Starting phenix.real_space_refine on Thu Jul 2 08:18:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k0k_22600/07_2026/7k0k_22600.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0k_22600/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7k0k_22600/07_2026/7k0k_22600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0k_22600/07_2026/7k0k_22600.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7k0k_22600/07_2026/7k0k_22600.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k0k_22600/07_2026/7k0k_22600.cif" model { file = "/net/cci-nas-00/data/ceres_data/7k0k_22600/07_2026/7k0k_22600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0k_22600/07_2026/7k0k_22600.cif" } 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-6108/lib/python3.11/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: 1.42, per 1000 atoms: 0.19 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: 0.52 Conformation dependent library (CDL) restraints added in 374.7 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: 0.19 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: 1.09 Time building geometry restraints manager: 0.72 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: 312 33.70 - 50.55: 63 50.55 - 67.40: 12 67.40 - 84.24: 4 Dihedral angle restraints: 4673 sinusoidal: 1889 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 4670 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: 4.750 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.260 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 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 : 12.436 84.244 2895 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/Z covalent geometry : bond 0.00583 / 0.26 ( 7771) covalent geometry : angle 0.68220 / 0.39 (10498) hydrogen bonds : bond 0.15145 / 9.94 ( 413) hydrogen bonds : angle 6.12457 / 4.55 ( 1161) Misc. bond : bond 0.02750 / 1.45 ( 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 : 0.256 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: 0.7087 time to fit residues: 73.1531 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 : 0.264 ------------------------------------------------------------------------------- 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... 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 = 0.3389 r_free = 0.3389 target = 0.113212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.098435 restraints weight = 9544.224| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.68 r_work: 0.3169 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7772 Z= 0.144 Angle : 0.534 6.392 10498 Z= 0.285 Chirality : 0.043 0.170 1157 Planarity : 0.004 0.048 1347 Dihedral : 5.285 55.228 1077 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.12 % Allowed : 6.72 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.00 (0.27), residues: 958 helix: 1.49 (0.24), residues: 462 sheet: 0.08 (0.52), residues: 93 loop : -0.07 (0.30), residues: 403 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 A 209 TRP 0.011 0.001 TRP B 134 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 7771) covalent geometry : angle 0.53396 / 0.28 (10498) hydrogen bonds : bond 0.04575 / 3.17 ( 413) hydrogen bonds : angle 5.00927 / 3.73 ( 1161) Misc. bond : bond 0.00064 / 0.03 ( 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 98 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.286 Fit side-chains REVERT: A 56 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7417 (mt-10) REVERT: A 150 ASP cc_start: 0.8256 (t70) cc_final: 0.7986 (t70) REVERT: A 225 GLU cc_start: 0.7809 (tt0) cc_final: 0.7099 (mt-10) REVERT: A 326 ASP cc_start: 0.8260 (m-30) cc_final: 0.7839 (m-30) REVERT: A 406 GLU cc_start: 0.7725 (pt0) cc_final: 0.7502 (tt0) REVERT: B 464 GLU cc_start: 0.7954 (pt0) cc_final: 0.7735 (pt0) REVERT: B 542 HIS cc_start: 0.7614 (m-70) cc_final: 0.7112 (m-70) outliers start: 9 outliers final: 3 residues processed: 93 average time/residue: 0.6055 time to fit residues: 59.1923 Evaluate side-chains 83 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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: 0.0670 chunk 62 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 65 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.116898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.102441 restraints weight = 9846.098| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.63 r_work: 0.3186 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7772 Z= 0.129 Angle : 0.494 6.388 10498 Z= 0.263 Chirality : 0.042 0.133 1157 Planarity : 0.004 0.046 1347 Dihedral : 5.117 60.213 1077 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.49 % Allowed : 8.58 % Favored : 89.93 % 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: 1.24 (0.27), residues: 958 helix: 1.78 (0.24), residues: 457 sheet: 0.03 (0.52), residues: 93 loop : -0.00 (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 0.005 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 7771) covalent geometry : angle 0.49434 / 0.26 (10498) hydrogen bonds : bond 0.04172 / 2.89 ( 413) hydrogen bonds : angle 4.77972 / 3.56 ( 1161) Misc. bond : bond 0.00089 / 0.05 ( 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 101 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.252 Fit side-chains REVERT: A 150 ASP cc_start: 0.8230 (t70) cc_final: 0.7978 (t70) REVERT: A 225 GLU cc_start: 0.7836 (tt0) cc_final: 0.7282 (mt-10) REVERT: A 326 ASP cc_start: 0.8261 (m-30) cc_final: 0.7836 (m-30) REVERT: A 375 LYS cc_start: 0.8373 (tttm) cc_final: 0.8070 (tptp) REVERT: B 68 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6701 (ttp) REVERT: B 281 LYS cc_start: 0.8625 (mmtt) cc_final: 0.8186 (mtpt) REVERT: B 464 GLU cc_start: 0.7986 (pt0) cc_final: 0.7778 (pt0) REVERT: B 542 HIS cc_start: 0.7601 (m-70) cc_final: 0.7357 (m-70) outliers start: 12 outliers final: 5 residues processed: 95 average time/residue: 0.6159 time to fit residues: 61.5271 Evaluate side-chains 85 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 420 MET 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: 0.7980 chunk 52 optimal weight: 0.9980 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: 1.9990 chunk 62 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.095853 restraints weight = 9749.465| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.68 r_work: 0.3138 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7772 Z= 0.222 Angle : 0.574 8.704 10498 Z= 0.300 Chirality : 0.045 0.154 1157 Planarity : 0.004 0.050 1347 Dihedral : 5.321 65.652 1077 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.62 % Allowed : 9.95 % Favored : 88.43 % 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: 1.04 (0.27), residues: 958 helix: 1.59 (0.24), residues: 456 sheet: 0.08 (0.54), residues: 88 loop : -0.11 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 207 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 0.011 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.22 ( 7771) covalent geometry : angle 0.57400 / 0.30 (10498) hydrogen bonds : bond 0.04911 / 3.42 ( 413) hydrogen bonds : angle 4.81559 / 3.58 ( 1161) Misc. bond : bond 0.00133 / 0.07 ( 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 93 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.307 Fit side-chains REVERT: A 225 GLU cc_start: 0.7859 (tt0) cc_final: 0.7152 (mt-10) REVERT: A 326 ASP cc_start: 0.8249 (m-30) cc_final: 0.7774 (m-30) REVERT: B 281 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8182 (mtpt) REVERT: B 464 GLU cc_start: 0.8052 (pt0) cc_final: 0.7836 (pt0) REVERT: B 542 HIS cc_start: 0.7651 (m-70) cc_final: 0.7278 (m-70) outliers start: 13 outliers final: 7 residues processed: 86 average time/residue: 0.5813 time to fit residues: 52.8767 Evaluate side-chains 83 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 43 optimal weight: 0.0670 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.113451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.098810 restraints weight = 9593.267| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.68 r_work: 0.3177 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7772 Z= 0.119 Angle : 0.488 7.537 10498 Z= 0.257 Chirality : 0.042 0.137 1157 Planarity : 0.004 0.045 1347 Dihedral : 5.026 60.745 1077 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.12 % Allowed : 10.82 % Favored : 88.06 % 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: 1.26 (0.27), residues: 958 helix: 1.82 (0.24), residues: 457 sheet: 0.02 (0.53), residues: 88 loop : -0.02 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 450 TYR 0.020 0.001 TYR C 20 PHE 0.015 0.001 PHE A 209 TRP 0.008 0.001 TRP B 134 HIS 0.005 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 7771) covalent geometry : angle 0.48781 / 0.26 (10498) hydrogen bonds : bond 0.03898 / 2.73 ( 413) hydrogen bonds : angle 4.63959 / 3.46 ( 1161) Misc. bond : bond 0.00092 / 0.05 ( 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 91 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.247 Fit side-chains REVERT: A 225 GLU cc_start: 0.7865 (tt0) cc_final: 0.7299 (mt-10) REVERT: A 227 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7003 (pm20) REVERT: A 326 ASP cc_start: 0.8197 (m-30) cc_final: 0.7758 (m-30) REVERT: B 206 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8218 (p) REVERT: B 281 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8199 (mtpt) REVERT: B 374 MET cc_start: 0.9198 (tmt) cc_final: 0.8985 (tmt) REVERT: B 464 GLU cc_start: 0.8024 (pt0) cc_final: 0.7810 (pt0) REVERT: B 542 HIS cc_start: 0.7790 (m-70) cc_final: 0.7544 (m-70) outliers start: 9 outliers final: 5 residues processed: 87 average time/residue: 0.5623 time to fit residues: 51.6302 Evaluate side-chains 87 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 83 optimal weight: 0.0060 chunk 67 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 24 optimal weight: 0.0770 chunk 78 optimal weight: 0.6980 overall best weight: 0.5154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.113471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.098834 restraints weight = 9613.187| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.68 r_work: 0.3175 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7772 Z= 0.127 Angle : 0.494 7.940 10498 Z= 0.258 Chirality : 0.042 0.135 1157 Planarity : 0.004 0.044 1347 Dihedral : 4.992 61.999 1077 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.24 % Allowed : 11.07 % Favored : 87.69 % 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: 1.31 (0.27), residues: 958 helix: 1.90 (0.24), residues: 457 sheet: 0.03 (0.52), residues: 88 loop : -0.04 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 233 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 0.005 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 7771) covalent geometry : angle 0.49394 / 0.26 (10498) hydrogen bonds : bond 0.03923 / 2.74 ( 413) hydrogen bonds : angle 4.61403 / 3.44 ( 1161) Misc. bond : bond 0.00089 / 0.05 ( 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 90 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.283 Fit side-chains REVERT: A 225 GLU cc_start: 0.7851 (tt0) cc_final: 0.7276 (mt-10) REVERT: A 326 ASP cc_start: 0.8200 (m-30) cc_final: 0.7750 (m-30) REVERT: B 206 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8233 (p) REVERT: B 281 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8193 (mtpt) REVERT: B 374 MET cc_start: 0.9221 (tmt) cc_final: 0.9009 (tmt) REVERT: B 464 GLU cc_start: 0.8023 (pt0) cc_final: 0.7815 (pt0) REVERT: B 530 GLU cc_start: 0.8144 (tt0) cc_final: 0.7898 (pt0) outliers start: 10 outliers final: 8 residues processed: 85 average time/residue: 0.6142 time to fit residues: 55.0327 Evaluate side-chains 88 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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 195 VAL 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: 0.5980 chunk 91 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 20 optimal weight: 0.0010 chunk 86 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.099906 restraints weight = 9480.339| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.62 r_work: 0.3181 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1516 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= 0.138 Angle : 0.504 8.968 10498 Z= 0.262 Chirality : 0.042 0.136 1157 Planarity : 0.004 0.045 1347 Dihedral : 5.003 63.237 1077 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.49 % Allowed : 10.82 % Favored : 87.69 % 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: 1.28 (0.27), residues: 958 helix: 1.89 (0.24), residues: 457 sheet: 0.02 (0.53), residues: 88 loop : -0.08 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 233 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/Z covalent geometry : bond 0.00327 / 0.14 ( 7771) covalent geometry : angle 0.50400 / 0.26 (10498) hydrogen bonds : bond 0.04017 / 2.81 ( 413) hydrogen bonds : angle 4.60792 / 3.44 ( 1161) Misc. bond : bond 0.00095 / 0.05 ( 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 94 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.291 Fit side-chains REVERT: A 181 ARG cc_start: 0.8579 (ttt180) cc_final: 0.8280 (ttm-80) REVERT: A 225 GLU cc_start: 0.7859 (tt0) cc_final: 0.7282 (mt-10) REVERT: A 326 ASP cc_start: 0.8207 (m-30) cc_final: 0.7738 (m-30) REVERT: B 206 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8204 (p) REVERT: B 281 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8160 (mtpt) REVERT: B 374 MET cc_start: 0.9221 (tmt) cc_final: 0.8967 (tmt) REVERT: B 464 GLU cc_start: 0.8013 (pt0) cc_final: 0.7803 (pt0) REVERT: B 530 GLU cc_start: 0.8109 (tt0) cc_final: 0.7812 (pt0) outliers start: 12 outliers final: 10 residues processed: 90 average time/residue: 0.5615 time to fit residues: 53.4290 Evaluate side-chains 91 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 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 B residue 503 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 51 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 469 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099439 restraints weight = 9575.667| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.64 r_work: 0.3175 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7772 Z= 0.149 Angle : 0.515 9.731 10498 Z= 0.267 Chirality : 0.043 0.137 1157 Planarity : 0.004 0.045 1347 Dihedral : 5.038 64.682 1077 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.99 % Allowed : 10.57 % Favored : 87.44 % 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: 1.24 (0.27), residues: 958 helix: 1.87 (0.24), residues: 457 sheet: 0.01 (0.53), residues: 88 loop : -0.12 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 233 TYR 0.021 0.001 TYR C 20 PHE 0.016 0.002 PHE A 209 TRP 0.008 0.001 TRP C 32 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 7771) covalent geometry : angle 0.51500 / 0.27 (10498) hydrogen bonds : bond 0.04132 / 2.89 ( 413) hydrogen bonds : angle 4.61723 / 3.44 ( 1161) Misc. bond : bond 0.00100 / 0.05 ( 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 : 0.338 Fit side-chains REVERT: A 181 ARG cc_start: 0.8595 (ttt180) cc_final: 0.8307 (ttm-80) REVERT: A 225 GLU cc_start: 0.7897 (tt0) cc_final: 0.7338 (mt-10) REVERT: A 326 ASP cc_start: 0.8209 (m-30) cc_final: 0.7758 (m-30) REVERT: B 206 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8253 (p) REVERT: B 281 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8205 (mtpt) REVERT: B 464 GLU cc_start: 0.8042 (pt0) cc_final: 0.7835 (pt0) REVERT: B 530 GLU cc_start: 0.8164 (tt0) cc_final: 0.7959 (tt0) outliers start: 16 outliers final: 11 residues processed: 88 average time/residue: 0.6381 time to fit residues: 59.5572 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 : 0.371 ------------------------------------------------------------------------------- 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 94 TRP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 320 MET 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: 1.9990 chunk 21 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.113292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.098884 restraints weight = 9470.326| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.63 r_work: 0.3166 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7772 Z= 0.168 Angle : 0.533 10.518 10498 Z= 0.276 Chirality : 0.044 0.280 1157 Planarity : 0.004 0.048 1347 Dihedral : 5.112 65.724 1077 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.74 % Allowed : 10.95 % Favored : 87.31 % 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: 1.17 (0.27), residues: 958 helix: 1.81 (0.24), residues: 457 sheet: 0.00 (0.53), residues: 88 loop : -0.16 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 233 TYR 0.020 0.001 TYR C 20 PHE 0.016 0.002 PHE A 209 TRP 0.008 0.001 TRP C 32 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 7771) covalent geometry : angle 0.53297 / 0.28 (10498) hydrogen bonds : bond 0.04293 / 3.01 ( 413) hydrogen bonds : angle 4.64407 / 3.46 ( 1161) Misc. bond : bond 0.00113 / 0.06 ( 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 93 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.264 Fit side-chains REVERT: A 181 ARG cc_start: 0.8594 (ttt180) cc_final: 0.8304 (ttm-80) REVERT: A 225 GLU cc_start: 0.7893 (tt0) cc_final: 0.7195 (mt-10) REVERT: A 326 ASP cc_start: 0.8188 (m-30) cc_final: 0.7759 (m-30) REVERT: B 206 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8253 (p) REVERT: B 281 LYS cc_start: 0.8612 (mmtt) cc_final: 0.8205 (mtpt) REVERT: B 464 GLU cc_start: 0.8043 (pt0) cc_final: 0.7835 (pt0) REVERT: C 28 MET cc_start: 0.9055 (mtp) cc_final: 0.8778 (mtp) outliers start: 14 outliers final: 10 residues processed: 87 average time/residue: 0.6440 time to fit residues: 59.2838 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 : 0.315 ------------------------------------------------------------------------------- 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 94 TRP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 320 MET 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 76 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.113249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098785 restraints weight = 9490.650| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.65 r_work: 0.3162 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1540 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 : 0.533 10.706 10498 Z= 0.276 Chirality : 0.044 0.245 1157 Planarity : 0.004 0.051 1347 Dihedral : 5.114 65.363 1077 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.62 % Allowed : 11.32 % 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: 1.09 (0.27), residues: 958 helix: 1.72 (0.24), residues: 463 sheet: 0.00 (0.53), residues: 88 loop : -0.22 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 233 TYR 0.021 0.001 TYR C 20 PHE 0.016 0.002 PHE A 209 TRP 0.008 0.001 TRP C 32 HIS 0.007 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 ( 7771) covalent geometry : angle 0.53283 / 0.28 (10498) hydrogen bonds : bond 0.04276 / 2.99 ( 413) hydrogen bonds : angle 4.65206 / 3.47 ( 1161) Misc. bond : bond 0.00107 / 0.06 ( 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 93 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.210 Fit side-chains REVERT: A 181 ARG cc_start: 0.8581 (ttt180) cc_final: 0.8293 (ttm-80) REVERT: A 225 GLU cc_start: 0.7852 (tt0) cc_final: 0.7159 (mt-10) REVERT: A 233 ARG cc_start: 0.6907 (mtm110) cc_final: 0.6390 (pmt170) REVERT: A 326 ASP cc_start: 0.8171 (m-30) cc_final: 0.7738 (m-30) REVERT: B 206 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8236 (p) REVERT: B 281 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8197 (mtpt) REVERT: B 464 GLU cc_start: 0.8026 (pt0) cc_final: 0.7817 (pt0) REVERT: B 530 GLU cc_start: 0.8193 (tt0) cc_final: 0.7974 (pt0) outliers start: 13 outliers final: 9 residues processed: 87 average time/residue: 0.6352 time to fit residues: 58.4127 Evaluate side-chains 89 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 37 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 12 optimal weight: 0.0970 chunk 39 optimal weight: 0.0670 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 0.0670 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 GLN A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.115230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.100660 restraints weight = 9532.993| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.68 r_work: 0.3208 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7772 Z= 0.100 Angle : 0.482 10.515 10498 Z= 0.250 Chirality : 0.042 0.245 1157 Planarity : 0.004 0.049 1347 Dihedral : 4.825 61.479 1077 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.37 % Allowed : 11.69 % 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: 1.23 (0.27), residues: 958 helix: 1.83 (0.24), residues: 469 sheet: -0.01 (0.52), residues: 88 loop : -0.15 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 233 TYR 0.021 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/Z covalent geometry : bond 0.00228 / 0.10 ( 7771) covalent geometry : angle 0.48212 / 0.25 (10498) hydrogen bonds : bond 0.03493 / 2.45 ( 413) hydrogen bonds : angle 4.51769 / 3.37 ( 1161) Misc. bond : bond 0.00075 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2415.45 seconds wall clock time: 42 minutes 4.55 seconds (2524.55 seconds total)