Starting phenix.real_space_refine on Tue Feb 3 17:43:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k0n_61948/02_2026/9k0n_61948.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k0n_61948/02_2026/9k0n_61948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k0n_61948/02_2026/9k0n_61948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k0n_61948/02_2026/9k0n_61948.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k0n_61948/02_2026/9k0n_61948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k0n_61948/02_2026/9k0n_61948.map" } resolution = 3.21 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= -0.002 sd= 0.097 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: 6 Type Number sf(0) Gaussians S 38 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3741 2.51 5 N 888 2.21 5 O 991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5661 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4070 Classifications: {'peptide': 538} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 28, 'TRANS': 509} Chain breaks: 1 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'PHE:plan': 5, 'HIS:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 7, 'TYR:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 160 Chain: "H" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 854 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "L" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 728 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'BAL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 1, ' NA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.54, per 1000 atoms: 0.27 Number of scatterers: 5661 At special positions: 0 Unit cell: (82.544, 80.4, 107.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 38 16.00 Na 2 11.00 O 991 8.00 N 888 7.00 C 3741 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " 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: 0.56 Conformation dependent library (CDL) restraints added in 406.1 milliseconds 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 57.2% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.620A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.788A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 removed outlier: 3.999A pdb=" N LEU A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 90 through 105 Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.649A pdb=" N ILE A 116 " --> pdb=" O CYS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 151 removed outlier: 3.696A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.848A pdb=" N HIS A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 250 through 266 removed outlier: 4.543A pdb=" N PHE A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.621A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.289A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.759A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 356 removed outlier: 3.502A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 380 Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.649A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 444 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.873A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 481 removed outlier: 3.779A pdb=" N LEU A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 533 through 535 No H-bonds generated for 'chain 'A' and resid 533 through 535' Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.996A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.646A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.843A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.517A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.612A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.619A pdb=" N VAL L 19 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.666A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.795A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 969 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 0.71 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: 1704 1.34 - 1.46: 1624 1.46 - 1.58: 2445 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 5827 Sorted by residual: bond pdb=" CB PRO A 502 " pdb=" CG PRO A 502 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.19e+00 bond pdb=" C BAL A 701 " pdb=" O BAL A 701 " ideal model delta sigma weight residual 1.231 1.259 -0.028 2.00e-02 2.50e+03 1.97e+00 bond pdb=" N VAL L 59 " pdb=" CA VAL L 59 " ideal model delta sigma weight residual 1.468 1.455 0.013 1.05e-02 9.07e+03 1.50e+00 bond pdb=" C VAL L 59 " pdb=" O VAL L 59 " ideal model delta sigma weight residual 1.245 1.231 0.014 1.34e-02 5.57e+03 1.07e+00 bond pdb=" CA ARG L 62 " pdb=" C ARG L 62 " ideal model delta sigma weight residual 1.523 1.510 0.013 1.34e-02 5.57e+03 9.59e-01 ... (remaining 5822 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 7752 1.31 - 2.61: 181 2.61 - 3.92: 34 3.92 - 5.22: 11 5.22 - 6.53: 7 Bond angle restraints: 7985 Sorted by residual: angle pdb=" N ILE A 116 " pdb=" CA ILE A 116 " pdb=" C ILE A 116 " ideal model delta sigma weight residual 111.45 108.59 2.86 9.30e-01 1.16e+00 9.45e+00 angle pdb=" CA TYR A 578 " pdb=" CB TYR A 578 " pdb=" CG TYR A 578 " ideal model delta sigma weight residual 113.90 118.85 -4.95 1.80e+00 3.09e-01 7.56e+00 angle pdb=" N ALA L 61 " pdb=" CA ALA L 61 " pdb=" C ALA L 61 " ideal model delta sigma weight residual 113.72 109.70 4.02 1.52e+00 4.33e-01 6.99e+00 angle pdb=" C ALA A 462 " pdb=" N ALA A 463 " pdb=" CA ALA A 463 " ideal model delta sigma weight residual 121.54 126.23 -4.69 1.91e+00 2.74e-01 6.04e+00 angle pdb=" N PRO L 60 " pdb=" CA PRO L 60 " pdb=" C PRO L 60 " ideal model delta sigma weight residual 114.20 111.45 2.75 1.20e+00 6.94e-01 5.25e+00 ... (remaining 7980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 2986 17.24 - 34.49: 236 34.49 - 51.73: 46 51.73 - 68.97: 8 68.97 - 86.21: 3 Dihedral angle restraints: 3279 sinusoidal: 1091 harmonic: 2188 Sorted by residual: dihedral pdb=" N BAL A 701 " pdb=" C BAL A 701 " pdb=" CA BAL A 701 " pdb=" CB BAL A 701 " ideal model delta harmonic sigma weight residual 122.80 36.59 86.21 0 2.50e+00 1.60e-01 1.19e+03 dihedral pdb=" C BAL A 701 " pdb=" N BAL A 701 " pdb=" CA BAL A 701 " pdb=" CB BAL A 701 " ideal model delta harmonic sigma weight residual -122.60 -97.47 -25.13 0 2.50e+00 1.60e-01 1.01e+02 dihedral pdb=" CA ASN A 63 " pdb=" CB ASN A 63 " pdb=" CG ASN A 63 " pdb=" OD1 ASN A 63 " ideal model delta sinusoidal sigma weight residual 120.00 -176.98 -63.02 2 2.00e+01 2.50e-03 9.53e+00 ... (remaining 3276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 596 0.029 - 0.058: 193 0.058 - 0.087: 81 0.087 - 0.116: 41 0.116 - 0.145: 4 Chirality restraints: 915 Sorted by residual: chirality pdb=" CB THR H 91 " pdb=" CA THR H 91 " pdb=" OG1 THR H 91 " pdb=" CG2 THR H 91 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA ILE L 76 " pdb=" N ILE L 76 " pdb=" C ILE L 76 " pdb=" CB ILE L 76 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE H 78 " pdb=" N ILE H 78 " pdb=" C ILE H 78 " pdb=" CB ILE H 78 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 912 not shown) Planarity restraints: 987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 501 " -0.047 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO A 502 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 502 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 502 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 374 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.39e+00 pdb=" N PRO A 375 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 40 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO H 41 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " 0.028 5.00e-02 4.00e+02 ... (remaining 984 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 36 2.61 - 3.18: 5059 3.18 - 3.76: 9007 3.76 - 4.33: 12409 4.33 - 4.90: 21145 Nonbonded interactions: 47656 Sorted by model distance: nonbonded pdb=" OD1 ASN A 333 " pdb="NA NA A 702 " model vdw 2.041 2.470 nonbonded pdb=" O GLY A 56 " pdb="NA NA A 703 " model vdw 2.049 2.470 nonbonded pdb=" O TYR A 247 " pdb=" OG1 THR A 251 " model vdw 2.189 3.040 nonbonded pdb=" OH TYR A 69 " pdb=" OD2 ASP A 459 " model vdw 2.270 3.040 nonbonded pdb=" OD2 ASP A 174 " pdb=" NZ LYS A 376 " model vdw 2.315 3.120 ... (remaining 47651 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 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: 1.510 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.100 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 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 : 0.002 0.074 5830 Z= 0.111 Angle : 0.528 6.529 7991 Z= 0.283 Chirality : 0.038 0.145 915 Planarity : 0.005 0.069 987 Dihedral : 13.182 79.835 1882 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 14.80 % Favored : 85.20 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 1.42 (0.32), residues: 755 helix: 2.00 (0.28), residues: 384 sheet: 0.48 (0.50), residues: 109 loop : -0.41 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 98 TYR 0.012 0.001 TYR A 69 PHE 0.011 0.001 PHE A 391 TRP 0.015 0.001 TRP A 541 HIS 0.002 0.001 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 5827) covalent geometry : angle 0.52753 ( 7985) SS BOND : bond 0.00126 ( 3) SS BOND : angle 0.99906 ( 6) hydrogen bonds : bond 0.16363 ( 336) hydrogen bonds : angle 6.29345 ( 969) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 125 TYR cc_start: 0.7926 (m-80) cc_final: 0.7624 (m-80) REVERT: A 197 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8256 (mt-10) REVERT: A 315 TYR cc_start: 0.8984 (m-80) cc_final: 0.8646 (m-80) REVERT: A 320 ASN cc_start: 0.7747 (t0) cc_final: 0.7530 (t0) REVERT: A 380 MET cc_start: 0.8495 (mmm) cc_final: 0.8205 (mmm) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0645 time to fit residues: 8.5928 Evaluate side-chains 89 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 151 GLN ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.127211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.107523 restraints weight = 7268.922| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.66 r_work: 0.3030 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.0515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.373 5830 Z= 0.329 Angle : 0.736 19.790 7991 Z= 0.417 Chirality : 0.045 0.259 915 Planarity : 0.006 0.060 987 Dihedral : 3.818 15.075 820 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.81 % Allowed : 13.00 % Favored : 85.20 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.98 (0.31), residues: 755 helix: 1.58 (0.27), residues: 381 sheet: 0.27 (0.49), residues: 110 loop : -0.47 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.013 0.002 TYR L 72 PHE 0.015 0.002 PHE A 276 TRP 0.012 0.001 TRP A 541 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00866 ( 5827) covalent geometry : angle 0.73539 ( 7985) SS BOND : bond 0.00197 ( 3) SS BOND : angle 1.50725 ( 6) hydrogen bonds : bond 0.06331 ( 336) hydrogen bonds : angle 5.39691 ( 969) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 125 TYR cc_start: 0.8219 (m-80) cc_final: 0.7860 (m-80) REVERT: A 197 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8508 (mt-10) REVERT: A 320 ASN cc_start: 0.8064 (t0) cc_final: 0.7862 (t0) REVERT: A 380 MET cc_start: 0.8631 (mmm) cc_final: 0.8326 (mmm) outliers start: 10 outliers final: 9 residues processed: 89 average time/residue: 0.0601 time to fit residues: 7.7542 Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 73 optimal weight: 0.0870 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 11 optimal weight: 0.0170 chunk 19 optimal weight: 0.0570 chunk 49 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.2514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.128469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.108807 restraints weight = 7107.372| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.66 r_work: 0.3026 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.373 5830 Z= 0.328 Angle : 0.736 19.785 7991 Z= 0.416 Chirality : 0.045 0.259 915 Planarity : 0.006 0.060 987 Dihedral : 3.818 15.075 820 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.62 % Allowed : 13.18 % Favored : 85.20 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.98 (0.31), residues: 755 helix: 1.58 (0.27), residues: 381 sheet: 0.27 (0.49), residues: 110 loop : -0.47 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.013 0.002 TYR L 72 PHE 0.015 0.002 PHE A 276 TRP 0.012 0.001 TRP A 541 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00866 ( 5827) covalent geometry : angle 0.73531 ( 7985) SS BOND : bond 0.00197 ( 3) SS BOND : angle 1.50710 ( 6) hydrogen bonds : bond 0.06331 ( 336) hydrogen bonds : angle 5.39689 ( 969) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 125 TYR cc_start: 0.8216 (m-80) cc_final: 0.7854 (m-80) REVERT: A 320 ASN cc_start: 0.8058 (t0) cc_final: 0.7853 (t0) REVERT: A 380 MET cc_start: 0.8620 (mmm) cc_final: 0.8316 (mmm) outliers start: 9 outliers final: 9 residues processed: 86 average time/residue: 0.0585 time to fit residues: 7.3307 Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 31 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 32 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: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.128469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.108695 restraints weight = 7183.671| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.68 r_work: 0.3025 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.0577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.373 5830 Z= 0.328 Angle : 0.736 19.785 7991 Z= 0.416 Chirality : 0.045 0.259 915 Planarity : 0.006 0.060 987 Dihedral : 3.818 15.075 820 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.62 % Allowed : 13.18 % Favored : 85.20 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.98 (0.31), residues: 755 helix: 1.58 (0.27), residues: 381 sheet: 0.27 (0.49), residues: 110 loop : -0.47 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.013 0.002 TYR L 72 PHE 0.015 0.002 PHE A 276 TRP 0.012 0.001 TRP A 541 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00866 ( 5827) covalent geometry : angle 0.73531 ( 7985) SS BOND : bond 0.00197 ( 3) SS BOND : angle 1.50710 ( 6) hydrogen bonds : bond 0.06331 ( 336) hydrogen bonds : angle 5.39689 ( 969) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 125 TYR cc_start: 0.8220 (m-80) cc_final: 0.7856 (m-80) REVERT: A 320 ASN cc_start: 0.8059 (t0) cc_final: 0.7854 (t0) REVERT: A 380 MET cc_start: 0.8623 (mmm) cc_final: 0.8317 (mmm) outliers start: 9 outliers final: 9 residues processed: 86 average time/residue: 0.0551 time to fit residues: 6.8954 Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 48 optimal weight: 0.3980 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.128469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.108756 restraints weight = 7277.818| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.67 r_work: 0.3025 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.0577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.373 5830 Z= 0.328 Angle : 0.736 19.785 7991 Z= 0.416 Chirality : 0.045 0.259 915 Planarity : 0.006 0.060 987 Dihedral : 3.818 15.075 820 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.62 % Allowed : 13.18 % Favored : 85.20 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.98 (0.31), residues: 755 helix: 1.58 (0.27), residues: 381 sheet: 0.27 (0.49), residues: 110 loop : -0.47 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.013 0.002 TYR L 72 PHE 0.015 0.002 PHE A 276 TRP 0.012 0.001 TRP A 541 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00866 ( 5827) covalent geometry : angle 0.73531 ( 7985) SS BOND : bond 0.00197 ( 3) SS BOND : angle 1.50710 ( 6) hydrogen bonds : bond 0.06331 ( 336) hydrogen bonds : angle 5.39689 ( 969) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 125 TYR cc_start: 0.8216 (m-80) cc_final: 0.7855 (m-80) REVERT: A 320 ASN cc_start: 0.8059 (t0) cc_final: 0.7855 (t0) REVERT: A 380 MET cc_start: 0.8622 (mmm) cc_final: 0.8319 (mmm) outliers start: 9 outliers final: 9 residues processed: 86 average time/residue: 0.0636 time to fit residues: 7.8654 Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.128469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.108694 restraints weight = 7186.839| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.68 r_work: 0.3024 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.373 5830 Z= 0.328 Angle : 0.736 19.785 7991 Z= 0.416 Chirality : 0.045 0.259 915 Planarity : 0.006 0.060 987 Dihedral : 3.818 15.075 820 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.62 % Allowed : 13.18 % Favored : 85.20 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.98 (0.31), residues: 755 helix: 1.58 (0.27), residues: 381 sheet: 0.27 (0.49), residues: 110 loop : -0.47 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.013 0.002 TYR L 72 PHE 0.015 0.002 PHE A 276 TRP 0.012 0.001 TRP A 541 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00866 ( 5827) covalent geometry : angle 0.73531 ( 7985) SS BOND : bond 0.00197 ( 3) SS BOND : angle 1.50710 ( 6) hydrogen bonds : bond 0.06331 ( 336) hydrogen bonds : angle 5.39689 ( 969) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 125 TYR cc_start: 0.8216 (m-80) cc_final: 0.7854 (m-80) REVERT: A 320 ASN cc_start: 0.8057 (t0) cc_final: 0.7851 (t0) REVERT: A 380 MET cc_start: 0.8623 (mmm) cc_final: 0.8321 (mmm) outliers start: 9 outliers final: 9 residues processed: 86 average time/residue: 0.0562 time to fit residues: 7.0874 Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 45 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 73 optimal weight: 0.0020 chunk 67 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.128469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.108597 restraints weight = 7267.189| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.69 r_work: 0.3023 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.0577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.373 5830 Z= 0.328 Angle : 0.736 19.785 7991 Z= 0.416 Chirality : 0.045 0.259 915 Planarity : 0.006 0.060 987 Dihedral : 3.818 15.075 820 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.62 % Allowed : 13.18 % Favored : 85.20 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.98 (0.31), residues: 755 helix: 1.58 (0.27), residues: 381 sheet: 0.27 (0.49), residues: 110 loop : -0.47 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.013 0.002 TYR L 72 PHE 0.015 0.002 PHE A 276 TRP 0.012 0.001 TRP A 541 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00866 ( 5827) covalent geometry : angle 0.73531 ( 7985) SS BOND : bond 0.00197 ( 3) SS BOND : angle 1.50710 ( 6) hydrogen bonds : bond 0.06331 ( 336) hydrogen bonds : angle 5.39689 ( 969) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 125 TYR cc_start: 0.8217 (m-80) cc_final: 0.7854 (m-80) REVERT: A 320 ASN cc_start: 0.8058 (t0) cc_final: 0.7853 (t0) REVERT: A 380 MET cc_start: 0.8622 (mmm) cc_final: 0.8320 (mmm) outliers start: 9 outliers final: 9 residues processed: 86 average time/residue: 0.0603 time to fit residues: 7.5421 Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 6 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 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 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.128469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.108786 restraints weight = 7152.127| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.66 r_work: 0.3026 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.373 5830 Z= 0.328 Angle : 0.736 19.785 7991 Z= 0.416 Chirality : 0.045 0.259 915 Planarity : 0.006 0.060 987 Dihedral : 3.818 15.075 820 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.62 % Allowed : 13.18 % Favored : 85.20 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.98 (0.31), residues: 755 helix: 1.58 (0.27), residues: 381 sheet: 0.27 (0.49), residues: 110 loop : -0.47 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.013 0.002 TYR L 72 PHE 0.015 0.002 PHE A 276 TRP 0.012 0.001 TRP A 541 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00866 ( 5827) covalent geometry : angle 0.73531 ( 7985) SS BOND : bond 0.00197 ( 3) SS BOND : angle 1.50710 ( 6) hydrogen bonds : bond 0.06331 ( 336) hydrogen bonds : angle 5.39689 ( 969) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 125 TYR cc_start: 0.8220 (m-80) cc_final: 0.7856 (m-80) REVERT: A 320 ASN cc_start: 0.8060 (t0) cc_final: 0.7856 (t0) REVERT: A 380 MET cc_start: 0.8623 (mmm) cc_final: 0.8318 (mmm) outliers start: 9 outliers final: 9 residues processed: 86 average time/residue: 0.0598 time to fit residues: 7.4778 Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 0.0070 chunk 73 optimal weight: 0.0670 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.128469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.108705 restraints weight = 7214.269| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.68 r_work: 0.3025 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.0577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.373 5830 Z= 0.328 Angle : 0.736 19.785 7991 Z= 0.416 Chirality : 0.045 0.259 915 Planarity : 0.006 0.060 987 Dihedral : 3.818 15.075 820 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.62 % Allowed : 13.18 % Favored : 85.20 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.98 (0.31), residues: 755 helix: 1.58 (0.27), residues: 381 sheet: 0.27 (0.49), residues: 110 loop : -0.47 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.013 0.002 TYR L 72 PHE 0.015 0.002 PHE A 276 TRP 0.012 0.001 TRP A 541 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00866 ( 5827) covalent geometry : angle 0.73531 ( 7985) SS BOND : bond 0.00197 ( 3) SS BOND : angle 1.50710 ( 6) hydrogen bonds : bond 0.06331 ( 336) hydrogen bonds : angle 5.39689 ( 969) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 125 TYR cc_start: 0.8217 (m-80) cc_final: 0.7854 (m-80) REVERT: A 320 ASN cc_start: 0.8056 (t0) cc_final: 0.7852 (t0) REVERT: A 380 MET cc_start: 0.8621 (mmm) cc_final: 0.8315 (mmm) outliers start: 9 outliers final: 9 residues processed: 86 average time/residue: 0.0571 time to fit residues: 7.1659 Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 9 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.128469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.108578 restraints weight = 7293.275| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.70 r_work: 0.3022 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.373 5830 Z= 0.328 Angle : 0.736 19.785 7991 Z= 0.416 Chirality : 0.045 0.259 915 Planarity : 0.006 0.060 987 Dihedral : 3.818 15.075 820 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.62 % Allowed : 13.18 % Favored : 85.20 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.98 (0.31), residues: 755 helix: 1.58 (0.27), residues: 381 sheet: 0.27 (0.49), residues: 110 loop : -0.47 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.013 0.002 TYR L 72 PHE 0.015 0.002 PHE A 276 TRP 0.012 0.001 TRP A 541 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00866 ( 5827) covalent geometry : angle 0.73531 ( 7985) SS BOND : bond 0.00197 ( 3) SS BOND : angle 1.50710 ( 6) hydrogen bonds : bond 0.06331 ( 336) hydrogen bonds : angle 5.39689 ( 969) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 125 TYR cc_start: 0.8219 (m-80) cc_final: 0.7858 (m-80) REVERT: A 320 ASN cc_start: 0.8058 (t0) cc_final: 0.7852 (t0) REVERT: A 380 MET cc_start: 0.8626 (mmm) cc_final: 0.8323 (mmm) outliers start: 9 outliers final: 9 residues processed: 86 average time/residue: 0.0510 time to fit residues: 6.4567 Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.128469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.108788 restraints weight = 7150.175| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.66 r_work: 0.3026 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.0577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.373 5830 Z= 0.328 Angle : 0.736 19.785 7991 Z= 0.416 Chirality : 0.045 0.259 915 Planarity : 0.006 0.060 987 Dihedral : 3.818 15.075 820 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.62 % Allowed : 13.18 % Favored : 85.20 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.98 (0.31), residues: 755 helix: 1.58 (0.27), residues: 381 sheet: 0.27 (0.49), residues: 110 loop : -0.47 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.013 0.002 TYR L 72 PHE 0.015 0.002 PHE A 276 TRP 0.012 0.001 TRP A 541 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00866 ( 5827) covalent geometry : angle 0.73531 ( 7985) SS BOND : bond 0.00197 ( 3) SS BOND : angle 1.50710 ( 6) hydrogen bonds : bond 0.06331 ( 336) hydrogen bonds : angle 5.39689 ( 969) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1405.11 seconds wall clock time: 24 minutes 52.31 seconds (1492.31 seconds total)