1.51 (0.30), residues: 288 sheet: 1.94 (0.77), residues: 54 loop : -0.48 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 18 HIS 0.002 0.001 HIS A 154 PHE 0.009 0.001 PHE A 86 TYR 0.012 0.002 TYR D 22 ARG 0.004 0.001 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.05515 ( 234) hydrogen bonds : angle 4.11707 ( 672) covalent geometry : bond 0.00343 ( 4384) covalent geometry : angle 0.60725 ( 5970) Misc. bond : bond 0.00147 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.478 Fit side-chains REVERT: A 22 LYS cc_start: 0.6146 (mptt) cc_final: 0.5867 (mmtm) REVERT: A 56 ARG cc_start: 0.6563 (mtt180) cc_final: 0.6312 (mtm-85) REVERT: D 33 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7782 (mt-10) REVERT: C 40 TYR cc_start: 0.6979 (m-80) cc_final: 0.6603 (m-80) REVERT: B 174 GLN cc_start: 0.7350 (tp40) cc_final: 0.6663 (mp10) outliers start: 17 outliers final: 9 residues processed: 76 average time/residue: 1.2447 time to fit residues: 98.0352 Evaluate side-chains 71 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.184046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.143771 restraints weight = 4684.633| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.06 r_work: 0.3681 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4386 Z= 0.125 Angle : 0.555 5.930 5970 Z= 0.284 Chirality : 0.040 0.134 688 Planarity : 0.005 0.056 774 Dihedral : 5.844 55.660 632 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.00 % Allowed : 20.67 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.37), residues: 548 helix: 1.65 (0.30), residues: 292 sheet: 1.88 (0.77), residues: 54 loop : -0.22 (0.48), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 18 HIS 0.003 0.001 HIS A 154 PHE 0.009 0.001 PHE A 86 TYR 0.010 0.001 TYR C 22 ARG 0.010 0.000 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.04689 ( 234) hydrogen bonds : angle 3.88125 ( 672) covalent geometry : bond 0.00284 ( 4384) covalent geometry : angle 0.55518 ( 5970) Misc. bond : bond 0.00121 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.469 Fit side-chains REVERT: A 22 LYS cc_start: 0.6219 (mttt) cc_final: 0.5928 (mmtm) REVERT: A 56 ARG cc_start: 0.6622 (mtt180) cc_final: 0.6366 (mtm-85) REVERT: A 62 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7742 (ttp) REVERT: D 33 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7659 (mt-10) REVERT: C 40 TYR cc_start: 0.6974 (m-80) cc_final: 0.6621 (m-80) REVERT: B 174 GLN cc_start: 0.7346 (tp40) cc_final: 0.6618 (mp10) outliers start: 18 outliers final: 9 residues processed: 72 average time/residue: 1.2975 time to fit residues: 96.5998 Evaluate side-chains 73 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.0010 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.179901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.138173 restraints weight = 4813.642| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.24 r_work: 0.3584 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4386 Z= 0.119 Angle : 0.546 5.698 5970 Z= 0.279 Chirality : 0.039 0.133 688 Planarity : 0.005 0.058 774 Dihedral : 5.733 53.259 632 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.56 % Allowed : 20.89 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.38), residues: 548 helix: 1.82 (0.30), residues: 292 sheet: 1.63 (0.78), residues: 54 loop : -0.13 (0.49), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 18 HIS 0.003 0.001 HIS A 154 PHE 0.009 0.001 PHE A 86 TYR 0.009 0.001 TYR D 22 ARG 0.015 0.000 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.04412 ( 234) hydrogen bonds : angle 3.78807 ( 672) covalent geometry : bond 0.00268 ( 4384) covalent geometry : angle 0.54572 ( 5970) Misc. bond : bond 0.00107 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.429 Fit side-chains REVERT: A 22 LYS cc_start: 0.5905 (mttt) cc_final: 0.5613 (mmtm) REVERT: A 56 ARG cc_start: 0.6636 (mtt180) cc_final: 0.6340 (mtm-85) REVERT: A 62 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7624 (ttp) REVERT: D 33 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7560 (mt-10) REVERT: C 40 TYR cc_start: 0.6822 (m-80) cc_final: 0.6469 (m-80) REVERT: B 174 GLN cc_start: 0.7310 (tp40) cc_final: 0.5851 (pm20) outliers start: 16 outliers final: 8 residues processed: 68 average time/residue: 1.3264 time to fit residues: 93.3166 Evaluate side-chains 68 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.177569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.135857 restraints weight = 4778.243| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.23 r_work: 0.3556 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4386 Z= 0.138 Angle : 0.582 6.114 5970 Z= 0.296 Chirality : 0.041 0.139 688 Planarity : 0.006 0.067 774 Dihedral : 5.691 48.323 632 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.00 % Allowed : 20.89 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.37), residues: 548 helix: 1.75 (0.30), residues: 290 sheet: 1.44 (0.77), residues: 54 loop : -0.22 (0.48), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 18 HIS 0.002 0.001 HIS A 154 PHE 0.010 0.001 PHE A 86 TYR 0.011 0.002 TYR D 22 ARG 0.015 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.04898 ( 234) hydrogen bonds : angle 3.91813 ( 672) covalent geometry : bond 0.00324 ( 4384) covalent geometry : angle 0.58162 ( 5970) Misc. bond : bond 0.00115 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.483 Fit side-chains REVERT: A 56 ARG cc_start: 0.6671 (mtt180) cc_final: 0.6364 (mtm-85) REVERT: A 62 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7647 (ttp) REVERT: A 147 SER cc_start: 0.7038 (t) cc_final: 0.6689 (p) REVERT: D 33 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7571 (mt-10) REVERT: C 40 TYR cc_start: 0.6821 (m-80) cc_final: 0.6049 (m-80) REVERT: B 174 GLN cc_start: 0.7405 (tp40) cc_final: 0.5871 (pm20) outliers start: 18 outliers final: 11 residues processed: 74 average time/residue: 1.2479 time to fit residues: 95.7211 Evaluate side-chains 75 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.0770 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 = 0.4078 r_free = 0.4078 target = 0.180029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.138438 restraints weight = 4811.799| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.23 r_work: 0.3588 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4386 Z= 0.116 Angle : 0.547 6.338 5970 Z= 0.280 Chirality : 0.039 0.133 688 Planarity : 0.006 0.074 774 Dihedral : 5.512 49.104 632 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.11 % Allowed : 22.00 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.38), residues: 548 helix: 1.95 (0.30), residues: 290 sheet: 1.42 (0.78), residues: 54 loop : -0.09 (0.48), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 18 HIS 0.003 0.001 HIS A 154 PHE 0.009 0.001 PHE A 86 TYR 0.008 0.001 TYR D 22 ARG 0.016 0.000 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 234) hydrogen bonds : angle 3.71838 ( 672) covalent geometry : bond 0.00264 ( 4384) covalent geometry : angle 0.54737 ( 5970) Misc. bond : bond 0.00091 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.427 Fit side-chains REVERT: A 56 ARG cc_start: 0.6602 (mtt180) cc_final: 0.6336 (mtm-85) REVERT: A 62 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7621 (ttp) REVERT: A 147 SER cc_start: 0.7024 (t) cc_final: 0.6680 (p) REVERT: D 33 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: C 40 TYR cc_start: 0.6829 (m-80) cc_final: 0.6079 (m-80) REVERT: B 174 GLN cc_start: 0.7467 (tp40) cc_final: 0.5930 (pm20) outliers start: 14 outliers final: 9 residues processed: 71 average time/residue: 1.3516 time to fit residues: 99.1301 Evaluate side-chains 72 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 50 optimal weight: 0.0980 chunk 19 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.179895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.138620 restraints weight = 4731.880| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.22 r_work: 0.3588 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4386 Z= 0.119 Angle : 0.556 6.565 5970 Z= 0.284 Chirality : 0.039 0.134 688 Planarity : 0.006 0.079 774 Dihedral : 5.272 49.004 630 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.33 % Allowed : 21.78 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.37), residues: 548 helix: 1.99 (0.30), residues: 290 sheet: 2.20 (0.79), residues: 42 loop : -0.01 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 18 HIS 0.003 0.001 HIS A 154 PHE 0.009 0.001 PHE A 86 TYR 0.008 0.001 TYR D 22 ARG 0.019 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 234) hydrogen bonds : angle 3.72998 ( 672) covalent geometry : bond 0.00273 ( 4384) covalent geometry : angle 0.55608 ( 5970) Misc. bond : bond 0.00093 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.459 Fit side-chains REVERT: A 56 ARG cc_start: 0.6578 (mmt180) cc_final: 0.6309 (mtm-85) REVERT: A 62 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7630 (ttp) REVERT: A 147 SER cc_start: 0.7017 (t) cc_final: 0.6671 (p) REVERT: D 33 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7621 (mt-10) REVERT: D 72 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6004 (mt-10) REVERT: C 40 TYR cc_start: 0.6813 (m-80) cc_final: 0.6083 (m-80) REVERT: B 45 GLU cc_start: 0.7052 (tt0) cc_final: 0.6597 (tm-30) REVERT: B 174 GLN cc_start: 0.7442 (tp40) cc_final: 0.5923 (pm20) outliers start: 15 outliers final: 9 residues processed: 69 average time/residue: 1.2696 time to fit residues: 90.7469 Evaluate side-chains 69 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.0060 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.179474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137966 restraints weight = 4837.058| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.25 r_work: 0.3580 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4386 Z= 0.124 Angle : 0.571 6.806 5970 Z= 0.290 Chirality : 0.040 0.137 688 Planarity : 0.006 0.083 774 Dihedral : 5.267 48.609 630 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.56 % Allowed : 21.33 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.38), residues: 548 helix: 1.94 (0.30), residues: 290 sheet: 1.41 (0.77), residues: 54 loop : -0.05 (0.49), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 18 HIS 0.002 0.001 HIS B 154 PHE 0.010 0.001 PHE A 86 TYR 0.009 0.001 TYR A 184 ARG 0.019 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 234) hydrogen bonds : angle 3.78923 ( 672) covalent geometry : bond 0.00290 ( 4384) covalent geometry : angle 0.57061 ( 5970) Misc. bond : bond 0.00104 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.438 Fit side-chains REVERT: A 56 ARG cc_start: 0.6689 (mmt180) cc_final: 0.6343 (mtm-85) REVERT: A 62 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7641 (ttp) REVERT: A 147 SER cc_start: 0.7014 (t) cc_final: 0.6657 (p) REVERT: A 158 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7140 (ttt) REVERT: D 33 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: C 36 ASP cc_start: 0.8130 (t0) cc_final: 0.6768 (t0) REVERT: C 40 TYR cc_start: 0.6810 (m-80) cc_final: 0.6005 (m-80) REVERT: C 95 MET cc_start: 0.4950 (mmm) cc_final: 0.3975 (tpt) REVERT: B 45 GLU cc_start: 0.6984 (tt0) cc_final: 0.6644 (tm-30) REVERT: B 174 GLN cc_start: 0.7511 (tp40) cc_final: 0.5959 (pm20) outliers start: 16 outliers final: 9 residues processed: 68 average time/residue: 1.3052 time to fit residues: 91.8997 Evaluate side-chains 72 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.0050 chunk 3 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.180113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.137857 restraints weight = 4710.222| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.26 r_work: 0.3576 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4386 Z= 0.125 Angle : 0.575 7.108 5970 Z= 0.293 Chirality : 0.040 0.136 688 Planarity : 0.006 0.087 774 Dihedral : 5.267 48.620 630 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.33 % Allowed : 21.56 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.38), residues: 548 helix: 1.96 (0.30), residues: 290 sheet: 1.36 (0.77), residues: 54 loop : -0.05 (0.49), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 18 HIS 0.002 0.001 HIS B 154 PHE 0.009 0.001 PHE A 86 TYR 0.007 0.001 TYR C 22 ARG 0.020 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 234) hydrogen bonds : angle 3.76441 ( 672) covalent geometry : bond 0.00291 ( 4384) covalent geometry : angle 0.57544 ( 5970) Misc. bond : bond 0.00106 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 1.104 Fit side-chains REVERT: A 18 TRP cc_start: 0.5977 (OUTLIER) cc_final: 0.5485 (m-10) REVERT: A 56 ARG cc_start: 0.6689 (mmt180) cc_final: 0.6377 (mtm-85) REVERT: A 62 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7644 (ttp) REVERT: A 147 SER cc_start: 0.7080 (t) cc_final: 0.6731 (p) REVERT: D 33 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: C 36 ASP cc_start: 0.8130 (t0) cc_final: 0.6786 (t0) REVERT: C 40 TYR cc_start: 0.6770 (m-80) cc_final: 0.6006 (m-80) REVERT: C 95 MET cc_start: 0.4926 (mmm) cc_final: 0.4017 (tpt) REVERT: B 174 GLN cc_start: 0.7522 (tp40) cc_final: 0.5913 (pm20) outliers start: 15 outliers final: 9 residues processed: 70 average time/residue: 1.4795 time to fit residues: 107.7365 Evaluate side-chains 72 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.0770 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.4078 r_free = 0.4078 target = 0.180308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.137680 restraints weight = 4754.636| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.30 r_work: 0.3580 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4386 Z= 0.121 Angle : 0.568 7.134 5970 Z= 0.289 Chirality : 0.039 0.136 688 Planarity : 0.006 0.088 774 Dihedral : 5.261 48.727 630 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.89 % Allowed : 21.78 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.38), residues: 548 helix: 2.01 (0.30), residues: 290 sheet: 1.45 (0.77), residues: 54 loop : -0.02 (0.49), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 18 HIS 0.002 0.001 HIS B 154 PHE 0.010 0.001 PHE A 86 TYR 0.008 0.001 TYR C 22 ARG 0.020 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 234) hydrogen bonds : angle 3.73016 ( 672) covalent geometry : bond 0.00281 ( 4384) covalent geometry : angle 0.56771 ( 5970) Misc. bond : bond 0.00100 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3866.52 seconds wall clock time: 66 minutes 55.98 seconds (4015.98 seconds total)