Starting phenix.real_space_refine on Sat Apr 26 19:43:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hnn_34917/04_2025/8hnn_34917.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnn_34917/04_2025/8hnn_34917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hnn_34917/04_2025/8hnn_34917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnn_34917/04_2025/8hnn_34917.map" model { file = "/net/cci-nas-00/data/ceres_data/8hnn_34917/04_2025/8hnn_34917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnn_34917/04_2025/8hnn_34917.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.080 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 S 17 5.16 5 Cl 2 4.86 5 C 1993 2.51 5 N 527 2.21 5 O 524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3063 Number of models: 1 Model: "" Number of chains: 3 Chain: "N" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 852 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2150 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'43I': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.87, per 1000 atoms: 0.94 Number of scatterers: 3063 At special positions: 0 Unit cell: (71.4, 52.7, 123.25, 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) Cl 2 17.00 S 17 16.00 O 524 8.00 N 527 7.00 C 1993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS R 124 " - pdb=" SG CYS R 203 " 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: 0.94 Conformation dependent library (CDL) restraints added in 379.5 milliseconds 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 722 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 4 sheets defined 56.6% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'N' and resid 88 through 92 Processing helix chain 'R' and resid 55 through 80 Processing helix chain 'R' and resid 86 through 105 removed outlier: 3.851A pdb=" N ASP R 99 " --> pdb=" O LEU R 95 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU R 101 " --> pdb=" O VAL R 97 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU R 102 " --> pdb=" O ALA R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 115 removed outlier: 3.909A pdb=" N TRP R 109 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 154 removed outlier: 4.064A pdb=" N PHE R 135 " --> pdb=" O PHE R 131 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR R 136 " --> pdb=" O ASN R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 189 Proline residue: R 185 - end of helix Processing helix chain 'R' and resid 211 through 244 Proline residue: R 227 - end of helix removed outlier: 3.889A pdb=" N SER R 244 " --> pdb=" O ALA R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 291 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 300 through 329 removed outlier: 4.207A pdb=" N CYS R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N CYS R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix removed outlier: 3.675A pdb=" N VAL R 329 " --> pdb=" O LEU R 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 4 through 9 Processing sheet with id=AA2, first strand: chain 'N' and resid 59 through 61 removed outlier: 6.842A pdb=" N TRP N 38 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER N 52 " --> pdb=" O MET N 36 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N MET N 36 " --> pdb=" O SER N 52 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU N 33 " --> pdb=" O ARG N 102 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG N 102 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP N 35 " --> pdb=" O GLU N 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 59 through 61 removed outlier: 6.842A pdb=" N TRP N 38 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER N 52 " --> pdb=" O MET N 36 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N MET N 36 " --> pdb=" O SER N 52 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU N 33 " --> pdb=" O ARG N 102 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG N 102 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP N 35 " --> pdb=" O GLU N 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 190 through 191 removed outlier: 4.145A pdb=" N SER R 191 " --> pdb=" O GLN R 204 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN R 204 " --> pdb=" O SER R 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 205 hydrogen bonds defined for protein. 591 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: 0.83 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 972 1.34 - 1.46: 711 1.46 - 1.58: 1424 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3131 Sorted by residual: bond pdb=" C19 43I R 401 " pdb=" C22 43I R 401 " ideal model delta sigma weight residual 1.437 1.379 0.058 2.00e-02 2.50e+03 8.44e+00 bond pdb=" C10 43I R 401 " pdb=" C11 43I R 401 " ideal model delta sigma weight residual 1.524 1.488 0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" C22 43I R 401 " pdb="CL2 43I R 401 " ideal model delta sigma weight residual 1.763 1.730 0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" C23 43I R 401 " pdb=" N6 43I R 401 " ideal model delta sigma weight residual 1.347 1.318 0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C14 43I R 401 " pdb=" C15 43I R 401 " ideal model delta sigma weight residual 1.388 1.359 0.029 2.00e-02 2.50e+03 2.07e+00 ... (remaining 3126 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 4138 1.61 - 3.21: 101 3.21 - 4.82: 17 4.82 - 6.42: 14 6.42 - 8.03: 2 Bond angle restraints: 4272 Sorted by residual: angle pdb=" C8 43I R 401 " pdb=" C7 43I R 401 " pdb=" N2 43I R 401 " ideal model delta sigma weight residual 115.50 123.35 -7.85 3.00e+00 1.11e-01 6.84e+00 angle pdb=" C LEU R 225 " pdb=" N LEU R 226 " pdb=" CA LEU R 226 " ideal model delta sigma weight residual 121.80 115.59 6.21 2.44e+00 1.68e-01 6.47e+00 angle pdb=" C HIS R 94 " pdb=" N LEU R 95 " pdb=" CA LEU R 95 " ideal model delta sigma weight residual 121.58 117.00 4.58 1.95e+00 2.63e-01 5.52e+00 angle pdb=" CA LEU R 95 " pdb=" CB LEU R 95 " pdb=" CG LEU R 95 " ideal model delta sigma weight residual 116.30 124.33 -8.03 3.50e+00 8.16e-02 5.26e+00 angle pdb=" C19 43I R 401 " pdb=" N1 43I R 401 " pdb=" C5 43I R 401 " ideal model delta sigma weight residual 118.45 124.82 -6.37 3.00e+00 1.11e-01 4.50e+00 ... (remaining 4267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.68: 1847 32.68 - 65.37: 34 65.37 - 98.05: 4 98.05 - 130.74: 6 130.74 - 163.42: 2 Dihedral angle restraints: 1893 sinusoidal: 765 harmonic: 1128 Sorted by residual: dihedral pdb=" CB CYS R 124 " pdb=" SG CYS R 124 " pdb=" SG CYS R 203 " pdb=" CB CYS R 203 " ideal model delta sinusoidal sigma weight residual 93.00 -178.02 -88.98 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" C11 43I R 401 " pdb=" C7 43I R 401 " pdb=" N2 43I R 401 " pdb=" C3 43I R 401 " ideal model delta sinusoidal sigma weight residual 198.38 34.96 163.42 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C11 43I R 401 " pdb=" C7 43I R 401 " pdb=" N2 43I R 401 " pdb=" C6 43I R 401 " ideal model delta sinusoidal sigma weight residual 63.87 -94.22 158.09 1 3.00e+01 1.11e-03 2.06e+01 ... (remaining 1890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.818: 507 0.818 - 1.635: 0 1.635 - 2.453: 0 2.453 - 3.271: 0 3.271 - 4.089: 1 Chirality restraints: 508 Sorted by residual: chirality pdb=" C7 43I R 401 " pdb=" C11 43I R 401 " pdb=" C8 43I R 401 " pdb=" N2 43I R 401 " both_signs ideal model delta sigma weight residual False 2.33 -1.76 4.09 2.00e-01 2.50e+01 4.18e+02 chirality pdb=" CG LEU R 321 " pdb=" CB LEU R 321 " pdb=" CD1 LEU R 321 " pdb=" CD2 LEU R 321 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA LEU R 106 " pdb=" N LEU R 106 " pdb=" C LEU R 106 " pdb=" CB LEU R 106 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 505 not shown) Planarity restraints: 521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 222 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C ALA R 222 " 0.028 2.00e-02 2.50e+03 pdb=" O ALA R 222 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY R 223 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 196 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.65e+00 pdb=" C GLU R 196 " 0.022 2.00e-02 2.50e+03 pdb=" O GLU R 196 " -0.008 2.00e-02 2.50e+03 pdb=" N ARG R 197 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 135 " 0.010 2.00e-02 2.50e+03 7.74e-03 1.05e+00 pdb=" CG PHE R 135 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE R 135 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 135 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 135 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 135 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE R 135 " 0.004 2.00e-02 2.50e+03 ... (remaining 518 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 318 2.74 - 3.28: 2951 3.28 - 3.82: 4849 3.82 - 4.36: 5235 4.36 - 4.90: 9449 Nonbonded interactions: 22802 Sorted by model distance: nonbonded pdb=" O ALA R 273 " pdb=" OG1 THR R 277 " model vdw 2.206 3.040 nonbonded pdb=" NZ LYS R 125 " pdb=" O LEU R 190 " model vdw 2.272 3.120 nonbonded pdb=" OG SER N 9 " pdb=" OG SER N 23 " model vdw 2.287 3.040 nonbonded pdb=" O GLN R 158 " pdb=" NH1 ARG R 162 " model vdw 2.317 3.120 nonbonded pdb=" O GLU R 253 " pdb=" ND2 ASN R 257 " model vdw 2.351 3.120 ... (remaining 22797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 1.450 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.090 Find NCS groups from input model: 0.030 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 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 : 0.004 0.058 3133 Z= 0.188 Angle : 0.688 8.025 4276 Z= 0.338 Chirality : 0.186 4.089 508 Planarity : 0.003 0.021 521 Dihedral : 17.325 163.420 1165 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.62 (0.44), residues: 386 helix: 1.05 (0.35), residues: 217 sheet: 2.72 (0.80), residues: 44 loop : -1.64 (0.54), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.017 0.001 PHE R 135 TYR 0.010 0.001 TYR R 233 ARG 0.002 0.000 ARG R 263 Details of bonding type rmsd hydrogen bonds : bond 0.11129 ( 197) hydrogen bonds : angle 4.86515 ( 591) SS BOND : bond 0.00285 ( 2) SS BOND : angle 0.55949 ( 4) covalent geometry : bond 0.00390 ( 3131) covalent geometry : angle 0.68828 ( 4272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 101 TYR cc_start: 0.8965 (p90) cc_final: 0.8449 (p90) REVERT: N 113 TRP cc_start: 0.8339 (m100) cc_final: 0.7985 (m-90) REVERT: R 254 LYS cc_start: 0.7462 (mtmt) cc_final: 0.7233 (ttpt) REVERT: R 274 LEU cc_start: 0.8379 (tt) cc_final: 0.8176 (tp) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1204 time to fit residues: 9.2268 Evaluate side-chains 56 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.0270 chunk 28 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 GLN R 318 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.196299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128901 restraints weight = 2875.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.133760 restraints weight = 1764.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.136612 restraints weight = 1368.457| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3133 Z= 0.129 Angle : 0.627 8.419 4276 Z= 0.298 Chirality : 0.039 0.119 508 Planarity : 0.003 0.021 521 Dihedral : 13.061 139.782 538 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.88 % Allowed : 8.97 % Favored : 88.14 % 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: 0.96 (0.44), residues: 386 helix: 1.29 (0.36), residues: 217 sheet: 2.21 (0.77), residues: 49 loop : -1.28 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.020 0.002 PHE R 328 TYR 0.009 0.001 TYR R 233 ARG 0.002 0.000 ARG R 162 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 197) hydrogen bonds : angle 4.02508 ( 591) SS BOND : bond 0.00241 ( 2) SS BOND : angle 0.32007 ( 4) covalent geometry : bond 0.00276 ( 3131) covalent geometry : angle 0.62750 ( 4272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 36 MET cc_start: 0.7842 (mtt) cc_final: 0.7549 (mmm) REVERT: N 113 TRP cc_start: 0.8306 (m100) cc_final: 0.7922 (m-90) REVERT: R 189 PHE cc_start: 0.8021 (m-10) cc_final: 0.7771 (m-10) outliers start: 9 outliers final: 6 residues processed: 59 average time/residue: 0.1157 time to fit residues: 8.7899 Evaluate side-chains 60 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 243 LYS Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 3 optimal weight: 0.0070 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.194557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.127337 restraints weight = 2841.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132155 restraints weight = 1772.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.134638 restraints weight = 1380.313| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3133 Z= 0.124 Angle : 0.601 9.302 4276 Z= 0.288 Chirality : 0.038 0.115 508 Planarity : 0.003 0.021 521 Dihedral : 12.606 140.746 538 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.21 % Allowed : 14.74 % Favored : 82.05 % 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: 1.09 (0.44), residues: 386 helix: 1.44 (0.37), residues: 217 sheet: 2.21 (0.77), residues: 49 loop : -1.27 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.018 0.002 PHE R 187 TYR 0.011 0.001 TYR N 101 ARG 0.001 0.000 ARG R 162 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 197) hydrogen bonds : angle 3.89442 ( 591) SS BOND : bond 0.00257 ( 2) SS BOND : angle 0.37037 ( 4) covalent geometry : bond 0.00264 ( 3131) covalent geometry : angle 0.60117 ( 4272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 36 MET cc_start: 0.7805 (mtt) cc_final: 0.7554 (mmm) REVERT: N 113 TRP cc_start: 0.8304 (m100) cc_final: 0.7889 (m-90) REVERT: R 189 PHE cc_start: 0.8020 (m-10) cc_final: 0.7760 (m-10) outliers start: 10 outliers final: 7 residues processed: 60 average time/residue: 0.1087 time to fit residues: 8.4878 Evaluate side-chains 62 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.190378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121865 restraints weight = 2924.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126189 restraints weight = 1853.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.128468 restraints weight = 1467.366| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3133 Z= 0.156 Angle : 0.658 11.630 4276 Z= 0.311 Chirality : 0.039 0.123 508 Planarity : 0.003 0.020 521 Dihedral : 12.539 140.934 538 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.49 % Allowed : 16.03 % Favored : 79.49 % 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: 1.10 (0.44), residues: 386 helix: 1.36 (0.37), residues: 218 sheet: 2.30 (0.76), residues: 49 loop : -1.16 (0.56), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.017 0.001 PHE R 135 TYR 0.011 0.001 TYR N 101 ARG 0.001 0.000 ARG R 167 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 197) hydrogen bonds : angle 3.99984 ( 591) SS BOND : bond 0.00346 ( 2) SS BOND : angle 0.40540 ( 4) covalent geometry : bond 0.00351 ( 3131) covalent geometry : angle 0.65852 ( 4272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8323 (m100) cc_final: 0.7916 (m-90) REVERT: R 189 PHE cc_start: 0.8048 (m-10) cc_final: 0.7706 (m-10) outliers start: 14 outliers final: 8 residues processed: 65 average time/residue: 0.1012 time to fit residues: 8.8052 Evaluate side-chains 64 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 27 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 75 ASN R 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.186614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.118317 restraints weight = 2919.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.122301 restraints weight = 1911.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.124323 restraints weight = 1543.133| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3133 Z= 0.180 Angle : 0.719 12.548 4276 Z= 0.337 Chirality : 0.041 0.136 508 Planarity : 0.003 0.019 521 Dihedral : 12.347 142.413 538 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.49 % Allowed : 17.95 % Favored : 77.56 % 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: 0.90 (0.44), residues: 386 helix: 1.19 (0.36), residues: 218 sheet: 2.24 (0.75), residues: 49 loop : -1.24 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.024 0.002 PHE R 187 TYR 0.012 0.001 TYR R 235 ARG 0.002 0.000 ARG R 259 Details of bonding type rmsd hydrogen bonds : bond 0.05259 ( 197) hydrogen bonds : angle 4.20394 ( 591) SS BOND : bond 0.00386 ( 2) SS BOND : angle 0.45856 ( 4) covalent geometry : bond 0.00414 ( 3131) covalent geometry : angle 0.71872 ( 4272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8318 (m100) cc_final: 0.7906 (m-90) REVERT: R 189 PHE cc_start: 0.8116 (m-10) cc_final: 0.7761 (m-10) outliers start: 14 outliers final: 11 residues processed: 62 average time/residue: 0.1074 time to fit residues: 8.7473 Evaluate side-chains 67 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 317 MET Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 17 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.196074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.133149 restraints weight = 2956.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.137629 restraints weight = 1840.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140195 restraints weight = 1438.881| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3133 Z= 0.158 Angle : 0.674 10.576 4276 Z= 0.318 Chirality : 0.039 0.127 508 Planarity : 0.003 0.020 521 Dihedral : 12.219 148.098 538 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.49 % Allowed : 19.23 % Favored : 76.28 % 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: 0.95 (0.44), residues: 386 helix: 1.28 (0.36), residues: 218 sheet: 2.18 (0.74), residues: 49 loop : -1.28 (0.54), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.017 0.001 PHE R 135 TYR 0.012 0.001 TYR N 101 ARG 0.001 0.000 ARG R 259 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 197) hydrogen bonds : angle 4.10057 ( 591) SS BOND : bond 0.00354 ( 2) SS BOND : angle 0.48872 ( 4) covalent geometry : bond 0.00359 ( 3131) covalent geometry : angle 0.67399 ( 4272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8260 (m100) cc_final: 0.7934 (m-90) REVERT: R 187 PHE cc_start: 0.8373 (m-80) cc_final: 0.8005 (m-80) REVERT: R 189 PHE cc_start: 0.8145 (m-10) cc_final: 0.7809 (m-10) outliers start: 14 outliers final: 10 residues processed: 62 average time/residue: 0.1019 time to fit residues: 8.2743 Evaluate side-chains 65 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 chunk 6 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 194 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.198080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.135878 restraints weight = 2872.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.140356 restraints weight = 1790.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.142655 restraints weight = 1408.195| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3133 Z= 0.137 Angle : 0.644 9.792 4276 Z= 0.304 Chirality : 0.038 0.121 508 Planarity : 0.003 0.020 521 Dihedral : 12.310 153.804 538 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.17 % Allowed : 19.87 % Favored : 75.96 % 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: 1.06 (0.44), residues: 386 helix: 1.41 (0.37), residues: 218 sheet: 2.27 (0.75), residues: 49 loop : -1.34 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.016 0.001 PHE R 135 TYR 0.012 0.001 TYR N 101 ARG 0.001 0.000 ARG R 259 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 197) hydrogen bonds : angle 4.00742 ( 591) SS BOND : bond 0.00285 ( 2) SS BOND : angle 0.44536 ( 4) covalent geometry : bond 0.00300 ( 3131) covalent geometry : angle 0.64401 ( 4272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8252 (m100) cc_final: 0.7935 (m-90) REVERT: R 187 PHE cc_start: 0.8423 (m-80) cc_final: 0.8086 (m-80) REVERT: R 189 PHE cc_start: 0.8086 (m-10) cc_final: 0.7735 (m-10) outliers start: 13 outliers final: 11 residues processed: 61 average time/residue: 0.1087 time to fit residues: 8.7010 Evaluate side-chains 65 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 25 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 0.0770 chunk 5 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 0.0370 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.4616 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.200227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.137907 restraints weight = 2854.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.142472 restraints weight = 1770.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.145011 restraints weight = 1393.430| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3133 Z= 0.121 Angle : 0.623 9.572 4276 Z= 0.292 Chirality : 0.037 0.114 508 Planarity : 0.003 0.021 521 Dihedral : 12.397 157.688 538 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.17 % Allowed : 20.51 % Favored : 75.32 % 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: 1.15 (0.44), residues: 386 helix: 1.54 (0.37), residues: 217 sheet: 2.29 (0.75), residues: 49 loop : -1.39 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.015 0.001 PHE R 135 TYR 0.010 0.001 TYR N 101 ARG 0.001 0.000 ARG R 259 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 197) hydrogen bonds : angle 3.91107 ( 591) SS BOND : bond 0.00260 ( 2) SS BOND : angle 0.37208 ( 4) covalent geometry : bond 0.00254 ( 3131) covalent geometry : angle 0.62325 ( 4272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8241 (m100) cc_final: 0.7928 (m-90) REVERT: R 187 PHE cc_start: 0.8381 (m-80) cc_final: 0.8054 (m-80) REVERT: R 189 PHE cc_start: 0.8025 (m-10) cc_final: 0.7724 (m-10) outliers start: 13 outliers final: 12 residues processed: 60 average time/residue: 0.1084 time to fit residues: 8.4705 Evaluate side-chains 67 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 317 MET Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.196126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133614 restraints weight = 2899.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.137977 restraints weight = 1833.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.140457 restraints weight = 1454.281| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3133 Z= 0.156 Angle : 0.658 9.813 4276 Z= 0.311 Chirality : 0.039 0.125 508 Planarity : 0.003 0.020 521 Dihedral : 12.665 161.490 538 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.49 % Allowed : 21.47 % Favored : 74.04 % 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: 1.03 (0.44), residues: 386 helix: 1.42 (0.37), residues: 218 sheet: 2.27 (0.74), residues: 49 loop : -1.43 (0.54), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.017 0.001 PHE R 135 TYR 0.010 0.001 TYR N 101 ARG 0.001 0.000 ARG R 259 Details of bonding type rmsd hydrogen bonds : bond 0.04735 ( 197) hydrogen bonds : angle 4.03778 ( 591) SS BOND : bond 0.00338 ( 2) SS BOND : angle 0.44897 ( 4) covalent geometry : bond 0.00353 ( 3131) covalent geometry : angle 0.65825 ( 4272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8254 (m100) cc_final: 0.7946 (m-90) REVERT: R 189 PHE cc_start: 0.8132 (m-10) cc_final: 0.7818 (m-10) outliers start: 14 outliers final: 12 residues processed: 62 average time/residue: 0.1064 time to fit residues: 8.6053 Evaluate side-chains 68 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 8 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.197848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.135804 restraints weight = 2821.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.140084 restraints weight = 1779.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.142783 restraints weight = 1401.015| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3133 Z= 0.140 Angle : 0.665 13.590 4276 Z= 0.309 Chirality : 0.038 0.118 508 Planarity : 0.003 0.020 521 Dihedral : 12.773 164.886 538 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.85 % Allowed : 21.47 % Favored : 74.68 % 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: 0.99 (0.44), residues: 386 helix: 1.38 (0.36), residues: 218 sheet: 2.49 (0.73), residues: 48 loop : -1.53 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.024 0.002 PHE R 187 TYR 0.011 0.001 TYR N 101 ARG 0.001 0.000 ARG R 259 Details of bonding type rmsd hydrogen bonds : bond 0.04493 ( 197) hydrogen bonds : angle 4.02013 ( 591) SS BOND : bond 0.00302 ( 2) SS BOND : angle 0.43698 ( 4) covalent geometry : bond 0.00308 ( 3131) covalent geometry : angle 0.66503 ( 4272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8255 (m100) cc_final: 0.7962 (m-90) REVERT: R 189 PHE cc_start: 0.8101 (m-10) cc_final: 0.7736 (m-10) outliers start: 12 outliers final: 12 residues processed: 60 average time/residue: 0.1072 time to fit residues: 8.4076 Evaluate side-chains 67 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.189476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.125387 restraints weight = 2943.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.128744 restraints weight = 2808.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.129444 restraints weight = 1952.337| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3133 Z= 0.153 Angle : 0.675 12.840 4276 Z= 0.317 Chirality : 0.039 0.126 508 Planarity : 0.003 0.020 521 Dihedral : 13.157 171.325 538 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.49 % Allowed : 20.83 % Favored : 74.68 % 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: 0.89 (0.44), residues: 386 helix: 1.32 (0.36), residues: 218 sheet: 2.20 (0.75), residues: 49 loop : -1.53 (0.53), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.017 0.002 PHE R 135 TYR 0.011 0.001 TYR N 39 ARG 0.001 0.000 ARG R 259 Details of bonding type rmsd hydrogen bonds : bond 0.04795 ( 197) hydrogen bonds : angle 4.07730 ( 591) SS BOND : bond 0.00337 ( 2) SS BOND : angle 0.45433 ( 4) covalent geometry : bond 0.00343 ( 3131) covalent geometry : angle 0.67520 ( 4272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1403.12 seconds wall clock time: 25 minutes 7.63 seconds (1507.63 seconds total)