Starting phenix.real_space_refine on Tue Mar 3 18:02:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k0k_22600/03_2026/7k0k_22600.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0k_22600/03_2026/7k0k_22600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k0k_22600/03_2026/7k0k_22600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0k_22600/03_2026/7k0k_22600.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k0k_22600/03_2026/7k0k_22600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0k_22600/03_2026/7k0k_22600.map" } resolution = 2.6 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= -0.001 sd= 0.107 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 4875 2.51 5 N 1293 2.21 5 O 1402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7615 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3287 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PLP': 1, 'VSD': 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: 1.57, per 1000 atoms: 0.21 Number of scatterers: 7615 At special positions: 0 Unit cell: (90.1, 90.1, 114.48, 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 1402 8.00 N 1293 7.00 C 4875 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: 0.62 Conformation dependent library (CDL) restraints added in 288.9 milliseconds 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: 39 helices and 8 sheets defined 52.8% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 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 156 Processing helix chain 'A' and resid 166 through 179 removed outlier: 4.466A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (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 Processing helix chain 'A' and resid 231 through 238 removed outlier: 3.514A pdb=" N ALA A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 321 through 332 removed outlier: 4.729A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 404 through 421 Processing helix chain 'A' and resid 453 through 472 Processing helix chain 'B' and resid 67 through 94 removed outlier: 3.589A pdb=" N TRP B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.510A pdb=" N ARG B 131 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 5.419A 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 Processing helix chain 'B' and resid 237 through 250 Proline residue: B 247 - end of helix 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 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 Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.839A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.502A 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 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95 removed outlier: 6.839A pdb=" N ALA A 425 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.519A 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: 6.575A pdb=" N ILE A 271 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N SER A 304 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU A 273 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N ASN A 306 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.396A 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: 4.110A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA5, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.541A pdb=" N VAL B 146 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 167 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ILE B 148 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ASN B 165 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLU B 150 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.582A pdb=" N ILE B 310 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N GLU B 315 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 317 through 318 Processing sheet with id=AA8, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.755A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1161 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: 1.15 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1961 1.33 - 1.45: 1397 1.45 - 1.57: 4341 1.57 - 1.69: 1 1.69 - 1.81: 71 Bond restraints: 7771 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 1.26e-02 6.30e+03 6.95e+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 5.64e+00 bond pdb=" N PHE B 118 " pdb=" CA PHE B 118 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.27e-02 6.20e+03 5.54e+00 bond pdb=" N PHE B 121 " pdb=" CA PHE B 121 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.88e+00 bond pdb=" C09 VSD B 602 " pdb=" C10 VSD B 602 " ideal model delta sigma weight residual 1.525 1.569 -0.044 2.00e-02 2.50e+03 4.81e+00 ... (remaining 7766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 10015 1.42 - 2.84: 392 2.84 - 4.25: 65 4.25 - 5.67: 17 5.67 - 7.09: 9 Bond angle restraints: 10498 Sorted by residual: angle pdb=" C LEU B 473 " pdb=" N TYR B 474 " pdb=" CA TYR B 474 " ideal model delta sigma weight residual 121.54 127.79 -6.25 1.91e+00 2.74e-01 1.07e+01 angle pdb=" N GLY A 315 " pdb=" CA GLY A 315 " pdb=" C GLY A 315 " ideal model delta sigma weight residual 111.85 115.12 -3.27 1.06e+00 8.90e-01 9.49e+00 angle pdb=" N GLU A 227 " pdb=" CA GLU A 227 " pdb=" CB GLU A 227 " ideal model delta sigma weight residual 110.28 114.72 -4.44 1.55e+00 4.16e-01 8.21e+00 angle pdb=" N GLY A 140 " pdb=" CA GLY A 140 " pdb=" C GLY A 140 " ideal model delta sigma weight residual 115.61 110.80 4.81 1.74e+00 3.30e-01 7.64e+00 angle pdb=" C PHE B 498 " pdb=" CA PHE B 498 " pdb=" CB PHE B 498 " ideal model delta sigma weight residual 112.76 107.79 4.97 1.86e+00 2.89e-01 7.13e+00 ... (remaining 10493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 4282 16.85 - 33.70: 318 33.70 - 50.55: 63 50.55 - 67.40: 12 67.40 - 84.24: 4 Dihedral angle restraints: 4679 sinusoidal: 1895 harmonic: 2784 Sorted by residual: dihedral pdb=" CA SER B 506 " pdb=" C SER B 506 " pdb=" N ARG B 507 " pdb=" CA ARG B 507 " ideal model delta harmonic sigma weight residual -180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+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 -161.92 -18.08 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA MET B 374 " pdb=" C MET B 374 " pdb=" N GLY B 375 " pdb=" CA GLY B 375 " ideal model delta harmonic sigma weight residual 180.00 162.19 17.81 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 4676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 858 0.046 - 0.092: 227 0.092 - 0.138: 69 0.138 - 0.184: 2 0.184 - 0.230: 1 Chirality restraints: 1157 Sorted by residual: chirality pdb=" CB ILE B 503 " pdb=" CA ILE B 503 " pdb=" CG1 ILE B 503 " pdb=" CG2 ILE B 503 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB VAL B 416 " pdb=" CA VAL B 416 " pdb=" CG1 VAL B 416 " pdb=" CG2 VAL B 416 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.04e-01 chirality pdb=" CA PRO B 301 " pdb=" N PRO B 301 " pdb=" C PRO B 301 " pdb=" CB PRO B 301 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 1154 not shown) Planarity restraints: 1347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 469 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO B 470 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 412 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO B 413 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 413 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 413 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 111 " -0.011 2.00e-02 2.50e+03 1.43e-02 3.59e+00 pdb=" CG PHE B 111 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE B 111 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 111 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 111 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 111 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 111 " -0.002 2.00e-02 2.50e+03 ... (remaining 1344 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 31 2.51 - 3.11: 5623 3.11 - 3.71: 11876 3.71 - 4.30: 18250 4.30 - 4.90: 30102 Nonbonded interactions: 65882 Sorted by model distance: nonbonded pdb=" C4A PLP B 601 " pdb=" N21 VSD B 602 " model vdw 1.915 3.420 nonbonded pdb=" OE1 GLU A 275 " pdb=" OG SER A 278 " model vdw 2.190 3.040 nonbonded pdb=" C4 PLP B 601 " pdb=" N21 VSD B 602 " model vdw 2.261 3.340 nonbonded pdb=" OG1 THR B 355 " pdb=" OE2 GLU B 361 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR B 448 " pdb=" OD1 ASP B 522 " model vdw 2.296 3.040 ... (remaining 65877 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: 5.060 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.250 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 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 : 0.006 0.055 7772 Z= 0.261 Angle : 0.682 7.090 10498 Z= 0.393 Chirality : 0.045 0.230 1157 Planarity : 0.004 0.054 1347 Dihedral : 12.491 84.244 2901 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.26), residues: 958 helix: 1.08 (0.24), residues: 453 sheet: -0.02 (0.50), residues: 107 loop : -0.29 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 233 TYR 0.023 0.002 TYR A 166 PHE 0.031 0.002 PHE B 111 TRP 0.011 0.002 TRP B 307 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 7771) covalent geometry : angle 0.68220 (10498) hydrogen bonds : bond 0.15145 ( 413) hydrogen bonds : angle 6.12457 ( 1161) Misc. bond : bond 0.02750 ( 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 99 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 225 GLU cc_start: 0.7286 (tt0) cc_final: 0.6895 (mt-10) REVERT: A 233 ARG cc_start: 0.6047 (mpp-170) cc_final: 0.5596 (ttm110) REVERT: B 464 GLU cc_start: 0.7386 (pt0) cc_final: 0.7176 (pt0) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.8263 time to fit residues: 85.2765 Evaluate side-chains 78 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0370 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS A 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.098446 restraints weight = 9542.727| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.68 r_work: 0.3170 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7772 Z= 0.144 Angle : 0.533 6.392 10498 Z= 0.285 Chirality : 0.043 0.164 1157 Planarity : 0.004 0.048 1347 Dihedral : 6.050 55.258 1083 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.12 % Allowed : 6.97 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.27), residues: 958 helix: 1.56 (0.24), residues: 456 sheet: 0.09 (0.52), residues: 93 loop : -0.02 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 151 TYR 0.019 0.001 TYR C 20 PHE 0.014 0.002 PHE B 280 TRP 0.011 0.001 TRP B 134 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 7771) covalent geometry : angle 0.53316 (10498) hydrogen bonds : bond 0.04570 ( 413) hydrogen bonds : angle 5.00541 ( 1161) Misc. bond : bond 0.00063 ( 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 99 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.229 Fit side-chains REVERT: A 56 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7413 (mt-10) REVERT: A 150 ASP cc_start: 0.8262 (t70) cc_final: 0.7992 (t70) REVERT: A 225 GLU cc_start: 0.7815 (tt0) cc_final: 0.7094 (mt-10) REVERT: A 326 ASP cc_start: 0.8272 (m-30) cc_final: 0.7846 (m-30) REVERT: A 406 GLU cc_start: 0.7718 (pt0) cc_final: 0.7495 (tt0) REVERT: B 464 GLU cc_start: 0.8003 (pt0) cc_final: 0.7782 (pt0) REVERT: B 542 HIS cc_start: 0.7600 (m-70) cc_final: 0.7096 (m-70) outliers start: 9 outliers final: 3 residues processed: 94 average time/residue: 0.6968 time to fit residues: 68.7990 Evaluate side-chains 84 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 423 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 0.0970 chunk 62 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 65 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 91 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.116820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102265 restraints weight = 9862.210| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.65 r_work: 0.3183 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7772 Z= 0.129 Angle : 0.496 6.384 10498 Z= 0.264 Chirality : 0.042 0.132 1157 Planarity : 0.004 0.045 1347 Dihedral : 5.793 59.163 1083 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.37 % Allowed : 8.58 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.27), residues: 958 helix: 1.77 (0.24), residues: 457 sheet: 0.05 (0.52), residues: 93 loop : -0.01 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 233 TYR 0.019 0.001 TYR C 20 PHE 0.015 0.001 PHE A 209 TRP 0.008 0.001 TRP B 134 HIS 0.006 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7771) covalent geometry : angle 0.49612 (10498) hydrogen bonds : bond 0.04172 ( 413) hydrogen bonds : angle 4.77628 ( 1161) Misc. bond : bond 0.00075 ( 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 100 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.294 Fit side-chains REVERT: A 150 ASP cc_start: 0.8236 (t70) cc_final: 0.7985 (t70) REVERT: A 225 GLU cc_start: 0.7842 (tt0) cc_final: 0.7282 (mt-10) REVERT: A 326 ASP cc_start: 0.8261 (m-30) cc_final: 0.7839 (m-30) REVERT: A 375 LYS cc_start: 0.8383 (tttm) cc_final: 0.8080 (tptp) REVERT: B 68 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6707 (ttp) REVERT: B 281 LYS cc_start: 0.8633 (mmtt) cc_final: 0.8192 (mtpt) REVERT: B 464 GLU cc_start: 0.7995 (pt0) cc_final: 0.7789 (pt0) REVERT: B 530 GLU cc_start: 0.8155 (tt0) cc_final: 0.7913 (tt0) REVERT: B 542 HIS cc_start: 0.7599 (m-70) cc_final: 0.7346 (m-70) outliers start: 11 outliers final: 4 residues processed: 95 average time/residue: 0.6910 time to fit residues: 68.9923 Evaluate side-chains 86 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 94 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 65 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3358 r_free = 0.3358 target = 0.110734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.096032 restraints weight = 9755.205| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.69 r_work: 0.3140 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7772 Z= 0.217 Angle : 0.567 8.456 10498 Z= 0.296 Chirality : 0.045 0.151 1157 Planarity : 0.004 0.049 1347 Dihedral : 5.797 62.369 1083 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.62 % Allowed : 9.83 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.27), residues: 958 helix: 1.60 (0.24), residues: 457 sheet: 0.05 (0.53), residues: 88 loop : -0.07 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 233 TYR 0.019 0.002 TYR C 20 PHE 0.017 0.002 PHE A 209 TRP 0.010 0.002 TRP C 32 HIS 0.010 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 7771) covalent geometry : angle 0.56692 (10498) hydrogen bonds : bond 0.04834 ( 413) hydrogen bonds : angle 4.80166 ( 1161) Misc. bond : bond 0.00105 ( 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 95 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.327 Fit side-chains REVERT: A 225 GLU cc_start: 0.7854 (tt0) cc_final: 0.7143 (mt-10) REVERT: A 326 ASP cc_start: 0.8257 (m-30) cc_final: 0.7788 (m-30) REVERT: B 152 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8488 (pt0) REVERT: B 281 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8181 (mtpt) REVERT: B 464 GLU cc_start: 0.8051 (pt0) cc_final: 0.7844 (pt0) REVERT: B 542 HIS cc_start: 0.7642 (m-70) cc_final: 0.7219 (m-70) outliers start: 13 outliers final: 7 residues processed: 88 average time/residue: 0.7089 time to fit residues: 65.7011 Evaluate side-chains 85 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 152 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 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 = 0.3405 r_free = 0.3405 target = 0.113668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.099192 restraints weight = 9510.073| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.63 r_work: 0.3171 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7772 Z= 0.140 Angle : 0.508 7.715 10498 Z= 0.267 Chirality : 0.042 0.140 1157 Planarity : 0.004 0.045 1347 Dihedral : 5.604 59.312 1083 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.24 % Allowed : 10.57 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.27), residues: 958 helix: 1.76 (0.24), residues: 457 sheet: 0.01 (0.53), residues: 88 loop : -0.05 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 207 TYR 0.020 0.001 TYR C 20 PHE 0.015 0.001 PHE A 209 TRP 0.008 0.001 TRP C 32 HIS 0.006 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 7771) covalent geometry : angle 0.50809 (10498) hydrogen bonds : bond 0.04176 ( 413) hydrogen bonds : angle 4.68980 ( 1161) Misc. bond : bond 0.00082 ( 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 93 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.305 Fit side-chains REVERT: A 225 GLU cc_start: 0.7873 (tt0) cc_final: 0.7188 (mt-10) REVERT: A 326 ASP cc_start: 0.8197 (m-30) cc_final: 0.7754 (m-30) REVERT: B 206 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8241 (m) REVERT: B 281 LYS cc_start: 0.8629 (mmtt) cc_final: 0.8192 (mtpt) REVERT: B 464 GLU cc_start: 0.8015 (pt0) cc_final: 0.7799 (pt0) REVERT: B 530 GLU cc_start: 0.8130 (tt0) cc_final: 0.7919 (tt0) REVERT: B 542 HIS cc_start: 0.7634 (m-70) cc_final: 0.7326 (m-70) outliers start: 10 outliers final: 6 residues processed: 89 average time/residue: 0.6534 time to fit residues: 61.4251 Evaluate side-chains 88 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 81 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 78 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN A 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.114042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.099635 restraints weight = 9902.746| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.64 r_work: 0.3147 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7772 Z= 0.201 Angle : 0.554 8.034 10498 Z= 0.289 Chirality : 0.044 0.159 1157 Planarity : 0.004 0.048 1347 Dihedral : 5.635 62.431 1083 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.49 % Allowed : 10.57 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.27), residues: 958 helix: 1.68 (0.24), residues: 456 sheet: 0.06 (0.53), residues: 88 loop : -0.14 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 207 TYR 0.020 0.002 TYR C 20 PHE 0.017 0.002 PHE A 209 TRP 0.010 0.002 TRP C 32 HIS 0.010 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 7771) covalent geometry : angle 0.55383 (10498) hydrogen bonds : bond 0.04646 ( 413) hydrogen bonds : angle 4.74221 ( 1161) Misc. bond : bond 0.00102 ( 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 89 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 181 ARG cc_start: 0.8585 (ttt180) cc_final: 0.8286 (ttm-80) REVERT: A 225 GLU cc_start: 0.7870 (tt0) cc_final: 0.7325 (mt-10) REVERT: A 326 ASP cc_start: 0.8175 (m-30) cc_final: 0.7749 (m-30) REVERT: B 206 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8303 (m) REVERT: B 281 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8217 (mtpt) REVERT: B 464 GLU cc_start: 0.8046 (pt0) cc_final: 0.7836 (pt0) outliers start: 12 outliers final: 9 residues processed: 83 average time/residue: 0.6615 time to fit residues: 57.9346 Evaluate side-chains 87 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 53 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.100388 restraints weight = 9845.781| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.64 r_work: 0.3157 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7772 Z= 0.164 Angle : 0.517 8.145 10498 Z= 0.272 Chirality : 0.043 0.140 1157 Planarity : 0.004 0.046 1347 Dihedral : 5.538 61.132 1083 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.87 % Allowed : 10.95 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.27), residues: 958 helix: 1.74 (0.24), residues: 457 sheet: 0.02 (0.53), residues: 88 loop : -0.14 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 207 TYR 0.021 0.001 TYR C 20 PHE 0.016 0.002 PHE A 209 TRP 0.009 0.001 TRP C 32 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 7771) covalent geometry : angle 0.51719 (10498) hydrogen bonds : bond 0.04336 ( 413) hydrogen bonds : angle 4.69977 ( 1161) Misc. bond : bond 0.00099 ( 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 95 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 181 ARG cc_start: 0.8607 (ttt180) cc_final: 0.8321 (ttm-80) REVERT: A 225 GLU cc_start: 0.7890 (tt0) cc_final: 0.7336 (mt-10) REVERT: A 326 ASP cc_start: 0.8202 (m-30) cc_final: 0.7765 (m-30) REVERT: B 206 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8272 (m) REVERT: B 281 LYS cc_start: 0.8668 (mmtt) cc_final: 0.8223 (mtpt) REVERT: B 464 GLU cc_start: 0.8043 (pt0) cc_final: 0.7840 (pt0) REVERT: B 472 MET cc_start: 0.9451 (mmp) cc_final: 0.9132 (mmp) REVERT: B 530 GLU cc_start: 0.8154 (tt0) cc_final: 0.7879 (pt0) outliers start: 15 outliers final: 10 residues processed: 88 average time/residue: 0.6581 time to fit residues: 60.9315 Evaluate side-chains 89 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 51 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 0.0770 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.115010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.100514 restraints weight = 9906.839| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.65 r_work: 0.3159 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7772 Z= 0.159 Angle : 0.517 8.260 10498 Z= 0.271 Chirality : 0.044 0.275 1157 Planarity : 0.004 0.048 1347 Dihedral : 5.477 61.445 1083 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.99 % Allowed : 11.07 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.27), residues: 958 helix: 1.78 (0.24), residues: 456 sheet: 0.01 (0.53), residues: 88 loop : -0.17 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 233 TYR 0.021 0.001 TYR C 20 PHE 0.016 0.002 PHE A 209 TRP 0.009 0.001 TRP C 32 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 7771) covalent geometry : angle 0.51674 (10498) hydrogen bonds : bond 0.04285 ( 413) hydrogen bonds : angle 4.67958 ( 1161) Misc. bond : bond 0.00097 ( 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 96 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 181 ARG cc_start: 0.8605 (ttt180) cc_final: 0.8318 (ttm-80) REVERT: A 225 GLU cc_start: 0.7891 (tt0) cc_final: 0.7195 (mt-10) REVERT: A 233 ARG cc_start: 0.7015 (mtm110) cc_final: 0.6497 (pmt170) REVERT: A 326 ASP cc_start: 0.8200 (m-30) cc_final: 0.7765 (m-30) REVERT: B 206 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8282 (m) REVERT: B 281 LYS cc_start: 0.8667 (mmtt) cc_final: 0.8221 (mtpt) REVERT: B 464 GLU cc_start: 0.8043 (pt0) cc_final: 0.7840 (pt0) REVERT: B 472 MET cc_start: 0.9460 (mmp) cc_final: 0.9064 (mmp) REVERT: B 530 GLU cc_start: 0.8142 (tt0) cc_final: 0.7940 (tt0) outliers start: 16 outliers final: 11 residues processed: 88 average time/residue: 0.6674 time to fit residues: 61.8693 Evaluate side-chains 91 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 19 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 0.0570 chunk 84 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.113523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099053 restraints weight = 9444.242| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.64 r_work: 0.3166 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7772 Z= 0.146 Angle : 0.506 8.364 10498 Z= 0.266 Chirality : 0.043 0.241 1157 Planarity : 0.004 0.051 1347 Dihedral : 5.399 61.249 1083 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.74 % Allowed : 11.19 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.27), residues: 958 helix: 1.80 (0.24), residues: 457 sheet: -0.00 (0.53), residues: 88 loop : -0.18 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 233 TYR 0.022 0.001 TYR C 20 PHE 0.015 0.001 PHE A 209 TRP 0.008 0.001 TRP C 32 HIS 0.006 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7771) covalent geometry : angle 0.50620 (10498) hydrogen bonds : bond 0.04145 ( 413) hydrogen bonds : angle 4.64955 ( 1161) Misc. bond : bond 0.00093 ( 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 97 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 181 ARG cc_start: 0.8573 (ttt180) cc_final: 0.8286 (ttm-80) REVERT: A 225 GLU cc_start: 0.7859 (tt0) cc_final: 0.7162 (mt-10) REVERT: A 233 ARG cc_start: 0.6999 (mtm110) cc_final: 0.6482 (pmt170) REVERT: A 326 ASP cc_start: 0.8179 (m-30) cc_final: 0.7751 (m-30) REVERT: B 206 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8268 (m) REVERT: B 281 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8214 (mtpt) REVERT: B 464 GLU cc_start: 0.8027 (pt0) cc_final: 0.7808 (pt0) REVERT: B 472 MET cc_start: 0.9459 (mmp) cc_final: 0.9099 (mmp) REVERT: B 530 GLU cc_start: 0.8131 (tt0) cc_final: 0.7916 (tt0) REVERT: C 28 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8774 (mtp) outliers start: 14 outliers final: 10 residues processed: 90 average time/residue: 0.6518 time to fit residues: 61.8651 Evaluate side-chains 91 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain C residue 28 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.097262 restraints weight = 9559.415| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.67 r_work: 0.3155 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7772 Z= 0.163 Angle : 0.525 8.430 10498 Z= 0.273 Chirality : 0.044 0.242 1157 Planarity : 0.004 0.048 1347 Dihedral : 5.409 62.132 1083 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.87 % Allowed : 11.19 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.27), residues: 958 helix: 1.77 (0.24), residues: 457 sheet: 0.01 (0.53), residues: 88 loop : -0.19 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 207 TYR 0.022 0.001 TYR C 20 PHE 0.016 0.002 PHE A 209 TRP 0.009 0.001 TRP C 32 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 7771) covalent geometry : angle 0.52472 (10498) hydrogen bonds : bond 0.04293 ( 413) hydrogen bonds : angle 4.68266 ( 1161) Misc. bond : bond 0.00097 ( 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 95 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 181 ARG cc_start: 0.8601 (ttt180) cc_final: 0.8317 (ttm-80) REVERT: A 225 GLU cc_start: 0.7845 (tt0) cc_final: 0.7144 (mt-10) REVERT: A 326 ASP cc_start: 0.8190 (m-30) cc_final: 0.7748 (m-30) REVERT: B 206 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8279 (m) REVERT: B 281 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8199 (mtpt) REVERT: B 464 GLU cc_start: 0.8030 (pt0) cc_final: 0.7808 (pt0) REVERT: B 472 MET cc_start: 0.9460 (mmp) cc_final: 0.9063 (mmp) REVERT: B 530 GLU cc_start: 0.8136 (tt0) cc_final: 0.7911 (tt0) outliers start: 15 outliers final: 11 residues processed: 87 average time/residue: 0.6588 time to fit residues: 60.4199 Evaluate side-chains 91 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 90 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 12 optimal weight: 0.2980 chunk 39 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 0.0000 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.114582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.100051 restraints weight = 9518.827| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.65 r_work: 0.3199 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 7772 Z= 0.106 Angle : 0.492 13.277 10498 Z= 0.254 Chirality : 0.042 0.226 1157 Planarity : 0.004 0.050 1347 Dihedral : 5.193 59.708 1083 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.62 % Allowed : 11.69 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.27), residues: 958 helix: 1.86 (0.24), residues: 463 sheet: -0.03 (0.52), residues: 88 loop : -0.14 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 233 TYR 0.024 0.001 TYR C 20 PHE 0.014 0.001 PHE A 209 TRP 0.010 0.001 TRP B 134 HIS 0.005 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 7771) covalent geometry : angle 0.49250 (10498) hydrogen bonds : bond 0.03633 ( 413) hydrogen bonds : angle 4.58586 ( 1161) Misc. bond : bond 0.00078 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2558.21 seconds wall clock time: 44 minutes 20.41 seconds (2660.41 seconds total)