Starting phenix.real_space_refine on Sun Jul 27 06:18:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j9z_61285/07_2025/9j9z_61285.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j9z_61285/07_2025/9j9z_61285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j9z_61285/07_2025/9j9z_61285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j9z_61285/07_2025/9j9z_61285.map" model { file = "/net/cci-nas-00/data/ceres_data/9j9z_61285/07_2025/9j9z_61285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j9z_61285/07_2025/9j9z_61285.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 5682 2.51 5 N 1454 2.21 5 O 1644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8820 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1682 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 211} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1624 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 4560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4560 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 19, 'TRANS': 569} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'2YP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.80, per 1000 atoms: 0.88 Number of scatterers: 8820 At special positions: 0 Unit cell: (90.2656, 102.254, 135.398, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1644 8.00 N 1454 7.00 C 5682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " 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: 2.51 Conformation dependent library (CDL) restraints added in 1.0 seconds 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 11 sheets defined 47.5% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.698A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.600A pdb=" N TRP H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 172 No H-bonds generated for 'chain 'H' and resid 170 through 172' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.700A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 98 Processing helix chain 'L' and resid 126 through 129 Processing helix chain 'L' and resid 185 through 189 Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 11 through 32 removed outlier: 3.830A pdb=" N ALA A 15 " --> pdb=" O GLN A 11 " (cutoff:3.500A) Proline residue: A 27 - end of helix removed outlier: 3.750A pdb=" N LEU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 42 Processing helix chain 'A' and resid 53 through 61 removed outlier: 3.780A pdb=" N GLN A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 72 removed outlier: 4.101A pdb=" N TRP A 65 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Proline residue: A 67 - end of helix Processing helix chain 'A' and resid 78 through 101 Processing helix chain 'A' and resid 109 through 136 Processing helix chain 'A' and resid 140 through 162 removed outlier: 3.507A pdb=" N LEU A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 171 through 194 removed outlier: 4.037A pdb=" N GLY A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Proline residue: A 186 - end of helix Processing helix chain 'A' and resid 200 through 216 Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.770A pdb=" N LYS A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 279 Processing helix chain 'A' and resid 282 through 297 Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.866A pdb=" N LYS A 302 " --> pdb=" O TYR A 299 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR A 303 " --> pdb=" O ILE A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 299 through 303' Processing helix chain 'A' and resid 311 through 324 Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 326 through 337 Processing helix chain 'A' and resid 338 through 354 removed outlier: 3.905A pdb=" N LEU A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N THR A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N THR A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 389 removed outlier: 3.738A pdb=" N TRP A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 415 Processing helix chain 'A' and resid 418 through 448 Processing helix chain 'A' and resid 452 through 483 removed outlier: 3.632A pdb=" N GLN A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 483 through 505 Proline residue: A 497 - end of helix Processing helix chain 'A' and resid 505 through 516 Processing helix chain 'A' and resid 526 through 555 Processing helix chain 'A' and resid 561 through 593 Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.666A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 136 through 138 removed outlier: 3.615A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL H 198 " --> pdb=" O ALA H 150 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL H 195 " --> pdb=" O HIS H 178 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 165 through 168 Processing sheet with id=AA5, first strand: chain 'H' and resid 183 through 184 removed outlier: 4.321A pdb=" N SER H 191 " --> pdb=" O VAL H 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.719A pdb=" N THR K 78 " --> pdb=" O ASP K 73 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP K 73 " --> pdb=" O THR K 78 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.586A pdb=" N THR K 118 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 20 through 25 Processing sheet with id=AA9, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.502A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 116 through 120 Processing sheet with id=AB2, first strand: chain 'L' and resid 147 through 150 508 hydrogen bonds defined for protein. 1434 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: 2.83 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2694 1.34 - 1.46: 1672 1.46 - 1.58: 4600 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 9030 Sorted by residual: bond pdb=" N ARG A 308 " pdb=" CA ARG A 308 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.28e-02 6.10e+03 6.97e+00 bond pdb=" N TRP A 109 " pdb=" CA TRP A 109 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.81e+00 bond pdb=" C LEU A 304 " pdb=" N GLY A 305 " ideal model delta sigma weight residual 1.331 1.297 0.034 1.46e-02 4.69e+03 5.35e+00 bond pdb=" CA PRO L 121 " pdb=" C PRO L 121 " ideal model delta sigma weight residual 1.514 1.502 0.012 5.50e-03 3.31e+04 4.90e+00 bond pdb=" CG LEU L 93 " pdb=" CD1 LEU L 93 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.71e+00 ... (remaining 9025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 11848 1.66 - 3.32: 347 3.32 - 4.98: 70 4.98 - 6.64: 22 6.64 - 8.30: 3 Bond angle restraints: 12290 Sorted by residual: angle pdb=" N GLU A 311 " pdb=" CA GLU A 311 " pdb=" C GLU A 311 " ideal model delta sigma weight residual 111.28 106.74 4.54 1.09e+00 8.42e-01 1.73e+01 angle pdb=" C LEU A 310 " pdb=" N GLU A 311 " pdb=" CA GLU A 311 " ideal model delta sigma weight residual 120.28 115.97 4.31 1.34e+00 5.57e-01 1.04e+01 angle pdb=" C ASN A 449 " pdb=" N LYS A 450 " pdb=" CA LYS A 450 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 1.00e+01 angle pdb=" CG MET A 69 " pdb=" SD MET A 69 " pdb=" CE MET A 69 " ideal model delta sigma weight residual 100.90 94.21 6.69 2.20e+00 2.07e-01 9.24e+00 angle pdb=" N PRO A 197 " pdb=" CA PRO A 197 " pdb=" C PRO A 197 " ideal model delta sigma weight residual 112.47 106.29 6.18 2.06e+00 2.36e-01 8.99e+00 ... (remaining 12285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.18: 4804 22.18 - 44.37: 438 44.37 - 66.55: 76 66.55 - 88.74: 15 88.74 - 110.92: 8 Dihedral angle restraints: 5341 sinusoidal: 2042 harmonic: 3299 Sorted by residual: dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 96 " pdb=" CB CYS K 96 " ideal model delta sinusoidal sigma weight residual -86.00 -140.68 54.68 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS L 24 " pdb=" SG CYS L 24 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 131.23 -38.23 1 1.00e+01 1.00e-02 2.06e+01 dihedral pdb=" CA TYR A 299 " pdb=" C TYR A 299 " pdb=" N ILE A 300 " pdb=" CA ILE A 300 " ideal model delta harmonic sigma weight residual -180.00 -158.32 -21.68 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 5338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 840 0.030 - 0.060: 388 0.060 - 0.090: 116 0.090 - 0.120: 57 0.120 - 0.150: 5 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CA LEU A 310 " pdb=" N LEU A 310 " pdb=" C LEU A 310 " pdb=" CB LEU A 310 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CA VAL A 306 " pdb=" N VAL A 306 " pdb=" C VAL A 306 " pdb=" CB VAL A 306 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA SER A 53 " pdb=" N SER A 53 " pdb=" C SER A 53 " pdb=" CB SER A 53 " 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 1403 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 582 " 0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ILE A 582 " -0.057 2.00e-02 2.50e+03 pdb=" O ILE A 582 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU A 583 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 575 " 0.016 2.00e-02 2.50e+03 3.16e-02 1.00e+01 pdb=" C ALA A 575 " -0.055 2.00e-02 2.50e+03 pdb=" O ALA A 575 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY A 576 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 571 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" C LEU A 571 " -0.054 2.00e-02 2.50e+03 pdb=" O LEU A 571 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE A 572 " 0.018 2.00e-02 2.50e+03 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 11 2.49 - 3.09: 6443 3.09 - 3.70: 13894 3.70 - 4.30: 20130 4.30 - 4.90: 32970 Nonbonded interactions: 73448 Sorted by model distance: nonbonded pdb=" CG2 THR K 91 " pdb=" O VAL K 119 " model vdw 1.888 3.460 nonbonded pdb=" OD1 ASP A 203 " pdb=" NH1 ARG A 308 " model vdw 2.227 3.120 nonbonded pdb=" CG2 THR K 91 " pdb=" N VAL K 119 " model vdw 2.328 3.540 nonbonded pdb=" CG2 THR L 23 " pdb=" OG1 THR L 73 " model vdw 2.340 3.460 nonbonded pdb=" CG1 VAL H 67 " pdb=" CG PHE H 71 " model vdw 2.384 3.680 ... (remaining 73443 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: 7.560 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.800 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:13.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 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 0.072 9035 Z= 0.213 Angle : 0.714 8.297 12300 Z= 0.389 Chirality : 0.040 0.150 1406 Planarity : 0.006 0.072 1539 Dihedral : 17.541 110.923 3216 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.39 % Favored : 95.52 % Rotamer: Outliers : 0.21 % Allowed : 29.80 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.20 (0.25), residues: 1138 helix: 1.07 (0.22), residues: 482 sheet: -0.89 (0.37), residues: 209 loop : -1.00 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 109 HIS 0.004 0.001 HIS H 214 PHE 0.016 0.002 PHE H 180 TYR 0.014 0.002 TYR L 92 ARG 0.045 0.001 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.10522 ( 508) hydrogen bonds : angle 6.96898 ( 1434) SS BOND : bond 0.00319 ( 5) SS BOND : angle 0.92891 ( 10) covalent geometry : bond 0.00391 ( 9030) covalent geometry : angle 0.71422 (12290) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: K 83 MET cc_start: 0.6248 (mpt) cc_final: 0.5806 (mpt) REVERT: A 39 MET cc_start: 0.4650 (mmp) cc_final: 0.3786 (mmp) REVERT: A 166 MET cc_start: 0.7577 (mtp) cc_final: 0.6926 (ptm) REVERT: A 215 ILE cc_start: 0.7054 (mt) cc_final: 0.6448 (mt) REVERT: A 365 MET cc_start: 0.6107 (ptp) cc_final: 0.5710 (ptt) REVERT: A 452 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8164 (p90) REVERT: A 548 MET cc_start: 0.0986 (mmm) cc_final: -0.0261 (ttp) outliers start: 2 outliers final: 1 residues processed: 126 average time/residue: 0.8434 time to fit residues: 117.1929 Evaluate side-chains 105 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain A residue 452 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN H 214 HIS K 39 GLN K 82 GLN L 39 GLN L 191 HIS A 10 GLN A 204 ASN ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.246646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.210618 restraints weight = 10147.508| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 2.03 r_work: 0.4190 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.4063 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9035 Z= 0.210 Angle : 0.694 10.470 12300 Z= 0.345 Chirality : 0.044 0.240 1406 Planarity : 0.005 0.056 1539 Dihedral : 9.081 80.626 1299 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 6.00 % Allowed : 26.90 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.25), residues: 1138 helix: 1.29 (0.23), residues: 484 sheet: -1.10 (0.34), residues: 228 loop : -1.06 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 328 HIS 0.002 0.001 HIS A 523 PHE 0.010 0.002 PHE A 561 TYR 0.017 0.002 TYR A 303 ARG 0.006 0.001 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 508) hydrogen bonds : angle 5.68950 ( 1434) SS BOND : bond 0.00470 ( 5) SS BOND : angle 1.19610 ( 10) covalent geometry : bond 0.00467 ( 9030) covalent geometry : angle 0.69346 (12290) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 116 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: H 9 GLU cc_start: 0.7618 (mp0) cc_final: 0.7418 (mt-10) REVERT: K 82 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7284 (mm-40) REVERT: L 110 ARG cc_start: 0.5852 (ttt-90) cc_final: 0.4651 (ttm110) REVERT: A 39 MET cc_start: 0.4937 (mmp) cc_final: 0.3843 (mmp) REVERT: A 166 MET cc_start: 0.7734 (mtp) cc_final: 0.6951 (ptm) REVERT: A 215 ILE cc_start: 0.7210 (mt) cc_final: 0.6358 (mt) REVERT: A 365 MET cc_start: 0.6066 (OUTLIER) cc_final: 0.5558 (ptm) REVERT: A 419 LEU cc_start: 0.5486 (OUTLIER) cc_final: 0.5206 (tp) REVERT: A 422 MET cc_start: 0.5964 (OUTLIER) cc_final: 0.5370 (tmm) REVERT: A 452 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8127 (p90) REVERT: A 471 VAL cc_start: 0.6929 (OUTLIER) cc_final: 0.6474 (m) REVERT: A 548 MET cc_start: 0.0772 (mmm) cc_final: -0.0515 (mtm) outliers start: 56 outliers final: 23 residues processed: 157 average time/residue: 0.8656 time to fit residues: 150.1754 Evaluate side-chains 127 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 582 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 46 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 39 GLN K 82 GLN ** A 513 GLN ** 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 = 0.4692 r_free = 0.4692 target = 0.248723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.212351 restraints weight = 10343.626| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 2.08 r_work: 0.4211 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.4079 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9035 Z= 0.144 Angle : 0.633 8.670 12300 Z= 0.310 Chirality : 0.041 0.207 1406 Planarity : 0.004 0.058 1539 Dihedral : 8.261 77.444 1299 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 5.25 % Allowed : 27.55 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.06 (0.26), residues: 1138 helix: 1.44 (0.23), residues: 489 sheet: -0.94 (0.35), residues: 228 loop : -1.00 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 65 HIS 0.003 0.001 HIS H 38 PHE 0.026 0.001 PHE H 180 TYR 0.021 0.001 TYR L 142 ARG 0.007 0.000 ARG A 354 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 508) hydrogen bonds : angle 5.33274 ( 1434) SS BOND : bond 0.00358 ( 5) SS BOND : angle 0.83297 ( 10) covalent geometry : bond 0.00311 ( 9030) covalent geometry : angle 0.63282 (12290) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 114 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: H 191 SER cc_start: 0.4303 (OUTLIER) cc_final: 0.3346 (p) REVERT: K 82 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7376 (tm-30) REVERT: L 46 LYS cc_start: 0.8407 (mttp) cc_final: 0.8184 (mptt) REVERT: L 110 ARG cc_start: 0.5551 (ttt-90) cc_final: 0.4310 (ttm110) REVERT: A 39 MET cc_start: 0.4965 (mmp) cc_final: 0.3994 (mmp) REVERT: A 166 MET cc_start: 0.7646 (mtp) cc_final: 0.6797 (ptm) REVERT: A 215 ILE cc_start: 0.6982 (mt) cc_final: 0.6023 (mt) REVERT: A 365 MET cc_start: 0.6044 (ptp) cc_final: 0.5520 (ptm) REVERT: A 419 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.5184 (tp) REVERT: A 452 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8126 (p90) REVERT: A 530 PHE cc_start: 0.6185 (OUTLIER) cc_final: 0.5943 (m-10) REVERT: A 548 MET cc_start: 0.0655 (mmm) cc_final: -0.0591 (mtm) REVERT: A 589 ARG cc_start: 0.5595 (OUTLIER) cc_final: 0.4205 (ttm170) outliers start: 49 outliers final: 25 residues processed: 154 average time/residue: 1.0214 time to fit residues: 175.1188 Evaluate side-chains 128 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 589 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 82 GLN ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.249299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.212776 restraints weight = 10130.640| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 2.13 r_work: 0.4198 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9035 Z= 0.153 Angle : 0.636 9.251 12300 Z= 0.311 Chirality : 0.041 0.180 1406 Planarity : 0.004 0.058 1539 Dihedral : 7.479 75.992 1299 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 6.00 % Allowed : 27.22 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.12 (0.26), residues: 1138 helix: 1.55 (0.23), residues: 487 sheet: -0.92 (0.35), residues: 231 loop : -1.02 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 65 HIS 0.003 0.001 HIS H 38 PHE 0.011 0.001 PHE A 22 TYR 0.017 0.001 TYR L 92 ARG 0.003 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 508) hydrogen bonds : angle 5.21661 ( 1434) SS BOND : bond 0.00285 ( 5) SS BOND : angle 0.91238 ( 10) covalent geometry : bond 0.00336 ( 9030) covalent geometry : angle 0.63596 (12290) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 107 time to evaluate : 1.526 Fit side-chains revert: symmetry clash REVERT: H 191 SER cc_start: 0.3378 (OUTLIER) cc_final: 0.2587 (p) REVERT: L 46 LYS cc_start: 0.8312 (mttp) cc_final: 0.8071 (mptt) REVERT: L 110 ARG cc_start: 0.5340 (ttt-90) cc_final: 0.4313 (ttm110) REVERT: A 39 MET cc_start: 0.4877 (mmp) cc_final: 0.3996 (mmp) REVERT: A 164 LEU cc_start: 0.5646 (OUTLIER) cc_final: 0.5238 (pp) REVERT: A 166 MET cc_start: 0.7620 (mtp) cc_final: 0.7273 (mtm) REVERT: A 215 ILE cc_start: 0.6890 (OUTLIER) cc_final: 0.5964 (mt) REVERT: A 296 ARG cc_start: 0.1971 (OUTLIER) cc_final: 0.1470 (mmt180) REVERT: A 365 MET cc_start: 0.6051 (ptp) cc_final: 0.5536 (ptm) REVERT: A 419 LEU cc_start: 0.5382 (OUTLIER) cc_final: 0.5071 (tp) REVERT: A 420 MET cc_start: 0.5498 (OUTLIER) cc_final: 0.5079 (mmt) REVERT: A 422 MET cc_start: 0.6065 (OUTLIER) cc_final: 0.5129 (tmm) REVERT: A 471 VAL cc_start: 0.7072 (OUTLIER) cc_final: 0.6646 (m) REVERT: A 548 MET cc_start: 0.0634 (mmm) cc_final: -0.0626 (mtm) REVERT: A 589 ARG cc_start: 0.5671 (OUTLIER) cc_final: 0.4229 (ttm170) outliers start: 56 outliers final: 31 residues processed: 148 average time/residue: 1.1421 time to fit residues: 185.3743 Evaluate side-chains 142 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 589 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 18 optimal weight: 0.0470 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 35 optimal weight: 0.0670 chunk 90 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** 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 = 0.4700 r_free = 0.4700 target = 0.249925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.213893 restraints weight = 10133.515| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 2.09 r_work: 0.4209 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9035 Z= 0.137 Angle : 0.619 9.199 12300 Z= 0.302 Chirality : 0.040 0.189 1406 Planarity : 0.004 0.058 1539 Dihedral : 6.817 74.076 1299 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 5.79 % Allowed : 27.22 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.23 (0.26), residues: 1138 helix: 1.66 (0.23), residues: 488 sheet: -0.86 (0.35), residues: 226 loop : -1.00 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 65 HIS 0.003 0.001 HIS H 38 PHE 0.027 0.001 PHE H 180 TYR 0.016 0.001 TYR L 92 ARG 0.005 0.000 ARG A 354 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 508) hydrogen bonds : angle 5.05479 ( 1434) SS BOND : bond 0.00241 ( 5) SS BOND : angle 0.81867 ( 10) covalent geometry : bond 0.00300 ( 9030) covalent geometry : angle 0.61861 (12290) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 107 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: H 191 SER cc_start: 0.3240 (OUTLIER) cc_final: 0.2472 (p) REVERT: L 46 LYS cc_start: 0.8302 (mttp) cc_final: 0.8054 (mptt) REVERT: A 39 MET cc_start: 0.4833 (mmp) cc_final: 0.4037 (mmp) REVERT: A 164 LEU cc_start: 0.5664 (OUTLIER) cc_final: 0.5233 (pp) REVERT: A 166 MET cc_start: 0.7632 (mtp) cc_final: 0.7300 (mtm) REVERT: A 215 ILE cc_start: 0.6840 (OUTLIER) cc_final: 0.5916 (mt) REVERT: A 296 ARG cc_start: 0.1958 (OUTLIER) cc_final: 0.1464 (mmt180) REVERT: A 365 MET cc_start: 0.6013 (ptp) cc_final: 0.5520 (ptm) REVERT: A 419 LEU cc_start: 0.5286 (OUTLIER) cc_final: 0.5021 (tp) REVERT: A 420 MET cc_start: 0.5455 (OUTLIER) cc_final: 0.5018 (mmt) REVERT: A 452 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8344 (p90) REVERT: A 471 VAL cc_start: 0.7049 (OUTLIER) cc_final: 0.6643 (m) REVERT: A 548 MET cc_start: 0.0503 (mmm) cc_final: -0.0741 (mtm) REVERT: A 589 ARG cc_start: 0.5614 (OUTLIER) cc_final: 0.4168 (ttm170) outliers start: 54 outliers final: 29 residues processed: 149 average time/residue: 0.7838 time to fit residues: 129.3955 Evaluate side-chains 135 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 589 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 89 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 178 HIS K 65 GLN A 278 ASN ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.244310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.206404 restraints weight = 10225.892| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 2.19 r_work: 0.4136 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9035 Z= 0.221 Angle : 0.691 9.777 12300 Z= 0.341 Chirality : 0.043 0.164 1406 Planarity : 0.004 0.056 1539 Dihedral : 6.309 76.000 1299 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.89 % Allowed : 28.19 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.07 (0.26), residues: 1138 helix: 1.47 (0.23), residues: 488 sheet: -1.11 (0.35), residues: 229 loop : -1.17 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 102 HIS 0.003 0.001 HIS H 38 PHE 0.014 0.002 PHE A 358 TYR 0.018 0.002 TYR L 92 ARG 0.009 0.001 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 508) hydrogen bonds : angle 5.29399 ( 1434) SS BOND : bond 0.00657 ( 5) SS BOND : angle 1.50246 ( 10) covalent geometry : bond 0.00496 ( 9030) covalent geometry : angle 0.69017 (12290) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 112 time to evaluate : 0.916 Fit side-chains REVERT: H 41 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7968 (ttm170) REVERT: H 191 SER cc_start: 0.3726 (OUTLIER) cc_final: 0.2976 (p) REVERT: H 203 LEU cc_start: -0.1399 (OUTLIER) cc_final: -0.1793 (mt) REVERT: L 46 LYS cc_start: 0.8331 (mttp) cc_final: 0.8072 (mptt) REVERT: L 110 ARG cc_start: 0.5822 (ttt-90) cc_final: 0.4575 (ttm110) REVERT: A 39 MET cc_start: 0.5067 (mmp) cc_final: 0.4616 (mmp) REVERT: A 166 MET cc_start: 0.7587 (mtp) cc_final: 0.7252 (mtm) REVERT: A 215 ILE cc_start: 0.7038 (mt) cc_final: 0.6130 (mt) REVERT: A 296 ARG cc_start: 0.1974 (OUTLIER) cc_final: 0.1400 (mmt180) REVERT: A 365 MET cc_start: 0.5940 (ptp) cc_final: 0.5441 (ptm) REVERT: A 419 LEU cc_start: 0.5356 (OUTLIER) cc_final: 0.5054 (tp) REVERT: A 420 MET cc_start: 0.5542 (OUTLIER) cc_final: 0.5094 (mmt) REVERT: A 422 MET cc_start: 0.6130 (OUTLIER) cc_final: 0.5188 (tmm) REVERT: A 452 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8189 (p90) REVERT: A 548 MET cc_start: 0.0463 (mmm) cc_final: -0.0791 (mtm) REVERT: A 589 ARG cc_start: 0.5540 (OUTLIER) cc_final: 0.4169 (ttm170) outliers start: 55 outliers final: 34 residues processed: 157 average time/residue: 0.8722 time to fit residues: 149.6627 Evaluate side-chains 147 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 104 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 589 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 0.7980 chunk 43 optimal weight: 0.0670 chunk 31 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 110 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** 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 = 0.4659 r_free = 0.4659 target = 0.245569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.209718 restraints weight = 10238.437| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 2.14 r_work: 0.4176 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9035 Z= 0.144 Angle : 0.652 11.245 12300 Z= 0.318 Chirality : 0.041 0.157 1406 Planarity : 0.004 0.059 1539 Dihedral : 5.997 75.807 1299 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 5.47 % Allowed : 29.47 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.09 (0.26), residues: 1138 helix: 1.60 (0.23), residues: 488 sheet: -1.01 (0.35), residues: 229 loop : -1.10 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 65 HIS 0.008 0.001 HIS H 178 PHE 0.028 0.001 PHE H 180 TYR 0.023 0.002 TYR L 142 ARG 0.007 0.000 ARG A 354 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 508) hydrogen bonds : angle 5.09403 ( 1434) SS BOND : bond 0.00346 ( 5) SS BOND : angle 1.02889 ( 10) covalent geometry : bond 0.00315 ( 9030) covalent geometry : angle 0.65193 (12290) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 105 time to evaluate : 1.016 Fit side-chains REVERT: H 191 SER cc_start: 0.3514 (OUTLIER) cc_final: 0.2818 (p) REVERT: L 46 LYS cc_start: 0.8285 (mttp) cc_final: 0.8022 (mptt) REVERT: L 110 ARG cc_start: 0.5483 (ttt-90) cc_final: 0.4416 (ttm110) REVERT: A 166 MET cc_start: 0.7553 (mtp) cc_final: 0.7241 (mtm) REVERT: A 215 ILE cc_start: 0.6823 (mt) cc_final: 0.5928 (mt) REVERT: A 296 ARG cc_start: 0.1855 (OUTLIER) cc_final: 0.1387 (mmt180) REVERT: A 365 MET cc_start: 0.6042 (ptp) cc_final: 0.5506 (ptm) REVERT: A 419 LEU cc_start: 0.5281 (OUTLIER) cc_final: 0.5010 (tp) REVERT: A 420 MET cc_start: 0.5467 (OUTLIER) cc_final: 0.5000 (mmt) REVERT: A 452 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8175 (p90) REVERT: A 471 VAL cc_start: 0.6988 (OUTLIER) cc_final: 0.6587 (m) REVERT: A 548 MET cc_start: 0.0471 (mmm) cc_final: -0.0802 (mtm) REVERT: A 579 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6740 (pt) REVERT: A 589 ARG cc_start: 0.5566 (mtm180) cc_final: 0.5104 (mtm180) outliers start: 51 outliers final: 28 residues processed: 149 average time/residue: 0.7171 time to fit residues: 119.7003 Evaluate side-chains 135 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 579 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 99 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 2 optimal weight: 0.0570 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.245800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.209936 restraints weight = 10253.356| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 2.14 r_work: 0.4179 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9035 Z= 0.148 Angle : 0.662 12.516 12300 Z= 0.319 Chirality : 0.042 0.400 1406 Planarity : 0.004 0.058 1539 Dihedral : 5.930 76.999 1299 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.14 % Allowed : 29.90 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.10 (0.26), residues: 1138 helix: 1.59 (0.23), residues: 488 sheet: -0.99 (0.34), residues: 230 loop : -1.07 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 65 HIS 0.006 0.001 HIS H 178 PHE 0.012 0.001 PHE A 22 TYR 0.019 0.002 TYR L 194 ARG 0.005 0.000 ARG H 41 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 508) hydrogen bonds : angle 5.04853 ( 1434) SS BOND : bond 0.00317 ( 5) SS BOND : angle 1.02973 ( 10) covalent geometry : bond 0.00327 ( 9030) covalent geometry : angle 0.66199 (12290) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 106 time to evaluate : 1.096 Fit side-chains REVERT: H 191 SER cc_start: 0.3462 (OUTLIER) cc_final: 0.2642 (t) REVERT: H 203 LEU cc_start: -0.1380 (OUTLIER) cc_final: -0.1778 (mt) REVERT: L 46 LYS cc_start: 0.8288 (mttp) cc_final: 0.8024 (mptt) REVERT: L 110 ARG cc_start: 0.5466 (ttt-90) cc_final: 0.4398 (ttm110) REVERT: A 166 MET cc_start: 0.7506 (mtp) cc_final: 0.7249 (mtm) REVERT: A 215 ILE cc_start: 0.6841 (OUTLIER) cc_final: 0.5991 (mt) REVERT: A 296 ARG cc_start: 0.1884 (OUTLIER) cc_final: 0.1421 (mmt180) REVERT: A 365 MET cc_start: 0.6017 (ptp) cc_final: 0.5466 (ptm) REVERT: A 419 LEU cc_start: 0.5263 (OUTLIER) cc_final: 0.4999 (tp) REVERT: A 420 MET cc_start: 0.5417 (OUTLIER) cc_final: 0.4904 (mtt) REVERT: A 452 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8187 (p90) REVERT: A 548 MET cc_start: 0.0393 (mmm) cc_final: -0.0842 (mtm) REVERT: A 589 ARG cc_start: 0.5547 (OUTLIER) cc_final: 0.5097 (mtm180) outliers start: 48 outliers final: 32 residues processed: 145 average time/residue: 0.7806 time to fit residues: 125.5778 Evaluate side-chains 139 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 589 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 102 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** 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 = 0.4640 r_free = 0.4640 target = 0.243743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.206362 restraints weight = 10299.785| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 2.37 r_work: 0.4137 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9035 Z= 0.208 Angle : 0.721 12.345 12300 Z= 0.348 Chirality : 0.044 0.383 1406 Planarity : 0.004 0.057 1539 Dihedral : 6.191 82.860 1299 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 5.25 % Allowed : 30.01 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.10 (0.25), residues: 1138 helix: 1.43 (0.23), residues: 489 sheet: -1.04 (0.35), residues: 216 loop : -1.24 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 102 HIS 0.006 0.001 HIS H 178 PHE 0.029 0.002 PHE H 180 TYR 0.029 0.002 TYR A 511 ARG 0.006 0.001 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 508) hydrogen bonds : angle 5.22256 ( 1434) SS BOND : bond 0.00501 ( 5) SS BOND : angle 1.35446 ( 10) covalent geometry : bond 0.00469 ( 9030) covalent geometry : angle 0.72001 (12290) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 106 time to evaluate : 0.906 Fit side-chains REVERT: H 191 SER cc_start: 0.3525 (OUTLIER) cc_final: 0.2758 (t) REVERT: H 194 SER cc_start: 0.7543 (OUTLIER) cc_final: 0.7194 (p) REVERT: H 203 LEU cc_start: -0.1309 (OUTLIER) cc_final: -0.1701 (mt) REVERT: L 110 ARG cc_start: 0.5728 (ttt-90) cc_final: 0.4554 (ttm110) REVERT: A 166 MET cc_start: 0.7545 (mtp) cc_final: 0.7293 (mtm) REVERT: A 215 ILE cc_start: 0.6905 (mt) cc_final: 0.6053 (mt) REVERT: A 296 ARG cc_start: 0.1820 (OUTLIER) cc_final: 0.1402 (mmt180) REVERT: A 365 MET cc_start: 0.5986 (ptp) cc_final: 0.5452 (ptm) REVERT: A 419 LEU cc_start: 0.5338 (OUTLIER) cc_final: 0.5090 (tp) REVERT: A 466 VAL cc_start: 0.7519 (OUTLIER) cc_final: 0.7262 (t) REVERT: A 520 MET cc_start: 0.7094 (tpp) cc_final: 0.6790 (tpp) REVERT: A 528 TYR cc_start: 0.7095 (m-80) cc_final: 0.6851 (m-80) REVERT: A 548 MET cc_start: 0.0301 (mmm) cc_final: -0.0861 (mtm) REVERT: A 589 ARG cc_start: 0.5459 (OUTLIER) cc_final: 0.5018 (mtm180) outliers start: 49 outliers final: 32 residues processed: 149 average time/residue: 0.7866 time to fit residues: 129.6883 Evaluate side-chains 140 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 101 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 589 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 8 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** 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 = 0.4657 r_free = 0.4657 target = 0.245593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.208941 restraints weight = 10229.948| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 2.19 r_work: 0.4162 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9035 Z= 0.165 Angle : 0.708 12.832 12300 Z= 0.341 Chirality : 0.043 0.349 1406 Planarity : 0.005 0.087 1539 Dihedral : 6.125 82.467 1299 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.18 % Allowed : 30.98 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.08 (0.25), residues: 1138 helix: 1.45 (0.23), residues: 489 sheet: -1.00 (0.35), residues: 219 loop : -1.25 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 65 HIS 0.006 0.001 HIS A 523 PHE 0.009 0.001 PHE A 358 TYR 0.026 0.002 TYR A 152 ARG 0.012 0.001 ARG A 521 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 508) hydrogen bonds : angle 5.15294 ( 1434) SS BOND : bond 0.00367 ( 5) SS BOND : angle 1.15744 ( 10) covalent geometry : bond 0.00368 ( 9030) covalent geometry : angle 0.70714 (12290) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 1.703 Fit side-chains REVERT: H 191 SER cc_start: 0.3541 (OUTLIER) cc_final: 0.2813 (p) REVERT: H 194 SER cc_start: 0.7511 (OUTLIER) cc_final: 0.7256 (p) REVERT: H 203 LEU cc_start: -0.1268 (OUTLIER) cc_final: -0.1669 (mt) REVERT: L 110 ARG cc_start: 0.5573 (ttt-90) cc_final: 0.4461 (ttm110) REVERT: A 166 MET cc_start: 0.7552 (mtp) cc_final: 0.7215 (mtm) REVERT: A 215 ILE cc_start: 0.6870 (mt) cc_final: 0.6048 (mt) REVERT: A 296 ARG cc_start: 0.1894 (OUTLIER) cc_final: 0.1464 (mmt180) REVERT: A 365 MET cc_start: 0.6078 (ptp) cc_final: 0.5528 (ptm) REVERT: A 419 LEU cc_start: 0.5343 (OUTLIER) cc_final: 0.5063 (tp) REVERT: A 466 VAL cc_start: 0.7441 (OUTLIER) cc_final: 0.7189 (t) REVERT: A 548 MET cc_start: 0.0316 (mmm) cc_final: -0.0862 (mtm) REVERT: A 589 ARG cc_start: 0.5493 (mtm180) cc_final: 0.5042 (mtm180) outliers start: 39 outliers final: 31 residues processed: 137 average time/residue: 1.1250 time to fit residues: 170.7570 Evaluate side-chains 138 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 71 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 0.0040 chunk 22 optimal weight: 9.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** 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 = 0.4665 r_free = 0.4665 target = 0.246666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.210530 restraints weight = 10214.763| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 2.15 r_work: 0.4173 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9035 Z= 0.151 Angle : 0.692 13.056 12300 Z= 0.331 Chirality : 0.042 0.324 1406 Planarity : 0.005 0.071 1539 Dihedral : 6.046 82.417 1299 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.39 % Allowed : 30.76 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.04 (0.26), residues: 1138 helix: 1.52 (0.23), residues: 489 sheet: -1.08 (0.34), residues: 227 loop : -1.22 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 65 HIS 0.003 0.001 HIS A 523 PHE 0.030 0.001 PHE H 180 TYR 0.024 0.002 TYR A 152 ARG 0.009 0.001 ARG A 521 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 508) hydrogen bonds : angle 5.06064 ( 1434) SS BOND : bond 0.00356 ( 5) SS BOND : angle 1.04889 ( 10) covalent geometry : bond 0.00337 ( 9030) covalent geometry : angle 0.69158 (12290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7057.13 seconds wall clock time: 127 minutes 51.87 seconds (7671.87 seconds total)