Starting phenix.real_space_refine on Wed Sep 17 14:30:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j9z_61285/09_2025/9j9z_61285.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j9z_61285/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9j9z_61285/09_2025/9j9z_61285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j9z_61285/09_2025/9j9z_61285.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j9z_61285/09_2025/9j9z_61285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j9z_61285/09_2025/9j9z_61285.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.98, per 1000 atoms: 0.22 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: 0.84 Conformation dependent library (CDL) restraints added in 331.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.31 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: 1.45 Time building geometry restraints manager: 1.06 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: 7.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.250 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.720 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.045 0.001 ARG A 108 TYR 0.014 0.002 TYR L 92 PHE 0.016 0.002 PHE H 180 TRP 0.013 0.001 TRP A 109 HIS 0.004 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 9030) covalent geometry : angle 0.71422 (12290) SS BOND : bond 0.00319 ( 5) SS BOND : angle 0.92891 ( 10) hydrogen bonds : bond 0.10522 ( 508) hydrogen bonds : angle 6.96898 ( 1434) *********************** 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 : 0.359 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: 0.5709 (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: 0.4141 time to fit residues: 57.2319 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 : 0.285 ------------------------------------------------------------------------------- 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 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 209 ASN ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.248001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.211728 restraints weight = 10208.927| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 2.07 r_work: 0.4205 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.4075 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9035 Z= 0.185 Angle : 0.673 10.313 12300 Z= 0.333 Chirality : 0.042 0.233 1406 Planarity : 0.004 0.056 1539 Dihedral : 9.105 81.475 1299 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.14 % Allowed : 28.19 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.25), residues: 1138 helix: 1.34 (0.23), residues: 484 sheet: -1.02 (0.34), residues: 228 loop : -1.02 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 108 TYR 0.016 0.002 TYR L 92 PHE 0.011 0.001 PHE A 561 TRP 0.013 0.002 TRP A 65 HIS 0.002 0.001 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9030) covalent geometry : angle 0.67263 (12290) SS BOND : bond 0.00381 ( 5) SS BOND : angle 1.03398 ( 10) hydrogen bonds : bond 0.04304 ( 508) hydrogen bonds : angle 5.63397 ( 1434) *********************** 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 163 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 115 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: K 82 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.7244 (mm-40) REVERT: L 110 ARG cc_start: 0.5594 (ttt-90) cc_final: 0.4402 (ttm110) REVERT: A 39 MET cc_start: 0.4854 (mmp) cc_final: 0.3775 (mmp) REVERT: A 166 MET cc_start: 0.7727 (mtp) cc_final: 0.6978 (ptm) REVERT: A 215 ILE cc_start: 0.7171 (mt) cc_final: 0.6279 (mt) REVERT: A 365 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.5512 (ptm) REVERT: A 412 LEU cc_start: 0.7132 (mt) cc_final: 0.6881 (mt) REVERT: A 416 ASP cc_start: 0.4198 (OUTLIER) cc_final: 0.3959 (m-30) REVERT: A 419 LEU cc_start: 0.5457 (OUTLIER) cc_final: 0.5169 (tp) REVERT: A 452 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8158 (p90) REVERT: A 471 VAL cc_start: 0.6881 (OUTLIER) cc_final: 0.6432 (m) REVERT: A 548 MET cc_start: 0.0714 (mmm) cc_final: -0.0538 (mtm) outliers start: 48 outliers final: 19 residues processed: 151 average time/residue: 0.3942 time to fit residues: 65.6102 Evaluate side-chains 123 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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 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 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 416 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 452 PHE 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: 0.7980 chunk 69 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 0.0670 chunk 83 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.4695 r_free = 0.4695 target = 0.248779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.212893 restraints weight = 10203.514| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 2.06 r_work: 0.4227 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.4099 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.1324 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= 0.152 Angle : 0.637 8.892 12300 Z= 0.314 Chirality : 0.041 0.210 1406 Planarity : 0.004 0.057 1539 Dihedral : 8.348 78.021 1299 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.47 % Allowed : 27.65 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.26), residues: 1138 helix: 1.46 (0.23), residues: 487 sheet: -0.91 (0.35), residues: 228 loop : -0.97 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 354 TYR 0.017 0.001 TYR A 152 PHE 0.026 0.001 PHE H 180 TRP 0.013 0.001 TRP A 65 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9030) covalent geometry : angle 0.63703 (12290) SS BOND : bond 0.00344 ( 5) SS BOND : angle 0.88821 ( 10) hydrogen bonds : bond 0.04013 ( 508) hydrogen bonds : angle 5.33974 ( 1434) *********************** 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 164 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 113 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: H 191 SER cc_start: 0.4234 (OUTLIER) cc_final: 0.3257 (t) REVERT: K 82 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: L 46 LYS cc_start: 0.8412 (mttp) cc_final: 0.8192 (mptt) REVERT: L 110 ARG cc_start: 0.5503 (ttt-90) cc_final: 0.4266 (ttm110) REVERT: A 39 MET cc_start: 0.4872 (mmp) cc_final: 0.3882 (mmp) REVERT: A 166 MET cc_start: 0.7648 (mtp) cc_final: 0.6809 (ptm) REVERT: A 215 ILE cc_start: 0.7001 (mt) cc_final: 0.6042 (mt) REVERT: A 365 MET cc_start: 0.6039 (ptp) cc_final: 0.5518 (ptm) REVERT: A 412 LEU cc_start: 0.7115 (mt) cc_final: 0.6773 (mt) REVERT: A 419 LEU cc_start: 0.5451 (OUTLIER) cc_final: 0.5191 (tp) REVERT: A 422 MET cc_start: 0.5942 (OUTLIER) cc_final: 0.5431 (tmm) REVERT: A 452 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8106 (p90) REVERT: A 530 PHE cc_start: 0.6149 (OUTLIER) cc_final: 0.5910 (m-10) REVERT: A 548 MET cc_start: 0.0669 (mmm) cc_final: -0.0579 (mtm) REVERT: A 589 ARG cc_start: 0.5630 (OUTLIER) cc_final: 0.4235 (ttm170) outliers start: 51 outliers final: 25 residues processed: 156 average time/residue: 0.3581 time to fit residues: 61.8211 Evaluate side-chains 131 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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 K residue 117 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 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 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 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 62 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 71 optimal weight: 0.0370 chunk 13 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 45 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.250103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.213907 restraints weight = 10256.267| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 2.13 r_work: 0.4192 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.1585 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= 0.147 Angle : 0.636 9.675 12300 Z= 0.310 Chirality : 0.041 0.212 1406 Planarity : 0.004 0.058 1539 Dihedral : 7.530 76.152 1299 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 5.89 % Allowed : 27.65 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.26), residues: 1138 helix: 1.57 (0.23), residues: 486 sheet: -0.92 (0.35), residues: 231 loop : -0.97 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 354 TYR 0.016 0.001 TYR L 92 PHE 0.011 0.001 PHE A 22 TRP 0.013 0.001 TRP A 65 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9030) covalent geometry : angle 0.63592 (12290) SS BOND : bond 0.00340 ( 5) SS BOND : angle 0.88864 ( 10) hydrogen bonds : bond 0.03862 ( 508) hydrogen bonds : angle 5.17980 ( 1434) *********************** 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 166 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 111 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: H 191 SER cc_start: 0.3250 (OUTLIER) cc_final: 0.2412 (t) REVERT: L 46 LYS cc_start: 0.8319 (mttp) cc_final: 0.8072 (mptt) REVERT: L 110 ARG cc_start: 0.5272 (ttt-90) cc_final: 0.4198 (ttm110) REVERT: A 39 MET cc_start: 0.4792 (mmp) cc_final: 0.3815 (mmp) REVERT: A 134 ASP cc_start: 0.7435 (m-30) cc_final: 0.7232 (m-30) REVERT: A 164 LEU cc_start: 0.5533 (OUTLIER) cc_final: 0.5153 (pp) REVERT: A 166 MET cc_start: 0.7600 (mtp) cc_final: 0.7263 (mtm) REVERT: A 215 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.5973 (mt) REVERT: A 296 ARG cc_start: 0.1933 (OUTLIER) cc_final: 0.1449 (mmt180) REVERT: A 365 MET cc_start: 0.6036 (ptp) cc_final: 0.5520 (ptm) REVERT: A 412 LEU cc_start: 0.6816 (mt) cc_final: 0.6495 (mt) REVERT: A 416 ASP cc_start: 0.3898 (OUTLIER) cc_final: 0.3529 (m-30) REVERT: A 419 LEU cc_start: 0.5327 (OUTLIER) cc_final: 0.5081 (tp) REVERT: A 422 MET cc_start: 0.5767 (OUTLIER) cc_final: 0.5235 (tmm) REVERT: A 452 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8243 (p90) REVERT: A 471 VAL cc_start: 0.7060 (OUTLIER) cc_final: 0.6636 (m) REVERT: A 548 MET cc_start: 0.0642 (mmm) cc_final: -0.0613 (mtm) REVERT: A 589 ARG cc_start: 0.5646 (OUTLIER) cc_final: 0.4204 (ttm170) outliers start: 55 outliers final: 28 residues processed: 155 average time/residue: 0.3844 time to fit residues: 65.6457 Evaluate side-chains 143 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 117 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 198 VAL 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 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 416 ASP Chi-restraints excluded: chain A residue 419 LEU 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 36 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 96 optimal weight: 0.2980 chunk 111 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.246945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.209749 restraints weight = 10229.559| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 2.18 r_work: 0.4166 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9035 Z= 0.170 Angle : 0.653 9.344 12300 Z= 0.319 Chirality : 0.042 0.207 1406 Planarity : 0.004 0.057 1539 Dihedral : 6.846 74.784 1299 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.79 % Allowed : 27.65 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.26), residues: 1138 helix: 1.54 (0.23), residues: 486 sheet: -0.92 (0.35), residues: 228 loop : -1.02 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 354 TYR 0.017 0.002 TYR L 92 PHE 0.028 0.001 PHE H 180 TRP 0.014 0.001 TRP A 65 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9030) covalent geometry : angle 0.65225 (12290) SS BOND : bond 0.00352 ( 5) SS BOND : angle 1.04055 ( 10) hydrogen bonds : bond 0.03968 ( 508) hydrogen bonds : angle 5.16735 ( 1434) *********************** 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 166 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 112 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: H 191 SER cc_start: 0.3492 (OUTLIER) cc_final: 0.2678 (t) REVERT: L 46 LYS cc_start: 0.8314 (mttp) cc_final: 0.8062 (mptt) REVERT: L 110 ARG cc_start: 0.5584 (ttt-90) cc_final: 0.4453 (ttm110) REVERT: L 163 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: A 39 MET cc_start: 0.4881 (mmp) cc_final: 0.4075 (mmp) REVERT: A 134 ASP cc_start: 0.7471 (m-30) cc_final: 0.7256 (m-30) REVERT: A 164 LEU cc_start: 0.5705 (OUTLIER) cc_final: 0.5243 (pp) REVERT: A 166 MET cc_start: 0.7633 (mtp) cc_final: 0.7287 (mtm) REVERT: A 215 ILE cc_start: 0.6933 (OUTLIER) cc_final: 0.5937 (mt) REVERT: A 296 ARG cc_start: 0.1977 (OUTLIER) cc_final: 0.1454 (mmt180) REVERT: A 365 MET cc_start: 0.5959 (ptp) cc_final: 0.5456 (ptm) REVERT: A 412 LEU cc_start: 0.6846 (mt) cc_final: 0.6536 (mt) REVERT: A 416 ASP cc_start: 0.3917 (OUTLIER) cc_final: 0.3504 (m-30) REVERT: A 419 LEU cc_start: 0.5339 (OUTLIER) cc_final: 0.5071 (tp) REVERT: A 420 MET cc_start: 0.5571 (OUTLIER) cc_final: 0.5152 (mmt) REVERT: A 422 MET cc_start: 0.5744 (OUTLIER) cc_final: 0.5192 (tmm) REVERT: A 452 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8282 (p90) REVERT: A 471 VAL cc_start: 0.7065 (OUTLIER) cc_final: 0.6629 (m) REVERT: A 548 MET cc_start: 0.0499 (mmm) cc_final: -0.0737 (mtm) REVERT: A 589 ARG cc_start: 0.5574 (OUTLIER) cc_final: 0.4202 (ttm170) outliers start: 54 outliers final: 32 residues processed: 155 average time/residue: 0.3791 time to fit residues: 65.1042 Evaluate side-chains 148 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 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 163 GLU 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 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 416 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 79 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 38 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.247741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.211486 restraints weight = 10290.746| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 2.27 r_work: 0.4184 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9035 Z= 0.146 Angle : 0.642 9.950 12300 Z= 0.311 Chirality : 0.041 0.183 1406 Planarity : 0.004 0.058 1539 Dihedral : 6.140 74.504 1299 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 6.22 % Allowed : 27.33 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.26), residues: 1138 helix: 1.59 (0.23), residues: 487 sheet: -0.85 (0.35), residues: 227 loop : -1.03 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 354 TYR 0.018 0.001 TYR L 194 PHE 0.011 0.001 PHE A 22 TRP 0.013 0.001 TRP A 65 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9030) covalent geometry : angle 0.64210 (12290) SS BOND : bond 0.00306 ( 5) SS BOND : angle 0.89346 ( 10) hydrogen bonds : bond 0.03840 ( 508) hydrogen bonds : angle 5.05451 ( 1434) *********************** 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 174 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 116 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: H 33 VAL cc_start: 0.9187 (OUTLIER) cc_final: 0.8978 (t) REVERT: H 191 SER cc_start: 0.3268 (OUTLIER) cc_final: 0.2476 (t) REVERT: H 203 LEU cc_start: -0.1415 (OUTLIER) cc_final: -0.1812 (mt) REVERT: L 46 LYS cc_start: 0.8281 (mttp) cc_final: 0.8025 (mptt) REVERT: L 110 ARG cc_start: 0.5412 (ttt-90) cc_final: 0.4273 (ttm110) REVERT: A 39 MET cc_start: 0.4801 (mmp) cc_final: 0.4101 (mmp) REVERT: A 166 MET cc_start: 0.7572 (mtp) cc_final: 0.7213 (mtm) REVERT: A 215 ILE cc_start: 0.6822 (OUTLIER) cc_final: 0.5817 (mt) REVERT: A 296 ARG cc_start: 0.1847 (OUTLIER) cc_final: 0.1411 (mmt180) REVERT: A 365 MET cc_start: 0.5972 (ptp) cc_final: 0.5475 (ptm) REVERT: A 416 ASP cc_start: 0.3935 (OUTLIER) cc_final: 0.3454 (m-30) REVERT: A 419 LEU cc_start: 0.5325 (OUTLIER) cc_final: 0.5069 (tp) REVERT: A 422 MET cc_start: 0.5672 (OUTLIER) cc_final: 0.5166 (tmm) REVERT: A 452 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8225 (p90) REVERT: A 471 VAL cc_start: 0.7030 (OUTLIER) cc_final: 0.6612 (m) REVERT: A 548 MET cc_start: 0.0410 (mmm) cc_final: -0.0786 (mtm) REVERT: A 589 ARG cc_start: 0.5517 (OUTLIER) cc_final: 0.5063 (mtm180) outliers start: 58 outliers final: 31 residues processed: 163 average time/residue: 0.3863 time to fit residues: 69.6264 Evaluate side-chains 151 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 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 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 65 TRP Chi-restraints excluded: chain A residue 85 VAL 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 416 ASP Chi-restraints excluded: chain A residue 419 LEU 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 95 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.246508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.209859 restraints weight = 10274.123| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 2.38 r_work: 0.4166 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9035 Z= 0.165 Angle : 0.654 10.123 12300 Z= 0.317 Chirality : 0.041 0.199 1406 Planarity : 0.004 0.058 1539 Dihedral : 6.008 75.788 1299 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 5.47 % Allowed : 29.15 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.26), residues: 1138 helix: 1.58 (0.23), residues: 488 sheet: -0.90 (0.35), residues: 227 loop : -1.06 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 354 TYR 0.018 0.002 TYR L 194 PHE 0.027 0.001 PHE H 180 TRP 0.013 0.001 TRP A 65 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 9030) covalent geometry : angle 0.65369 (12290) SS BOND : bond 0.00353 ( 5) SS BOND : angle 0.95066 ( 10) hydrogen bonds : bond 0.03851 ( 508) hydrogen bonds : angle 5.05971 ( 1434) *********************** 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 163 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 112 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: H 191 SER cc_start: 0.3505 (OUTLIER) cc_final: 0.2719 (p) REVERT: H 203 LEU cc_start: -0.1422 (OUTLIER) cc_final: -0.1812 (mt) REVERT: L 46 LYS cc_start: 0.8296 (mttp) cc_final: 0.8045 (mptt) REVERT: L 110 ARG cc_start: 0.5473 (ttt-90) cc_final: 0.4304 (ttm110) REVERT: L 163 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7646 (mt-10) REVERT: A 39 MET cc_start: 0.4834 (mmp) cc_final: 0.4276 (mmp) REVERT: A 110 MET cc_start: 0.5696 (mmt) cc_final: 0.5479 (mmt) REVERT: A 166 MET cc_start: 0.7549 (mtp) cc_final: 0.7233 (mtm) REVERT: A 215 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.5975 (mt) REVERT: A 296 ARG cc_start: 0.1873 (OUTLIER) cc_final: 0.1402 (mmt180) REVERT: A 365 MET cc_start: 0.5966 (ptp) cc_final: 0.5474 (ptm) REVERT: A 419 LEU cc_start: 0.5319 (OUTLIER) cc_final: 0.5057 (tp) REVERT: A 420 MET cc_start: 0.5550 (OUTLIER) cc_final: 0.5151 (mmt) REVERT: A 422 MET cc_start: 0.5664 (OUTLIER) cc_final: 0.5091 (tmm) REVERT: A 452 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8244 (p90) REVERT: A 471 VAL cc_start: 0.7006 (OUTLIER) cc_final: 0.6605 (m) REVERT: A 548 MET cc_start: 0.0374 (mmm) cc_final: -0.0838 (mtm) REVERT: A 589 ARG cc_start: 0.5524 (OUTLIER) cc_final: 0.5067 (mtm180) outliers start: 51 outliers final: 30 residues processed: 153 average time/residue: 0.3739 time to fit residues: 63.1073 Evaluate side-chains 147 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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 163 GLU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 76 optimal weight: 0.4980 chunk 83 optimal weight: 0.4980 chunk 71 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 31 optimal weight: 0.0070 overall best weight: 0.3798 ------------------------------------------------------------------------------- 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 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.248962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.213310 restraints weight = 10340.979| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 2.26 r_work: 0.4201 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.2125 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= 0.129 Angle : 0.647 10.508 12300 Z= 0.311 Chirality : 0.041 0.196 1406 Planarity : 0.004 0.059 1539 Dihedral : 5.862 76.099 1299 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.18 % Allowed : 30.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.26), residues: 1138 helix: 1.69 (0.23), residues: 488 sheet: -0.91 (0.35), residues: 232 loop : -0.95 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 354 TYR 0.024 0.001 TYR A 511 PHE 0.013 0.001 PHE A 22 TRP 0.013 0.001 TRP A 65 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9030) covalent geometry : angle 0.64658 (12290) SS BOND : bond 0.00229 ( 5) SS BOND : angle 0.72170 ( 10) hydrogen bonds : bond 0.03728 ( 508) hydrogen bonds : angle 4.93480 ( 1434) *********************** 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 153 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: H 33 VAL cc_start: 0.9092 (m) cc_final: 0.8839 (t) REVERT: L 46 LYS cc_start: 0.8263 (mttp) cc_final: 0.7999 (mptt) REVERT: A 39 MET cc_start: 0.4724 (mmp) cc_final: 0.4166 (mmp) REVERT: A 110 MET cc_start: 0.5625 (mmt) cc_final: 0.5404 (mmt) REVERT: A 166 MET cc_start: 0.7535 (mtp) cc_final: 0.7222 (mtm) REVERT: A 215 ILE cc_start: 0.6708 (OUTLIER) cc_final: 0.5892 (mt) REVERT: A 296 ARG cc_start: 0.1938 (OUTLIER) cc_final: 0.1433 (mmt180) REVERT: A 365 MET cc_start: 0.6009 (ptp) cc_final: 0.5508 (ptm) REVERT: A 412 LEU cc_start: 0.6818 (mt) cc_final: 0.6540 (mt) REVERT: A 419 LEU cc_start: 0.5390 (OUTLIER) cc_final: 0.5098 (tp) REVERT: A 422 MET cc_start: 0.5814 (OUTLIER) cc_final: 0.5168 (tmm) REVERT: A 452 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8325 (p90) REVERT: A 471 VAL cc_start: 0.6977 (OUTLIER) cc_final: 0.6591 (m) REVERT: A 548 MET cc_start: 0.0349 (mmm) cc_final: -0.0850 (mtm) REVERT: A 589 ARG cc_start: 0.5501 (mtm180) cc_final: 0.5055 (mtm180) outliers start: 39 outliers final: 24 residues processed: 147 average time/residue: 0.3451 time to fit residues: 56.6085 Evaluate side-chains 136 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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 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 198 VAL Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 65 TRP 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 350 THR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 419 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 29 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 85 optimal weight: 0.0980 chunk 109 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 88 GLN ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.247305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.211092 restraints weight = 10243.406| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 2.06 r_work: 0.4191 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9035 Z= 0.149 Angle : 0.672 14.474 12300 Z= 0.321 Chirality : 0.042 0.219 1406 Planarity : 0.004 0.058 1539 Dihedral : 5.951 81.340 1299 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.50 % Allowed : 30.33 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.26), residues: 1138 helix: 1.63 (0.23), residues: 490 sheet: -0.93 (0.35), residues: 231 loop : -0.98 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 354 TYR 0.021 0.002 TYR A 511 PHE 0.031 0.001 PHE H 180 TRP 0.014 0.001 TRP A 65 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9030) covalent geometry : angle 0.67218 (12290) SS BOND : bond 0.00286 ( 5) SS BOND : angle 0.92400 ( 10) hydrogen bonds : bond 0.03783 ( 508) hydrogen bonds : angle 4.95664 ( 1434) *********************** 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 151 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: H 191 SER cc_start: 0.3271 (OUTLIER) cc_final: 0.2520 (p) REVERT: H 203 LEU cc_start: -0.1399 (OUTLIER) cc_final: -0.1795 (mt) REVERT: L 46 LYS cc_start: 0.8287 (mttp) cc_final: 0.8032 (mptt) REVERT: L 110 ARG cc_start: 0.5416 (ttt-90) cc_final: 0.4447 (ttm110) REVERT: A 39 MET cc_start: 0.4743 (mmp) cc_final: 0.4261 (mmp) REVERT: A 110 MET cc_start: 0.5531 (mmt) cc_final: 0.5311 (mmt) REVERT: A 166 MET cc_start: 0.7527 (mtp) cc_final: 0.7214 (mtm) REVERT: A 215 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.6064 (mt) REVERT: A 296 ARG cc_start: 0.1885 (OUTLIER) cc_final: 0.1446 (mmt180) REVERT: A 365 MET cc_start: 0.6052 (ptp) cc_final: 0.5539 (ptm) REVERT: A 412 LEU cc_start: 0.6827 (mt) cc_final: 0.6600 (mt) REVERT: A 419 LEU cc_start: 0.5361 (OUTLIER) cc_final: 0.5092 (tp) REVERT: A 422 MET cc_start: 0.5903 (OUTLIER) cc_final: 0.5245 (tmm) REVERT: A 452 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8373 (p90) REVERT: A 521 ARG cc_start: 0.6518 (ptt180) cc_final: 0.5891 (ptp-170) REVERT: A 528 TYR cc_start: 0.7065 (m-80) cc_final: 0.6865 (m-80) REVERT: A 548 MET cc_start: 0.0316 (mmm) cc_final: -0.0884 (mtm) REVERT: A 589 ARG cc_start: 0.5511 (mtm180) cc_final: 0.5074 (mtm180) outliers start: 42 outliers final: 28 residues processed: 144 average time/residue: 0.3775 time to fit residues: 60.0509 Evaluate side-chains 139 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 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 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 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 350 THR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 419 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 72 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 0.0770 chunk 105 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.250343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.214012 restraints weight = 10292.254| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 2.28 r_work: 0.4173 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.2263 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= 0.152 Angle : 0.684 13.535 12300 Z= 0.325 Chirality : 0.041 0.196 1406 Planarity : 0.004 0.058 1539 Dihedral : 5.943 81.814 1299 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.50 % Allowed : 30.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.26), residues: 1138 helix: 1.59 (0.23), residues: 490 sheet: -0.98 (0.34), residues: 236 loop : -0.99 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 90 TYR 0.022 0.002 TYR A 511 PHE 0.010 0.001 PHE A 22 TRP 0.012 0.001 TRP A 65 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9030) covalent geometry : angle 0.68392 (12290) SS BOND : bond 0.00428 ( 5) SS BOND : angle 0.88160 ( 10) hydrogen bonds : bond 0.03790 ( 508) hydrogen bonds : angle 4.97620 ( 1434) ********************** 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 152 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: H 191 SER cc_start: 0.3456 (OUTLIER) cc_final: 0.2692 (p) REVERT: H 203 LEU cc_start: -0.1413 (OUTLIER) cc_final: -0.1804 (mt) REVERT: L 46 LYS cc_start: 0.8306 (mttp) cc_final: 0.8048 (mptt) REVERT: L 110 ARG cc_start: 0.5485 (ttt-90) cc_final: 0.4472 (ttm110) REVERT: A 39 MET cc_start: 0.4798 (mmp) cc_final: 0.4312 (mmp) REVERT: A 110 MET cc_start: 0.5574 (mmt) cc_final: 0.5357 (mmt) REVERT: A 166 MET cc_start: 0.7549 (mtp) cc_final: 0.7250 (mtm) REVERT: A 215 ILE cc_start: 0.6854 (OUTLIER) cc_final: 0.6110 (mt) REVERT: A 296 ARG cc_start: 0.1865 (OUTLIER) cc_final: 0.1406 (mmt180) REVERT: A 365 MET cc_start: 0.6026 (ptp) cc_final: 0.5492 (ptm) REVERT: A 412 LEU cc_start: 0.6853 (mt) cc_final: 0.6631 (mt) REVERT: A 419 LEU cc_start: 0.5397 (OUTLIER) cc_final: 0.5106 (tp) REVERT: A 422 MET cc_start: 0.5928 (OUTLIER) cc_final: 0.5306 (tmm) REVERT: A 452 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8316 (p90) REVERT: A 521 ARG cc_start: 0.6521 (ptt180) cc_final: 0.5891 (ptp-170) REVERT: A 528 TYR cc_start: 0.7093 (m-80) cc_final: 0.6891 (m-80) REVERT: A 548 MET cc_start: 0.0371 (mmm) cc_final: -0.0846 (mtm) REVERT: A 589 ARG cc_start: 0.5442 (mtm180) cc_final: 0.5005 (mtm180) outliers start: 42 outliers final: 28 residues processed: 145 average time/residue: 0.3879 time to fit residues: 62.2272 Evaluate side-chains 143 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 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 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 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 350 THR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 419 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 85 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 124 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 = 0.4671 r_free = 0.4671 target = 0.247174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.210272 restraints weight = 10197.504| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 2.26 r_work: 0.4145 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2381 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= 0.200 Angle : 0.720 15.637 12300 Z= 0.348 Chirality : 0.043 0.178 1406 Planarity : 0.004 0.057 1539 Dihedral : 6.148 83.730 1299 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.29 % Allowed : 30.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.26), residues: 1138 helix: 1.49 (0.23), residues: 488 sheet: -0.99 (0.36), residues: 218 loop : -1.25 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 108 TYR 0.021 0.002 TYR L 194 PHE 0.032 0.002 PHE H 180 TRP 0.013 0.002 TRP H 102 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 9030) covalent geometry : angle 0.71903 (12290) SS BOND : bond 0.00514 ( 5) SS BOND : angle 1.34463 ( 10) hydrogen bonds : bond 0.04030 ( 508) hydrogen bonds : angle 5.15506 ( 1434) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3093.80 seconds wall clock time: 53 minutes 45.64 seconds (3225.64 seconds total)