Starting phenix.real_space_refine on Fri Aug 22 14:18:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zam_39880/08_2025/8zam_39880_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zam_39880/08_2025/8zam_39880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zam_39880/08_2025/8zam_39880_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zam_39880/08_2025/8zam_39880_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zam_39880/08_2025/8zam_39880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zam_39880/08_2025/8zam_39880.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 34 5.16 5 C 2660 2.51 5 N 634 2.21 5 O 670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4000 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1949 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1949 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'L9Q': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'L9Q': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.08, per 1000 atoms: 0.27 Number of scatterers: 4000 At special positions: 0 Unit cell: (59.85, 75.95, 80.15, 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 34 16.00 P 2 15.00 O 670 8.00 N 634 7.00 C 2660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS B 36 " distance=2.03 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS B 34 " 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: 0.35 Conformation dependent library (CDL) restraints added in 172.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 884 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 79.3% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 47 through 76 Processing helix chain 'A' and resid 80 through 101 removed outlier: 3.769A pdb=" N ILE A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 136 Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 146 through 168 removed outlier: 3.553A pdb=" N MET A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 203 Processing helix chain 'A' and resid 206 through 233 Proline residue: A 227 - end of helix Processing helix chain 'A' and resid 240 through 257 Processing helix chain 'A' and resid 257 through 278 Processing helix chain 'B' and resid 47 through 76 Processing helix chain 'B' and resid 80 through 101 removed outlier: 3.769A pdb=" N ILE B 84 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 136 Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 146 through 168 removed outlier: 3.553A pdb=" N MET B 150 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 203 Processing helix chain 'B' and resid 206 through 233 Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 240 through 257 Processing helix chain 'B' and resid 257 through 278 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 108 Processing sheet with id=AA2, first strand: chain 'B' and resid 107 through 108 312 hydrogen bonds defined for protein. 930 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: 0.48 Time building geometry restraints manager: 0.48 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: 1125 1.34 - 1.46: 826 1.46 - 1.58: 2115 1.58 - 1.70: 4 1.70 - 1.82: 50 Bond restraints: 4120 Sorted by residual: bond pdb=" C39 L9Q B 401 " pdb=" C40 L9Q B 401 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C39 L9Q A 401 " pdb=" C40 L9Q A 401 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.05e+01 bond pdb=" C11 L9Q B 401 " pdb=" O3 L9Q B 401 " ideal model delta sigma weight residual 1.327 1.456 -0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C31 L9Q B 401 " pdb=" O2 L9Q B 401 " ideal model delta sigma weight residual 1.330 1.455 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C11 L9Q A 401 " pdb=" O3 L9Q A 401 " ideal model delta sigma weight residual 1.327 1.452 -0.125 2.00e-02 2.50e+03 3.88e+01 ... (remaining 4115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 5534 3.44 - 6.87: 37 6.87 - 10.31: 7 10.31 - 13.75: 2 13.75 - 17.19: 2 Bond angle restraints: 5582 Sorted by residual: angle pdb=" C38 L9Q A 401 " pdb=" C39 L9Q A 401 " pdb=" C40 L9Q A 401 " ideal model delta sigma weight residual 127.57 110.38 17.19 3.00e+00 1.11e-01 3.28e+01 angle pdb=" C38 L9Q B 401 " pdb=" C39 L9Q B 401 " pdb=" C40 L9Q B 401 " ideal model delta sigma weight residual 127.57 110.61 16.96 3.00e+00 1.11e-01 3.20e+01 angle pdb=" C39 L9Q B 401 " pdb=" C40 L9Q B 401 " pdb=" C41 L9Q B 401 " ideal model delta sigma weight residual 127.59 114.62 12.97 3.00e+00 1.11e-01 1.87e+01 angle pdb=" C39 L9Q A 401 " pdb=" C40 L9Q A 401 " pdb=" C41 L9Q A 401 " ideal model delta sigma weight residual 127.59 114.75 12.84 3.00e+00 1.11e-01 1.83e+01 angle pdb=" N THR A 170 " pdb=" CA THR A 170 " pdb=" C THR A 170 " ideal model delta sigma weight residual 111.02 116.24 -5.22 1.25e+00 6.40e-01 1.74e+01 ... (remaining 5577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 2187 35.42 - 70.85: 116 70.85 - 106.27: 11 106.27 - 141.69: 2 141.69 - 177.11: 4 Dihedral angle restraints: 2320 sinusoidal: 920 harmonic: 1400 Sorted by residual: dihedral pdb=" CB CYS A 34 " pdb=" SG CYS A 34 " pdb=" SG CYS B 36 " pdb=" CB CYS B 36 " ideal model delta sinusoidal sigma weight residual 93.00 50.49 42.51 1 1.00e+01 1.00e-02 2.52e+01 dihedral pdb=" CB CYS A 36 " pdb=" SG CYS A 36 " pdb=" SG CYS B 34 " pdb=" CB CYS B 34 " ideal model delta sinusoidal sigma weight residual 93.00 50.50 42.50 1 1.00e+01 1.00e-02 2.52e+01 dihedral pdb=" C23 L9Q B 401 " pdb=" C24 L9Q B 401 " pdb=" C25 L9Q B 401 " pdb=" C26 L9Q B 401 " ideal model delta sinusoidal sigma weight residual 179.70 -3.19 -177.11 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 2317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 416 0.038 - 0.076: 146 0.076 - 0.113: 38 0.113 - 0.151: 0 0.151 - 0.189: 6 Chirality restraints: 606 Sorted by residual: chirality pdb=" C2 L9Q B 401 " pdb=" C1 L9Q B 401 " pdb=" C3 L9Q B 401 " pdb=" O2 L9Q B 401 " both_signs ideal model delta sigma weight residual False 2.36 2.55 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CA THR A 170 " pdb=" N THR A 170 " pdb=" C THR A 170 " pdb=" CB THR A 170 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CA THR B 170 " pdb=" N THR B 170 " pdb=" C THR B 170 " pdb=" CB THR B 170 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 603 not shown) Planarity restraints: 666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 L9Q B 401 " -0.208 2.00e-02 2.50e+03 2.16e-01 4.66e+02 pdb=" C39 L9Q B 401 " 0.184 2.00e-02 2.50e+03 pdb=" C40 L9Q B 401 " 0.245 2.00e-02 2.50e+03 pdb=" C41 L9Q B 401 " -0.221 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 L9Q A 401 " 0.205 2.00e-02 2.50e+03 2.13e-01 4.55e+02 pdb=" C39 L9Q A 401 " -0.180 2.00e-02 2.50e+03 pdb=" C40 L9Q A 401 " -0.244 2.00e-02 2.50e+03 pdb=" C41 L9Q A 401 " 0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 203 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO B 204 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 204 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 204 " -0.016 5.00e-02 4.00e+02 ... (remaining 663 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1028 2.79 - 3.32: 3977 3.32 - 3.85: 7431 3.85 - 4.37: 8711 4.37 - 4.90: 14518 Nonbonded interactions: 35665 Sorted by model distance: nonbonded pdb=" OG SER A 77 " pdb=" N THR A 78 " model vdw 2.265 3.120 nonbonded pdb=" OG SER B 77 " pdb=" N THR B 78 " model vdw 2.265 3.120 nonbonded pdb=" O TYR A 70 " pdb=" OG1 THR A 74 " model vdw 2.270 3.040 nonbonded pdb=" O TYR B 70 " pdb=" OG1 THR B 74 " model vdw 2.270 3.040 nonbonded pdb=" O ALA A 59 " pdb=" OG SER A 63 " model vdw 2.335 3.040 ... (remaining 35660 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: 0.01 Found NCS groups: 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: 20.700 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: 0.280 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.350 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:7.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 : 0.007 0.190 4122 Z= 0.339 Angle : 0.868 17.187 5586 Z= 0.402 Chirality : 0.042 0.189 606 Planarity : 0.012 0.216 666 Dihedral : 22.820 177.109 1430 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.46 % Allowed : 26.11 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.38), residues: 488 helix: 2.06 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -2.34 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 120 TYR 0.010 0.001 TYR B 85 PHE 0.012 0.001 PHE B 177 TRP 0.006 0.001 TRP B 118 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00680 ( 4120) covalent geometry : angle 0.86805 ( 5582) SS BOND : bond 0.00312 ( 2) SS BOND : angle 0.76950 ( 4) hydrogen bonds : bond 0.08605 ( 312) hydrogen bonds : angle 5.19131 ( 930) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.099 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 52 average time/residue: 0.3809 time to fit residues: 20.7379 Evaluate side-chains 50 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 203 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.0070 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.127029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108856 restraints weight = 4317.918| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.60 r_work: 0.3122 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.0715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4122 Z= 0.142 Angle : 0.528 6.195 5586 Z= 0.281 Chirality : 0.040 0.144 606 Planarity : 0.003 0.023 666 Dihedral : 16.862 132.695 632 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.43 % Allowed : 20.20 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.38), residues: 488 helix: 2.01 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -1.87 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 207 TYR 0.011 0.001 TYR A 109 PHE 0.010 0.001 PHE B 177 TRP 0.006 0.001 TRP A 118 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4120) covalent geometry : angle 0.52829 ( 5582) SS BOND : bond 0.00170 ( 2) SS BOND : angle 0.31539 ( 4) hydrogen bonds : bond 0.04132 ( 312) hydrogen bonds : angle 4.70420 ( 930) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.147 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 54 average time/residue: 0.3646 time to fit residues: 20.6007 Evaluate side-chains 44 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 0.0470 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN A 137 ASN A 201 HIS B 104 ASN B 137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.127183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108814 restraints weight = 4245.415| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.59 r_work: 0.3126 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4122 Z= 0.139 Angle : 0.529 8.604 5586 Z= 0.276 Chirality : 0.039 0.143 606 Planarity : 0.003 0.023 666 Dihedral : 14.440 112.538 626 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.69 % Allowed : 20.94 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.38), residues: 488 helix: 2.05 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -1.92 (0.61), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 207 TYR 0.011 0.001 TYR B 109 PHE 0.009 0.001 PHE A 177 TRP 0.007 0.001 TRP A 118 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4120) covalent geometry : angle 0.52863 ( 5582) SS BOND : bond 0.00179 ( 2) SS BOND : angle 0.34040 ( 4) hydrogen bonds : bond 0.04089 ( 312) hydrogen bonds : angle 4.66206 ( 930) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.118 Fit side-chains REVERT: A 104 ASN cc_start: 0.7338 (OUTLIER) cc_final: 0.7128 (t0) REVERT: B 104 ASN cc_start: 0.7332 (OUTLIER) cc_final: 0.7125 (t0) REVERT: B 194 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7282 (mttt) outliers start: 15 outliers final: 8 residues processed: 57 average time/residue: 0.3864 time to fit residues: 23.0608 Evaluate side-chains 49 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 257 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 137 ASN A 210 GLN B 137 ASN B 210 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.124708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.106186 restraints weight = 4246.727| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.60 r_work: 0.3086 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4122 Z= 0.177 Angle : 0.553 6.530 5586 Z= 0.292 Chirality : 0.041 0.145 606 Planarity : 0.003 0.022 666 Dihedral : 14.033 109.276 626 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 5.17 % Allowed : 19.21 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.38), residues: 488 helix: 2.02 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.94 (0.60), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 207 TYR 0.012 0.002 TYR B 109 PHE 0.012 0.002 PHE A 177 TRP 0.008 0.001 TRP B 118 HIS 0.005 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 4120) covalent geometry : angle 0.55272 ( 5582) SS BOND : bond 0.00250 ( 2) SS BOND : angle 0.34226 ( 4) hydrogen bonds : bond 0.04238 ( 312) hydrogen bonds : angle 4.73215 ( 930) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.178 Fit side-chains REVERT: A 194 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7297 (mttt) REVERT: B 194 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7291 (mttt) outliers start: 21 outliers final: 12 residues processed: 62 average time/residue: 0.4098 time to fit residues: 26.5567 Evaluate side-chains 54 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 257 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 210 GLN B 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.125467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107214 restraints weight = 4218.866| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.58 r_work: 0.3105 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4122 Z= 0.147 Angle : 0.550 10.702 5586 Z= 0.283 Chirality : 0.039 0.140 606 Planarity : 0.003 0.023 666 Dihedral : 13.501 102.711 626 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 5.42 % Allowed : 18.47 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.38), residues: 488 helix: 2.03 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -1.68 (0.62), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 207 TYR 0.011 0.001 TYR A 109 PHE 0.009 0.001 PHE B 177 TRP 0.008 0.001 TRP A 118 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4120) covalent geometry : angle 0.55037 ( 5582) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.27902 ( 4) hydrogen bonds : bond 0.04077 ( 312) hydrogen bonds : angle 4.68754 ( 930) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 0.111 Fit side-chains REVERT: A 104 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.7195 (t0) REVERT: A 194 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7311 (mttt) REVERT: B 104 ASN cc_start: 0.7478 (OUTLIER) cc_final: 0.7211 (t0) REVERT: B 194 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7303 (mttt) outliers start: 22 outliers final: 10 residues processed: 67 average time/residue: 0.3415 time to fit residues: 24.0091 Evaluate side-chains 53 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 257 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 210 GLN B 137 ASN B 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.125442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106854 restraints weight = 4338.987| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.62 r_work: 0.3093 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4122 Z= 0.151 Angle : 0.537 8.664 5586 Z= 0.280 Chirality : 0.039 0.141 606 Planarity : 0.003 0.023 666 Dihedral : 12.862 95.356 626 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.43 % Allowed : 18.47 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.38), residues: 488 helix: 2.10 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -1.83 (0.61), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 207 TYR 0.012 0.001 TYR A 109 PHE 0.009 0.001 PHE A 177 TRP 0.008 0.001 TRP B 118 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 4120) covalent geometry : angle 0.53700 ( 5582) SS BOND : bond 0.00192 ( 2) SS BOND : angle 0.29855 ( 4) hydrogen bonds : bond 0.04090 ( 312) hydrogen bonds : angle 4.68395 ( 930) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.158 Fit side-chains REVERT: A 194 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7326 (mttt) outliers start: 18 outliers final: 13 residues processed: 61 average time/residue: 0.4147 time to fit residues: 26.4254 Evaluate side-chains 55 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 257 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 210 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.125912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107095 restraints weight = 4353.656| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.64 r_work: 0.3096 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4122 Z= 0.150 Angle : 0.566 12.457 5586 Z= 0.287 Chirality : 0.039 0.148 606 Planarity : 0.003 0.023 666 Dihedral : 12.283 88.720 626 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.94 % Allowed : 18.97 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.38), residues: 488 helix: 2.08 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -1.79 (0.62), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 207 TYR 0.011 0.001 TYR B 109 PHE 0.009 0.001 PHE A 177 TRP 0.008 0.001 TRP B 118 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4120) covalent geometry : angle 0.56567 ( 5582) SS BOND : bond 0.00174 ( 2) SS BOND : angle 0.27305 ( 4) hydrogen bonds : bond 0.04071 ( 312) hydrogen bonds : angle 4.68451 ( 930) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.136 Fit side-chains REVERT: A 194 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7331 (mttt) REVERT: B 194 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7329 (mttt) outliers start: 16 outliers final: 10 residues processed: 56 average time/residue: 0.3796 time to fit residues: 22.2234 Evaluate side-chains 50 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 257 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.125426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106845 restraints weight = 4211.475| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.60 r_work: 0.3092 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4122 Z= 0.155 Angle : 0.565 11.592 5586 Z= 0.288 Chirality : 0.039 0.148 606 Planarity : 0.003 0.023 666 Dihedral : 11.454 77.143 626 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.45 % Allowed : 19.70 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.38), residues: 488 helix: 2.07 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -1.86 (0.61), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 207 TYR 0.011 0.001 TYR A 109 PHE 0.010 0.001 PHE B 177 TRP 0.008 0.001 TRP B 118 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 4120) covalent geometry : angle 0.56474 ( 5582) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.30744 ( 4) hydrogen bonds : bond 0.04099 ( 312) hydrogen bonds : angle 4.68934 ( 930) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.170 Fit side-chains REVERT: A 194 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7343 (mttt) REVERT: B 194 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7328 (mttt) outliers start: 14 outliers final: 7 residues processed: 53 average time/residue: 0.4477 time to fit residues: 24.7731 Evaluate side-chains 47 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 257 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 0.0060 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108857 restraints weight = 4276.400| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.64 r_work: 0.3120 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4122 Z= 0.133 Angle : 0.538 10.990 5586 Z= 0.275 Chirality : 0.038 0.144 606 Planarity : 0.003 0.023 666 Dihedral : 10.956 68.370 626 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.22 % Allowed : 20.20 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.38), residues: 488 helix: 2.18 (0.25), residues: 388 sheet: None (None), residues: 0 loop : -1.85 (0.61), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 207 TYR 0.010 0.001 TYR B 109 PHE 0.008 0.001 PHE A 177 TRP 0.008 0.001 TRP A 118 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4120) covalent geometry : angle 0.53835 ( 5582) SS BOND : bond 0.00170 ( 2) SS BOND : angle 0.28051 ( 4) hydrogen bonds : bond 0.03949 ( 312) hydrogen bonds : angle 4.62528 ( 930) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.100 Fit side-chains REVERT: A 194 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7345 (mttt) REVERT: B 194 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7321 (mttt) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.4540 time to fit residues: 22.6340 Evaluate side-chains 46 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 0.0670 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.127305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108651 restraints weight = 4220.104| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.61 r_work: 0.3117 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4122 Z= 0.137 Angle : 0.541 10.767 5586 Z= 0.277 Chirality : 0.038 0.144 606 Planarity : 0.003 0.023 666 Dihedral : 10.665 59.797 626 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.22 % Allowed : 20.44 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.38), residues: 488 helix: 2.14 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -1.69 (0.61), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 207 TYR 0.010 0.001 TYR A 109 PHE 0.009 0.001 PHE A 177 TRP 0.008 0.001 TRP B 118 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4120) covalent geometry : angle 0.54137 ( 5582) SS BOND : bond 0.00163 ( 2) SS BOND : angle 0.33793 ( 4) hydrogen bonds : bond 0.03963 ( 312) hydrogen bonds : angle 4.63089 ( 930) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.161 Fit side-chains REVERT: A 194 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7332 (mttt) REVERT: B 194 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7328 (mttt) outliers start: 9 outliers final: 6 residues processed: 49 average time/residue: 0.3963 time to fit residues: 20.3566 Evaluate side-chains 47 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 19 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 0.0570 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.109202 restraints weight = 4260.462| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.63 r_work: 0.3123 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4122 Z= 0.133 Angle : 0.535 10.536 5586 Z= 0.274 Chirality : 0.038 0.143 606 Planarity : 0.003 0.023 666 Dihedral : 10.326 58.487 626 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.22 % Allowed : 20.44 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.38), residues: 488 helix: 2.16 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -1.66 (0.61), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 207 TYR 0.010 0.001 TYR B 109 PHE 0.008 0.001 PHE B 177 TRP 0.008 0.001 TRP B 118 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 4120) covalent geometry : angle 0.53482 ( 5582) SS BOND : bond 0.00175 ( 2) SS BOND : angle 0.27367 ( 4) hydrogen bonds : bond 0.03922 ( 312) hydrogen bonds : angle 4.61342 ( 930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1950.71 seconds wall clock time: 34 minutes 7.53 seconds (2047.53 seconds total)