Starting phenix.real_space_refine on Wed Jun 11 14:33:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rlc_19338/06_2025/8rlc_19338_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rlc_19338/06_2025/8rlc_19338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rlc_19338/06_2025/8rlc_19338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rlc_19338/06_2025/8rlc_19338.map" model { file = "/net/cci-nas-00/data/ceres_data/8rlc_19338/06_2025/8rlc_19338_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rlc_19338/06_2025/8rlc_19338_trim.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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 S 32 5.16 5 C 4219 2.51 5 N 1116 2.21 5 O 1214 1.98 5 H 6330 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12911 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 3212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3212 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 10, 'TRANS': 206} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1612 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1671 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 6392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 6392 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 12, 'TRANS': 408} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.83, per 1000 atoms: 0.53 Number of scatterers: 12911 At special positions: 0 Unit cell: (60.58, 87.608, 132.344, 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 32 16.00 O 1214 8.00 N 1116 7.00 C 4219 6.00 H 6330 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS C 11 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.0 seconds 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 50.2% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'B' and resid 56 through 67 removed outlier: 4.086A pdb=" N LEU B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'D' and resid 83 through 88 removed outlier: 3.520A pdb=" N ALA D 88 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'A' and resid 101 through 125 removed outlier: 4.657A pdb=" N VAL A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ALA A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A 124 " --> pdb=" O TYR A 120 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 136 through 165 removed outlier: 3.702A pdb=" N LEU A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 166 through 187 removed outlier: 3.690A pdb=" N ILE A 170 " --> pdb=" O ASN A 166 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 222 removed outlier: 3.501A pdb=" N VAL A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Proline residue: A 215 - end of helix removed outlier: 3.785A pdb=" N PHE A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 257 removed outlier: 4.271A pdb=" N THR A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Proline residue: A 239 - end of helix Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 261 through 281 removed outlier: 4.460A pdb=" N SER A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Proline residue: A 267 - end of helix removed outlier: 3.517A pdb=" N ILE A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 311 removed outlier: 4.222A pdb=" N ARG A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 347 Proline residue: A 337 - end of helix Processing helix chain 'A' and resid 360 through 392 removed outlier: 3.608A pdb=" N LEU A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 391 " --> pdb=" O TRP A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 421 removed outlier: 4.355A pdb=" N PHE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 451 removed outlier: 3.733A pdb=" N ALA A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N TRP A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ALA A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 455 through 471 Processing helix chain 'A' and resid 474 through 490 Processing helix chain 'A' and resid 493 through 506 Processing helix chain 'A' and resid 506 through 525 removed outlier: 4.358A pdb=" N PHE A 510 " --> pdb=" O MET A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 539 removed outlier: 3.712A pdb=" N ASP A 529 " --> pdb=" O PHE A 525 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 22 removed outlier: 5.528A pdb=" N ASN B 149 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LYS B 166 " --> pdb=" O ASN B 149 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE B 161 " --> pdb=" O ASN B 185 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 119 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN B 121 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 123 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.725A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLY D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N MET D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 94 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR D 100 " --> pdb=" O VAL D 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.571A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ASN C 50 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N THR C 34 " --> pdb=" O ASN C 50 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1242 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: 4.68 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6320 1.03 - 1.23: 12 1.23 - 1.42: 2898 1.42 - 1.62: 3781 1.62 - 1.81: 48 Bond restraints: 13059 Sorted by residual: bond pdb=" C3' LMT A 601 " pdb=" O3' LMT A 601 " ideal model delta sigma weight residual 1.404 1.362 0.042 2.00e-02 2.50e+03 4.31e+00 bond pdb=" C7 LMT A 601 " pdb=" C8 LMT A 601 " ideal model delta sigma weight residual 1.529 1.490 0.039 2.00e-02 2.50e+03 3.90e+00 bond pdb=" C8 LMT A 601 " pdb=" C9 LMT A 601 " ideal model delta sigma weight residual 1.531 1.494 0.037 2.00e-02 2.50e+03 3.50e+00 bond pdb=" C6' LMT A 601 " pdb=" O6' LMT A 601 " ideal model delta sigma weight residual 1.407 1.371 0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" C2 LMT A 601 " pdb=" C3 LMT A 601 " ideal model delta sigma weight residual 1.529 1.495 0.034 2.00e-02 2.50e+03 2.97e+00 ... (remaining 13054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 23315 1.88 - 3.76: 106 3.76 - 5.65: 15 5.65 - 7.53: 0 7.53 - 9.41: 3 Bond angle restraints: 23439 Sorted by residual: angle pdb=" C2 LMT A 601 " pdb=" C3 LMT A 601 " pdb=" C4 LMT A 601 " ideal model delta sigma weight residual 117.09 107.68 9.41 3.00e+00 1.11e-01 9.84e+00 angle pdb=" C10 LMT A 601 " pdb=" C9 LMT A 601 " pdb=" C8 LMT A 601 " ideal model delta sigma weight residual 116.03 107.57 8.46 3.00e+00 1.11e-01 7.95e+00 angle pdb=" C GLY A 471 " pdb=" N ASP A 472 " pdb=" CA ASP A 472 " ideal model delta sigma weight residual 121.54 126.74 -5.20 1.91e+00 2.74e-01 7.41e+00 angle pdb=" C6 LMT A 601 " pdb=" C7 LMT A 601 " pdb=" C8 LMT A 601 " ideal model delta sigma weight residual 117.26 109.23 8.03 3.00e+00 1.11e-01 7.17e+00 angle pdb=" C ILE A 336 " pdb=" CA ILE A 336 " pdb=" CB ILE A 336 " ideal model delta sigma weight residual 114.00 110.90 3.10 1.31e+00 5.83e-01 5.61e+00 ... (remaining 23434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 5566 16.00 - 32.00: 444 32.00 - 48.00: 124 48.00 - 64.00: 96 64.00 - 80.00: 5 Dihedral angle restraints: 6235 sinusoidal: 3270 harmonic: 2965 Sorted by residual: dihedral pdb=" CA ARG C 101 " pdb=" C ARG C 101 " pdb=" N PHE C 102 " pdb=" CA PHE C 102 " ideal model delta harmonic sigma weight residual -180.00 -162.78 -17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA MET A 448 " pdb=" C MET A 448 " pdb=" N TYR A 449 " pdb=" CA TYR A 449 " ideal model delta harmonic sigma weight residual 180.00 163.81 16.19 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CG ARG D 38 " pdb=" CD ARG D 38 " pdb=" NE ARG D 38 " pdb=" CZ ARG D 38 " ideal model delta sinusoidal sigma weight residual -90.00 -133.73 43.73 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 6232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 809 0.041 - 0.082: 160 0.082 - 0.123: 62 0.123 - 0.164: 4 0.164 - 0.206: 2 Chirality restraints: 1037 Sorted by residual: chirality pdb=" C5' LMT A 601 " pdb=" C4' LMT A 601 " pdb=" C6' LMT A 601 " pdb=" O5' LMT A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.30 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C4' LMT A 601 " pdb=" C3' LMT A 601 " pdb=" C5' LMT A 601 " pdb=" O1B LMT A 601 " both_signs ideal model delta sigma weight residual False -2.55 -2.76 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 1034 not shown) Planarity restraints: 1994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 452 " -0.055 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO A 453 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 453 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 453 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 449 " -0.012 2.00e-02 2.50e+03 7.13e-03 1.52e+00 pdb=" CG TYR A 449 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 449 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 449 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 449 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 449 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 449 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 449 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TYR A 449 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR A 449 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR A 449 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR A 449 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 508 " 0.015 5.00e-02 4.00e+02 2.28e-02 8.32e-01 pdb=" N PRO A 509 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 509 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 509 " 0.013 5.00e-02 4.00e+02 ... (remaining 1991 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 1861 2.27 - 2.85: 29200 2.85 - 3.43: 33425 3.43 - 4.02: 45112 4.02 - 4.60: 68338 Nonbonded interactions: 177936 Sorted by model distance: nonbonded pdb=" OE1 GLN A 190 " pdb=" H GLN A 190 " model vdw 1.687 2.450 nonbonded pdb=" O SER A 319 " pdb=" HG SER A 323 " model vdw 1.687 2.450 nonbonded pdb=" HG SER A 250 " pdb=" O ALA A 360 " model vdw 1.689 2.450 nonbonded pdb=" O ALA A 237 " pdb=" H GLY A 241 " model vdw 1.690 2.450 nonbonded pdb=" O ILE A 213 " pdb=" HG1 THR A 216 " model vdw 1.699 2.450 ... (remaining 177931 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.520 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: 0.250 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.960 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.050 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 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 : 0.003 0.042 6732 Z= 0.126 Angle : 0.495 9.412 9149 Z= 0.253 Chirality : 0.040 0.206 1037 Planarity : 0.003 0.083 1165 Dihedral : 13.208 80.004 2347 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.29), residues: 854 helix: 2.21 (0.27), residues: 390 sheet: 0.06 (0.34), residues: 211 loop : 0.11 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.004 0.000 HIS B 181 PHE 0.011 0.001 PHE A 151 TYR 0.021 0.001 TYR A 449 ARG 0.003 0.000 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.09893 ( 437) hydrogen bonds : angle 5.32657 ( 1242) SS BOND : bond 0.00221 ( 3) SS BOND : angle 0.58014 ( 6) covalent geometry : bond 0.00252 ( 6729) covalent geometry : angle 0.49461 ( 9143) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 VAL cc_start: 0.6726 (t) cc_final: 0.6511 (t) REVERT: A 472 ASP cc_start: 0.7892 (t70) cc_final: 0.7605 (t0) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.3388 time to fit residues: 71.7233 Evaluate side-chains 126 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 0.0770 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.201298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.165714 restraints weight = 26453.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.171051 restraints weight = 13491.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.174333 restraints weight = 8326.653| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6732 Z= 0.115 Angle : 0.472 4.964 9149 Z= 0.253 Chirality : 0.038 0.136 1037 Planarity : 0.003 0.051 1165 Dihedral : 4.500 52.710 971 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.07 % Allowed : 6.80 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.29), residues: 854 helix: 2.30 (0.26), residues: 395 sheet: 0.28 (0.34), residues: 209 loop : 0.14 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 178 HIS 0.007 0.001 HIS B 199 PHE 0.018 0.001 PHE B 71 TYR 0.015 0.001 TYR A 116 ARG 0.002 0.000 ARG C 98 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 437) hydrogen bonds : angle 4.70722 ( 1242) SS BOND : bond 0.00276 ( 3) SS BOND : angle 0.43419 ( 6) covalent geometry : bond 0.00240 ( 6729) covalent geometry : angle 0.47251 ( 9143) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 ASP cc_start: 0.7576 (m-30) cc_final: 0.7335 (m-30) REVERT: C 13 LYS cc_start: 0.6245 (pttt) cc_final: 0.5930 (pttp) REVERT: A 472 ASP cc_start: 0.8280 (t70) cc_final: 0.8076 (t0) outliers start: 14 outliers final: 12 residues processed: 132 average time/residue: 0.3286 time to fit residues: 60.8559 Evaluate side-chains 127 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 489 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 80 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.206182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.171841 restraints weight = 27398.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.177910 restraints weight = 13334.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.181544 restraints weight = 8046.231| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6732 Z= 0.125 Angle : 0.468 5.104 9149 Z= 0.251 Chirality : 0.039 0.205 1037 Planarity : 0.003 0.037 1165 Dihedral : 4.266 42.850 971 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.07 % Allowed : 7.99 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.29), residues: 854 helix: 2.47 (0.26), residues: 393 sheet: 0.24 (0.34), residues: 212 loop : 0.19 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 178 HIS 0.004 0.001 HIS B 181 PHE 0.012 0.001 PHE A 151 TYR 0.014 0.001 TYR A 116 ARG 0.002 0.000 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.04033 ( 437) hydrogen bonds : angle 4.58611 ( 1242) SS BOND : bond 0.00251 ( 3) SS BOND : angle 0.51761 ( 6) covalent geometry : bond 0.00273 ( 6729) covalent geometry : angle 0.46760 ( 9143) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.6362 (pttt) cc_final: 0.6126 (pttp) REVERT: A 472 ASP cc_start: 0.8296 (t70) cc_final: 0.8063 (t0) outliers start: 14 outliers final: 12 residues processed: 123 average time/residue: 0.3319 time to fit residues: 56.6049 Evaluate side-chains 123 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 163 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.205086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.170165 restraints weight = 27370.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.175820 restraints weight = 13756.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.179348 restraints weight = 8561.641| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6732 Z= 0.129 Angle : 0.478 5.274 9149 Z= 0.259 Chirality : 0.039 0.192 1037 Planarity : 0.003 0.034 1165 Dihedral : 4.175 46.774 971 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.37 % Allowed : 8.58 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.29), residues: 854 helix: 2.49 (0.26), residues: 394 sheet: 0.15 (0.34), residues: 216 loop : 0.12 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 178 HIS 0.004 0.001 HIS B 181 PHE 0.011 0.001 PHE A 151 TYR 0.027 0.001 TYR A 449 ARG 0.006 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 437) hydrogen bonds : angle 4.55718 ( 1242) SS BOND : bond 0.00226 ( 3) SS BOND : angle 0.49748 ( 6) covalent geometry : bond 0.00279 ( 6729) covalent geometry : angle 0.47782 ( 9143) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.6436 (pttt) cc_final: 0.6185 (pttp) REVERT: A 472 ASP cc_start: 0.8312 (t70) cc_final: 0.8091 (t0) outliers start: 16 outliers final: 14 residues processed: 127 average time/residue: 0.3455 time to fit residues: 61.6170 Evaluate side-chains 126 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 489 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 24 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.194158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.156807 restraints weight = 27847.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.162325 restraints weight = 14683.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.165558 restraints weight = 9341.818| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 6732 Z= 0.244 Angle : 0.623 8.165 9149 Z= 0.350 Chirality : 0.042 0.188 1037 Planarity : 0.005 0.046 1165 Dihedral : 4.971 48.103 971 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.96 % Allowed : 10.21 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.28), residues: 854 helix: 1.83 (0.26), residues: 393 sheet: -0.04 (0.34), residues: 223 loop : -0.19 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 178 HIS 0.004 0.002 HIS B 148 PHE 0.021 0.003 PHE A 518 TYR 0.018 0.002 TYR C 108 ARG 0.004 0.001 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.05307 ( 437) hydrogen bonds : angle 5.16828 ( 1242) SS BOND : bond 0.00136 ( 3) SS BOND : angle 1.00535 ( 6) covalent geometry : bond 0.00539 ( 6729) covalent geometry : angle 0.62226 ( 9143) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 17 residues processed: 130 average time/residue: 0.3264 time to fit residues: 59.2414 Evaluate side-chains 123 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 489 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.197256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.162281 restraints weight = 28022.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.167329 restraints weight = 15230.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.170471 restraints weight = 9829.273| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6732 Z= 0.130 Angle : 0.493 5.934 9149 Z= 0.269 Chirality : 0.039 0.185 1037 Planarity : 0.004 0.041 1165 Dihedral : 4.600 48.967 971 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.66 % Allowed : 12.13 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.29), residues: 854 helix: 2.19 (0.26), residues: 393 sheet: 0.10 (0.34), residues: 222 loop : 0.07 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 178 HIS 0.004 0.001 HIS B 199 PHE 0.017 0.002 PHE A 176 TYR 0.015 0.001 TYR A 246 ARG 0.002 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04557 ( 437) hydrogen bonds : angle 4.74133 ( 1242) SS BOND : bond 0.00077 ( 3) SS BOND : angle 0.46910 ( 6) covalent geometry : bond 0.00278 ( 6729) covalent geometry : angle 0.49291 ( 9143) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 16 residues processed: 127 average time/residue: 0.3600 time to fit residues: 61.7745 Evaluate side-chains 123 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 489 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.196294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.159746 restraints weight = 27560.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.165303 restraints weight = 14273.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.168801 restraints weight = 9013.371| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6732 Z= 0.141 Angle : 0.495 5.926 9149 Z= 0.272 Chirality : 0.039 0.216 1037 Planarity : 0.004 0.043 1165 Dihedral : 4.590 53.319 971 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.96 % Allowed : 12.43 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.29), residues: 854 helix: 2.30 (0.26), residues: 393 sheet: 0.16 (0.34), residues: 222 loop : -0.01 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 178 HIS 0.029 0.002 HIS B 181 PHE 0.011 0.001 PHE A 236 TYR 0.014 0.001 TYR A 116 ARG 0.002 0.000 ARG A 530 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 437) hydrogen bonds : angle 4.74639 ( 1242) SS BOND : bond 0.00048 ( 3) SS BOND : angle 0.64356 ( 6) covalent geometry : bond 0.00305 ( 6729) covalent geometry : angle 0.49492 ( 9143) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 MET cc_start: 0.6593 (mmm) cc_final: 0.6310 (mmm) outliers start: 20 outliers final: 17 residues processed: 122 average time/residue: 0.3418 time to fit residues: 57.4729 Evaluate side-chains 126 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 489 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.194721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.159461 restraints weight = 27822.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.164444 restraints weight = 15238.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.167535 restraints weight = 9987.181| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6732 Z= 0.154 Angle : 0.506 6.093 9149 Z= 0.279 Chirality : 0.039 0.224 1037 Planarity : 0.004 0.042 1165 Dihedral : 4.655 56.208 971 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.40 % Allowed : 12.72 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.29), residues: 854 helix: 2.23 (0.26), residues: 393 sheet: 0.09 (0.34), residues: 231 loop : -0.03 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 178 HIS 0.024 0.002 HIS B 181 PHE 0.011 0.002 PHE A 236 TYR 0.015 0.001 TYR A 449 ARG 0.003 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.04529 ( 437) hydrogen bonds : angle 4.76964 ( 1242) SS BOND : bond 0.00068 ( 3) SS BOND : angle 0.58757 ( 6) covalent geometry : bond 0.00337 ( 6729) covalent geometry : angle 0.50638 ( 9143) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 MET cc_start: 0.6577 (mmm) cc_final: 0.6306 (mmm) outliers start: 23 outliers final: 19 residues processed: 128 average time/residue: 0.3483 time to fit residues: 61.3241 Evaluate side-chains 131 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 489 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.191598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.156072 restraints weight = 27902.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.160917 restraints weight = 15373.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.163921 restraints weight = 10156.304| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6732 Z= 0.189 Angle : 0.547 6.681 9149 Z= 0.305 Chirality : 0.040 0.215 1037 Planarity : 0.005 0.044 1165 Dihedral : 4.928 57.311 971 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.11 % Allowed : 13.61 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.29), residues: 854 helix: 2.03 (0.26), residues: 393 sheet: -0.10 (0.33), residues: 237 loop : -0.15 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 178 HIS 0.023 0.002 HIS B 181 PHE 0.014 0.002 PHE A 518 TYR 0.013 0.002 TYR A 246 ARG 0.002 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 437) hydrogen bonds : angle 4.96491 ( 1242) SS BOND : bond 0.00071 ( 3) SS BOND : angle 0.65368 ( 6) covalent geometry : bond 0.00417 ( 6729) covalent geometry : angle 0.54673 ( 9143) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 MET cc_start: 0.6625 (mmm) cc_final: 0.6354 (mmm) outliers start: 21 outliers final: 19 residues processed: 129 average time/residue: 0.3628 time to fit residues: 65.0592 Evaluate side-chains 132 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 489 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 78 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.0770 chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.194811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.158586 restraints weight = 27689.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.164205 restraints weight = 13906.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.167674 restraints weight = 8687.129| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6732 Z= 0.123 Angle : 0.494 5.580 9149 Z= 0.270 Chirality : 0.039 0.211 1037 Planarity : 0.004 0.042 1165 Dihedral : 4.733 59.531 971 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.81 % Allowed : 14.79 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.29), residues: 854 helix: 2.26 (0.26), residues: 393 sheet: 0.12 (0.34), residues: 227 loop : -0.14 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 178 HIS 0.022 0.002 HIS B 181 PHE 0.013 0.001 PHE A 236 TYR 0.013 0.001 TYR A 449 ARG 0.002 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.04472 ( 437) hydrogen bonds : angle 4.73564 ( 1242) SS BOND : bond 0.00072 ( 3) SS BOND : angle 0.50997 ( 6) covalent geometry : bond 0.00265 ( 6729) covalent geometry : angle 0.49356 ( 9143) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 18 residues processed: 131 average time/residue: 0.3892 time to fit residues: 71.3661 Evaluate side-chains 135 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 489 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 83 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 40 optimal weight: 0.0040 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 0.0070 chunk 65 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.5210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.187935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.150529 restraints weight = 27406.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155542 restraints weight = 14694.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.158752 restraints weight = 9526.190| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6732 Z= 0.123 Angle : 0.488 5.583 9149 Z= 0.267 Chirality : 0.039 0.211 1037 Planarity : 0.004 0.045 1165 Dihedral : 4.628 58.934 971 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.81 % Allowed : 14.94 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.29), residues: 854 helix: 2.33 (0.26), residues: 394 sheet: 0.04 (0.34), residues: 228 loop : 0.02 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 178 HIS 0.019 0.002 HIS B 181 PHE 0.011 0.001 PHE A 236 TYR 0.013 0.001 TYR A 449 ARG 0.002 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.04345 ( 437) hydrogen bonds : angle 4.67795 ( 1242) SS BOND : bond 0.00205 ( 3) SS BOND : angle 1.32687 ( 6) covalent geometry : bond 0.00266 ( 6729) covalent geometry : angle 0.48721 ( 9143) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4662.21 seconds wall clock time: 80 minutes 5.67 seconds (4805.67 seconds total)