Starting phenix.real_space_refine on Fri Jul 25 17:06:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k0l_22601/07_2025/7k0l_22601.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0l_22601/07_2025/7k0l_22601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k0l_22601/07_2025/7k0l_22601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0l_22601/07_2025/7k0l_22601.map" model { file = "/net/cci-nas-00/data/ceres_data/7k0l_22601/07_2025/7k0l_22601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0l_22601/07_2025/7k0l_22601.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 44 5.16 5 C 4877 2.51 5 N 1293 2.21 5 O 1404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7619 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3284 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 409 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'PLP': 1, 'VRP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.79, per 1000 atoms: 0.76 Number of scatterers: 7619 At special positions: 0 Unit cell: (95.475, 96.48, 115.575, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 1 15.00 O 1404 8.00 N 1293 7.00 C 4877 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.0 seconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1778 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 52.3% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 142 through 157 removed outlier: 3.713A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 179 removed outlier: 3.501A pdb=" N THR A 170 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 213 through 231 removed outlier: 3.515A pdb=" N LEU A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 359 Processing helix chain 'A' and resid 361 through 378 removed outlier: 3.660A pdb=" N GLN A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 422 Processing helix chain 'A' and resid 453 through 472 Processing helix chain 'B' and resid 67 through 94 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 116 through 126 removed outlier: 4.704A pdb=" N TYR B 122 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.612A pdb=" N ARG B 131 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ASP B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.526A pdb=" N GLU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 Proline residue: B 247 - end of helix removed outlier: 3.570A pdb=" N VAL B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 273 Processing helix chain 'B' and resid 284 through 299 Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.614A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 433 through 457 removed outlier: 3.865A pdb=" N GLU B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.528A pdb=" N ILE B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 25 through 29 Processing helix chain 'C' and resid 30 through 56 removed outlier: 3.542A pdb=" N PHE C 55 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 4.060A pdb=" N VAL A 94 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA A 425 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.690A pdb=" N LEU A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP A 188 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLU A 245 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 386 removed outlier: 4.437A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.995A pdb=" N ILE B 148 " --> pdb=" O LYS B 168 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LYS B 168 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU B 150 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE B 166 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N GLN B 152 " --> pdb=" O GLY B 164 " (cutoff:3.500A) removed outlier: 9.404A pdb=" N GLY B 164 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.681A pdb=" N ILE B 310 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP B 259 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N GLU B 315 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.501A pdb=" N ARG B 507 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1137 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 2.70 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: 2465 1.34 - 1.46: 1174 1.46 - 1.58: 4063 1.58 - 1.70: 2 1.70 - 1.82: 71 Bond restraints: 7775 Sorted by residual: bond pdb=" N ASN B 120 " pdb=" CA ASN B 120 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.13e+00 bond pdb=" N GLU B 119 " pdb=" CA GLU B 119 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.84e+00 bond pdb=" N PHE B 121 " pdb=" CA PHE B 121 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.71e+00 bond pdb=" N PHE B 118 " pdb=" CA PHE B 118 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.25e-02 6.40e+03 5.54e+00 bond pdb=" C18 VRP B 602 " pdb=" C19 VRP B 602 " ideal model delta sigma weight residual 1.538 1.572 -0.034 2.00e-02 2.50e+03 2.94e+00 ... (remaining 7770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 10164 1.49 - 2.99: 289 2.99 - 4.48: 41 4.48 - 5.98: 7 5.98 - 7.47: 5 Bond angle restraints: 10506 Sorted by residual: angle pdb=" CB MET B 285 " pdb=" CG MET B 285 " pdb=" SD MET B 285 " ideal model delta sigma weight residual 112.70 120.17 -7.47 3.00e+00 1.11e-01 6.21e+00 angle pdb=" N ASN B 120 " pdb=" CA ASN B 120 " pdb=" C ASN B 120 " ideal model delta sigma weight residual 113.16 110.18 2.98 1.24e+00 6.50e-01 5.79e+00 angle pdb=" C TYR B 176 " pdb=" N ASN B 177 " pdb=" CA ASN B 177 " ideal model delta sigma weight residual 121.54 126.08 -4.54 1.91e+00 2.74e-01 5.64e+00 angle pdb=" CA CYS A 133 " pdb=" C CYS A 133 " pdb=" N GLY A 134 " ideal model delta sigma weight residual 115.67 118.55 -2.88 1.23e+00 6.61e-01 5.50e+00 angle pdb=" CA GLU B 119 " pdb=" C GLU B 119 " pdb=" O GLU B 119 " ideal model delta sigma weight residual 120.55 118.10 2.45 1.06e+00 8.90e-01 5.34e+00 ... (remaining 10501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.52: 4438 22.52 - 45.03: 236 45.03 - 67.55: 14 67.55 - 90.07: 3 90.07 - 112.58: 1 Dihedral angle restraints: 4692 sinusoidal: 1908 harmonic: 2784 Sorted by residual: dihedral pdb=" C5A PLP B 601 " pdb=" O4P PLP B 601 " pdb=" P PLP B 601 " pdb=" O1P PLP B 601 " ideal model delta sinusoidal sigma weight residual 76.43 -170.99 -112.58 1 2.00e+01 2.50e-03 3.32e+01 dihedral pdb=" CA THR B 400 " pdb=" C THR B 400 " pdb=" N HIS B 401 " pdb=" CA HIS B 401 " ideal model delta harmonic sigma weight residual -180.00 -164.35 -15.65 0 5.00e+00 4.00e-02 9.80e+00 dihedral pdb=" CB GLU B 197 " pdb=" CG GLU B 197 " pdb=" CD GLU B 197 " pdb=" OE1 GLU B 197 " ideal model delta sinusoidal sigma weight residual 0.00 80.48 -80.48 1 3.00e+01 1.11e-03 8.90e+00 ... (remaining 4689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 884 0.044 - 0.087: 189 0.087 - 0.131: 82 0.131 - 0.174: 3 0.174 - 0.218: 1 Chirality restraints: 1159 Sorted by residual: chirality pdb=" C18 VRP B 602 " pdb=" C17 VRP B 602 " pdb=" C19 VRP B 602 " pdb=" O28 VRP B 602 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASN B 177 " pdb=" N ASN B 177 " pdb=" C ASN B 177 " pdb=" CB ASN B 177 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE A 242 " pdb=" N ILE A 242 " pdb=" C ILE A 242 " pdb=" CB ILE A 242 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 1156 not shown) Planarity restraints: 1348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 498 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO B 499 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 499 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 499 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 412 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO B 413 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 413 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 413 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 469 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO B 470 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " -0.023 5.00e-02 4.00e+02 ... (remaining 1345 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 125 2.69 - 3.24: 7377 3.24 - 3.80: 11385 3.80 - 4.35: 14945 4.35 - 4.90: 26010 Nonbonded interactions: 59842 Sorted by model distance: nonbonded pdb=" OH TYR B 176 " pdb=" O24 VRP B 602 " model vdw 2.141 3.040 nonbonded pdb=" OD2 ASP B 259 " pdb=" OH TYR B 318 " model vdw 2.187 3.040 nonbonded pdb=" OG SER A 401 " pdb=" OD2 ASP A 408 " model vdw 2.246 3.040 nonbonded pdb=" NE2 HIS B 263 " pdb=" O27 VRP B 602 " model vdw 2.270 3.120 nonbonded pdb=" OG1 THR A 402 " pdb=" OD1 ASP A 408 " model vdw 2.300 3.040 ... (remaining 59837 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.310 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 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 0.116 7776 Z= 0.227 Angle : 0.601 7.474 10506 Z= 0.360 Chirality : 0.042 0.218 1159 Planarity : 0.004 0.061 1348 Dihedral : 12.662 112.583 2914 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.27), residues: 958 helix: 1.86 (0.25), residues: 432 sheet: 0.64 (0.48), residues: 124 loop : -0.49 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.003 0.001 HIS B 403 PHE 0.012 0.001 PHE A 209 TYR 0.023 0.001 TYR A 166 ARG 0.004 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.16052 ( 398) hydrogen bonds : angle 5.93674 ( 1137) covalent geometry : bond 0.00387 ( 7775) covalent geometry : angle 0.60143 (10506) Misc. bond : bond 0.11625 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.947 Fit side-chains REVERT: B 472 MET cc_start: 0.8708 (mmm) cc_final: 0.8463 (mmm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2113 time to fit residues: 19.0964 Evaluate side-chains 56 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.094266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.081799 restraints weight = 16095.010| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.27 r_work: 0.3091 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7776 Z= 0.137 Angle : 0.503 6.631 10506 Z= 0.271 Chirality : 0.042 0.146 1159 Planarity : 0.004 0.055 1348 Dihedral : 5.380 74.340 1098 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.50 % Allowed : 5.23 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), residues: 958 helix: 1.97 (0.25), residues: 445 sheet: 0.57 (0.46), residues: 131 loop : -0.48 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 32 HIS 0.006 0.001 HIS B 403 PHE 0.012 0.001 PHE A 209 TYR 0.025 0.001 TYR A 166 ARG 0.005 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04760 ( 398) hydrogen bonds : angle 4.70279 ( 1137) covalent geometry : bond 0.00317 ( 7775) covalent geometry : angle 0.50346 (10506) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.914 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.1911 time to fit residues: 15.6861 Evaluate side-chains 58 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 47 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.094841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.082223 restraints weight = 16349.879| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.30 r_work: 0.3094 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7776 Z= 0.129 Angle : 0.479 6.612 10506 Z= 0.257 Chirality : 0.041 0.147 1159 Planarity : 0.004 0.051 1348 Dihedral : 5.081 84.421 1098 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.87 % Allowed : 6.23 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), residues: 958 helix: 2.04 (0.25), residues: 445 sheet: 0.41 (0.45), residues: 129 loop : -0.51 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 32 HIS 0.004 0.001 HIS B 403 PHE 0.012 0.001 PHE A 209 TYR 0.020 0.001 TYR A 166 ARG 0.004 0.000 ARG B 136 Details of bonding type rmsd hydrogen bonds : bond 0.04224 ( 398) hydrogen bonds : angle 4.48176 ( 1137) covalent geometry : bond 0.00300 ( 7775) covalent geometry : angle 0.47879 (10506) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.940 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.1898 time to fit residues: 17.1738 Evaluate side-chains 60 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 47 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.4980 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.094408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.081864 restraints weight = 16237.707| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.28 r_work: 0.3088 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7776 Z= 0.138 Angle : 0.478 6.645 10506 Z= 0.256 Chirality : 0.041 0.140 1159 Planarity : 0.004 0.050 1348 Dihedral : 4.880 82.662 1098 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.87 % Allowed : 7.72 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.27), residues: 958 helix: 2.04 (0.25), residues: 445 sheet: 0.35 (0.45), residues: 129 loop : -0.50 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 32 HIS 0.004 0.001 HIS B 403 PHE 0.013 0.001 PHE A 209 TYR 0.018 0.001 TYR A 166 ARG 0.002 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 398) hydrogen bonds : angle 4.40778 ( 1137) covalent geometry : bond 0.00326 ( 7775) covalent geometry : angle 0.47795 (10506) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.925 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 0.1703 time to fit residues: 15.4390 Evaluate side-chains 60 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 47 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.094369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.081919 restraints weight = 16173.463| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.28 r_work: 0.3093 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7776 Z= 0.131 Angle : 0.464 6.640 10506 Z= 0.249 Chirality : 0.041 0.139 1159 Planarity : 0.004 0.050 1348 Dihedral : 4.603 71.548 1098 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.00 % Allowed : 8.84 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.27), residues: 958 helix: 2.08 (0.25), residues: 445 sheet: 0.30 (0.45), residues: 129 loop : -0.48 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 32 HIS 0.004 0.001 HIS B 403 PHE 0.013 0.001 PHE A 209 TYR 0.017 0.001 TYR A 166 ARG 0.002 0.000 ARG B 136 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 398) hydrogen bonds : angle 4.33528 ( 1137) covalent geometry : bond 0.00308 ( 7775) covalent geometry : angle 0.46402 (10506) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.923 Fit side-chains REVERT: B 505 GLU cc_start: 0.8292 (mp0) cc_final: 0.7912 (mp0) outliers start: 8 outliers final: 5 residues processed: 63 average time/residue: 0.1691 time to fit residues: 16.1059 Evaluate side-chains 61 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 47 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.094472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.082018 restraints weight = 16136.617| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.28 r_work: 0.3091 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7776 Z= 0.127 Angle : 0.463 6.637 10506 Z= 0.248 Chirality : 0.041 0.138 1159 Planarity : 0.004 0.049 1348 Dihedral : 4.441 63.918 1098 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.37 % Allowed : 9.71 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.27), residues: 958 helix: 2.10 (0.25), residues: 445 sheet: 0.26 (0.45), residues: 129 loop : -0.48 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 32 HIS 0.003 0.001 HIS B 403 PHE 0.013 0.001 PHE A 209 TYR 0.014 0.001 TYR C 50 ARG 0.001 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 398) hydrogen bonds : angle 4.33730 ( 1137) covalent geometry : bond 0.00298 ( 7775) covalent geometry : angle 0.46318 (10506) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.918 Fit side-chains REVERT: A 77 HIS cc_start: 0.8527 (OUTLIER) cc_final: 0.8013 (m170) REVERT: A 469 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7525 (mp-120) REVERT: B 505 GLU cc_start: 0.8292 (mp0) cc_final: 0.7877 (mp0) outliers start: 11 outliers final: 6 residues processed: 67 average time/residue: 0.1581 time to fit residues: 16.1320 Evaluate side-chains 64 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 47 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 52 optimal weight: 3.9990 chunk 6 optimal weight: 0.0970 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.094835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.082225 restraints weight = 16142.350| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.28 r_work: 0.3101 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7776 Z= 0.118 Angle : 0.461 6.616 10506 Z= 0.248 Chirality : 0.041 0.137 1159 Planarity : 0.004 0.049 1348 Dihedral : 4.316 58.289 1098 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.37 % Allowed : 10.46 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.27), residues: 958 helix: 2.07 (0.25), residues: 445 sheet: 0.23 (0.44), residues: 129 loop : -0.44 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 32 HIS 0.003 0.001 HIS B 403 PHE 0.012 0.001 PHE A 209 TYR 0.013 0.001 TYR C 50 ARG 0.001 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 398) hydrogen bonds : angle 4.34378 ( 1137) covalent geometry : bond 0.00276 ( 7775) covalent geometry : angle 0.46141 (10506) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.937 Fit side-chains REVERT: A 77 HIS cc_start: 0.8506 (OUTLIER) cc_final: 0.8049 (m170) REVERT: A 469 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7517 (mp-120) REVERT: B 505 GLU cc_start: 0.8266 (mp0) cc_final: 0.7872 (mp0) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 0.1578 time to fit residues: 15.7240 Evaluate side-chains 66 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 47 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 34 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 12 optimal weight: 0.0010 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.099389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.086683 restraints weight = 16249.244| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.29 r_work: 0.3181 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7776 Z= 0.106 Angle : 0.471 11.782 10506 Z= 0.252 Chirality : 0.041 0.209 1159 Planarity : 0.004 0.048 1348 Dihedral : 4.189 53.404 1098 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.49 % Allowed : 10.21 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.27), residues: 958 helix: 2.13 (0.25), residues: 445 sheet: 0.23 (0.44), residues: 129 loop : -0.39 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 32 HIS 0.003 0.000 HIS B 403 PHE 0.011 0.001 PHE A 209 TYR 0.012 0.001 TYR C 50 ARG 0.001 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 398) hydrogen bonds : angle 4.32875 ( 1137) covalent geometry : bond 0.00243 ( 7775) covalent geometry : angle 0.47127 (10506) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 1.059 Fit side-chains REVERT: A 77 HIS cc_start: 0.8547 (OUTLIER) cc_final: 0.8116 (m170) REVERT: A 469 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7541 (mp-120) REVERT: B 86 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7860 (t80) outliers start: 12 outliers final: 7 residues processed: 65 average time/residue: 0.1566 time to fit residues: 15.9024 Evaluate side-chains 66 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 47 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 28 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 0.0470 chunk 8 optimal weight: 2.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.099279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.086896 restraints weight = 16297.251| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.28 r_work: 0.3180 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7776 Z= 0.110 Angle : 0.473 10.243 10506 Z= 0.253 Chirality : 0.041 0.178 1159 Planarity : 0.004 0.049 1348 Dihedral : 4.119 49.634 1098 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.37 % Allowed : 9.96 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.27), residues: 958 helix: 2.25 (0.25), residues: 438 sheet: 0.20 (0.44), residues: 129 loop : -0.46 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 32 HIS 0.003 0.001 HIS B 403 PHE 0.012 0.001 PHE A 209 TYR 0.012 0.001 TYR C 50 ARG 0.002 0.000 ARG A 459 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 398) hydrogen bonds : angle 4.32259 ( 1137) covalent geometry : bond 0.00256 ( 7775) covalent geometry : angle 0.47284 (10506) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 1.056 Fit side-chains REVERT: A 77 HIS cc_start: 0.8541 (OUTLIER) cc_final: 0.8104 (m170) REVERT: A 214 MET cc_start: 0.8855 (mmt) cc_final: 0.8625 (mmp) REVERT: A 226 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7562 (tp) REVERT: A 469 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7553 (mp-120) REVERT: B 86 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7818 (t80) outliers start: 11 outliers final: 7 residues processed: 64 average time/residue: 0.1542 time to fit residues: 15.5916 Evaluate side-chains 67 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 494 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 82 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.0670 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.099292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.086887 restraints weight = 16336.400| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.29 r_work: 0.3180 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7776 Z= 0.112 Angle : 0.475 10.225 10506 Z= 0.253 Chirality : 0.041 0.173 1159 Planarity : 0.004 0.049 1348 Dihedral : 4.063 45.015 1098 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.37 % Allowed : 10.21 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.27), residues: 958 helix: 2.22 (0.25), residues: 438 sheet: 0.18 (0.44), residues: 129 loop : -0.48 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 10 HIS 0.003 0.001 HIS B 403 PHE 0.012 0.001 PHE A 209 TYR 0.012 0.001 TYR C 50 ARG 0.002 0.000 ARG B 507 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 398) hydrogen bonds : angle 4.31017 ( 1137) covalent geometry : bond 0.00263 ( 7775) covalent geometry : angle 0.47538 (10506) Misc. bond : bond 0.00008 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.851 Fit side-chains REVERT: A 77 HIS cc_start: 0.8546 (OUTLIER) cc_final: 0.8105 (m170) REVERT: A 226 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7577 (tp) REVERT: A 469 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7563 (mp-120) REVERT: B 86 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7820 (t80) outliers start: 11 outliers final: 7 residues processed: 68 average time/residue: 0.1460 time to fit residues: 15.6030 Evaluate side-chains 69 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 494 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.0020 chunk 41 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.094985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.082693 restraints weight = 16192.964| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.27 r_work: 0.3107 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7776 Z= 0.123 Angle : 0.488 10.035 10506 Z= 0.258 Chirality : 0.041 0.177 1159 Planarity : 0.004 0.048 1348 Dihedral : 4.057 41.102 1098 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.37 % Allowed : 10.09 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.27), residues: 958 helix: 2.22 (0.25), residues: 438 sheet: 0.13 (0.43), residues: 131 loop : -0.46 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 10 HIS 0.003 0.001 HIS B 403 PHE 0.012 0.001 PHE A 209 TYR 0.013 0.001 TYR C 50 ARG 0.002 0.000 ARG B 507 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 398) hydrogen bonds : angle 4.30412 ( 1137) covalent geometry : bond 0.00291 ( 7775) covalent geometry : angle 0.48763 (10506) Misc. bond : bond 0.00007 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3783.56 seconds wall clock time: 65 minutes 49.91 seconds (3949.91 seconds total)