Starting phenix.real_space_refine on Thu May 15 08:11:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rlc_19338/05_2025/8rlc_19338_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rlc_19338/05_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_19338/05_2025/8rlc_19338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rlc_19338/05_2025/8rlc_19338.map" model { file = "/net/cci-nas-00/data/ceres_data/8rlc_19338/05_2025/8rlc_19338_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rlc_19338/05_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-5687/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: 6.35, per 1000 atoms: 0.49 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: 3.05 Conformation dependent library (CDL) restraints added in 955.5 milliseconds 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: 0.97 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: 4.23 Time building geometry restraints manager: 3.71 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: 3.240 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: 0.240 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 27.960 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.730 ------------------------------------------------------------------------------- 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 : 0.908 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: 0.3400 time to fit residues: 71.5820 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 : 0.934 ------------------------------------------------------------------------------- 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: 0.9980 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 = 55)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.165712 restraints weight = 26453.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.171086 restraints weight = 13491.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.174341 restraints weight = 8317.434| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 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 52.711 971 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 4.70724 ( 1242) SS BOND : bond 0.00276 ( 3) SS BOND : angle 0.43416 ( 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 : 0.902 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: 0.7577 (m-30) cc_final: 0.7336 (m-30) REVERT: C 13 LYS cc_start: 0.6247 (pttt) cc_final: 0.5931 (pttp) REVERT: A 472 ASP cc_start: 0.8279 (t70) cc_final: 0.8076 (t0) outliers start: 14 outliers final: 12 residues processed: 132 average time/residue: 0.3082 time to fit residues: 56.9427 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 : 0.904 ------------------------------------------------------------------------------- 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: 2.9990 chunk 64 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 23 optimal weight: 0.0470 chunk 13 optimal weight: 0.9990 chunk 80 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- 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 = 0.4391 r_free = 0.4391 target = 0.206641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.172221 restraints weight = 27490.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.178030 restraints weight = 13807.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.181588 restraints weight = 8487.555| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6732 Z= 0.133 Angle : 0.475 5.254 9149 Z= 0.255 Chirality : 0.039 0.202 1037 Planarity : 0.003 0.036 1165 Dihedral : 4.303 43.274 971 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.92 % Allowed : 8.14 % 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: 1.82 (0.29), residues: 854 helix: 2.46 (0.26), residues: 393 sheet: 0.23 (0.34), residues: 212 loop : 0.17 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 178 HIS 0.011 0.002 HIS B 181 PHE 0.012 0.001 PHE A 151 TYR 0.015 0.001 TYR A 116 ARG 0.002 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 437) hydrogen bonds : angle 4.60267 ( 1242) SS BOND : bond 0.00270 ( 3) SS BOND : angle 0.53974 ( 6) covalent geometry : bond 0.00292 ( 6729) covalent geometry : angle 0.47473 ( 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 133 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 1.045 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: D 86 ASP cc_start: 0.7624 (m-30) cc_final: 0.7419 (m-30) REVERT: C 13 LYS cc_start: 0.6384 (pttt) cc_final: 0.6150 (pttp) REVERT: A 472 ASP cc_start: 0.8320 (t70) cc_final: 0.8089 (t0) outliers start: 13 outliers final: 11 residues processed: 127 average time/residue: 0.3373 time to fit residues: 59.0941 Evaluate side-chains 124 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 63 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 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 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 = 0.4346 r_free = 0.4346 target = 0.202027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.166539 restraints weight = 27422.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.172103 restraints weight = 13955.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.175635 restraints weight = 8738.758| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2283 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= 0.153 Angle : 0.508 5.943 9149 Z= 0.277 Chirality : 0.040 0.195 1037 Planarity : 0.004 0.036 1165 Dihedral : 4.313 47.688 971 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.51 % Allowed : 8.73 % Favored : 88.76 % 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: 1.67 (0.29), residues: 854 helix: 2.37 (0.26), residues: 394 sheet: 0.10 (0.34), residues: 218 loop : 0.05 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 178 HIS 0.005 0.001 HIS B 181 PHE 0.022 0.002 PHE C 102 TYR 0.028 0.001 TYR A 449 ARG 0.008 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 437) hydrogen bonds : angle 4.68202 ( 1242) SS BOND : bond 0.00267 ( 3) SS BOND : angle 0.52254 ( 6) covalent geometry : bond 0.00336 ( 6729) covalent geometry : angle 0.50819 ( 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 127 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.884 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: 0.6536 (pttt) cc_final: 0.6303 (pttp) REVERT: A 472 ASP cc_start: 0.8433 (t70) cc_final: 0.8195 (t0) outliers start: 17 outliers final: 14 residues processed: 120 average time/residue: 0.3335 time to fit residues: 54.9184 Evaluate side-chains 122 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 81 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 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: 0.9990 chunk 13 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.200966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.165161 restraints weight = 27594.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.170815 restraints weight = 14135.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.174238 restraints weight = 8807.282| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2584 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= 0.134 Angle : 0.478 5.424 9149 Z= 0.260 Chirality : 0.039 0.181 1037 Planarity : 0.004 0.037 1165 Dihedral : 4.237 46.747 971 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.37 % Allowed : 10.36 % Favored : 87.28 % 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: 1.75 (0.29), residues: 854 helix: 2.46 (0.26), residues: 394 sheet: 0.08 (0.34), residues: 223 loop : 0.15 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 178 HIS 0.004 0.001 HIS B 199 PHE 0.010 0.001 PHE A 151 TYR 0.012 0.001 TYR A 246 ARG 0.004 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 437) hydrogen bonds : angle 4.57107 ( 1242) SS BOND : bond 0.00174 ( 3) SS BOND : angle 0.58704 ( 6) covalent geometry : bond 0.00289 ( 6729) covalent geometry : angle 0.47803 ( 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 135 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.934 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: C 13 LYS cc_start: 0.6576 (pttt) cc_final: 0.6338 (pttp) REVERT: A 472 ASP cc_start: 0.8356 (t70) cc_final: 0.8128 (t0) outliers start: 16 outliers final: 14 residues processed: 127 average time/residue: 0.3625 time to fit residues: 62.2058 Evaluate side-chains 125 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 D residue 82 LEU 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 163 ASP Chi-restraints excluded: chain A residue 364 LEU 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: 2.9990 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.197759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.161455 restraints weight = 27966.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.167172 restraints weight = 14329.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.170758 restraints weight = 8951.792| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6732 Z= 0.152 Angle : 0.493 5.836 9149 Z= 0.271 Chirality : 0.039 0.218 1037 Planarity : 0.004 0.038 1165 Dihedral : 4.386 53.551 971 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.37 % Allowed : 11.83 % Favored : 85.80 % 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: 1.70 (0.29), residues: 854 helix: 2.42 (0.26), residues: 394 sheet: 0.18 (0.34), residues: 217 loop : -0.03 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 178 HIS 0.024 0.002 HIS B 181 PHE 0.011 0.002 PHE A 151 TYR 0.014 0.001 TYR A 116 ARG 0.002 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 437) hydrogen bonds : angle 4.66027 ( 1242) SS BOND : bond 0.00206 ( 3) SS BOND : angle 0.54516 ( 6) covalent geometry : bond 0.00331 ( 6729) covalent geometry : angle 0.49308 ( 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 132 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.895 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 3 GLN cc_start: 0.7534 (tp-100) cc_final: 0.7230 (tp-100) REVERT: A 176 PHE cc_start: 0.8412 (m-80) cc_final: 0.8030 (m-80) REVERT: A 472 ASP cc_start: 0.8371 (t70) cc_final: 0.8171 (t0) outliers start: 16 outliers final: 15 residues processed: 125 average time/residue: 0.3458 time to fit residues: 59.3174 Evaluate side-chains 128 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 D residue 106 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.196258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.159651 restraints weight = 27499.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.165313 restraints weight = 14193.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.168748 restraints weight = 8951.828| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6732 Z= 0.164 Angle : 0.504 6.088 9149 Z= 0.279 Chirality : 0.039 0.209 1037 Planarity : 0.004 0.040 1165 Dihedral : 4.554 54.529 971 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.96 % Allowed : 11.83 % 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: 1.60 (0.29), residues: 854 helix: 2.30 (0.26), residues: 400 sheet: 0.04 (0.33), residues: 232 loop : 0.03 (0.41), residues: 222 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 0.027 0.002 PHE C 47 TYR 0.014 0.001 TYR A 246 ARG 0.002 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04517 ( 437) hydrogen bonds : angle 4.72458 ( 1242) SS BOND : bond 0.00121 ( 3) SS BOND : angle 0.63914 ( 6) covalent geometry : bond 0.00351 ( 6729) covalent geometry : angle 0.50409 ( 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 140 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.974 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 176 PHE cc_start: 0.8475 (m-80) cc_final: 0.8063 (m-80) outliers start: 20 outliers final: 17 residues processed: 132 average time/residue: 0.3335 time to fit residues: 60.7414 Evaluate side-chains 124 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 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 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 118 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 0.0270 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.195862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.159311 restraints weight = 27740.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.165039 restraints weight = 14257.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.168580 restraints weight = 8915.542| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6732 Z= 0.145 Angle : 0.494 5.794 9149 Z= 0.272 Chirality : 0.039 0.204 1037 Planarity : 0.004 0.058 1165 Dihedral : 4.548 56.440 971 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.25 % Allowed : 13.02 % Favored : 83.73 % 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: 1.66 (0.29), residues: 854 helix: 2.34 (0.26), residues: 400 sheet: 0.25 (0.35), residues: 217 loop : -0.14 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 178 HIS 0.019 0.002 HIS B 181 PHE 0.014 0.002 PHE C 47 TYR 0.018 0.001 TYR A 449 ARG 0.005 0.000 ARG A 530 Details of bonding type rmsd hydrogen bonds : bond 0.04440 ( 437) hydrogen bonds : angle 4.66751 ( 1242) SS BOND : bond 0.00429 ( 3) SS BOND : angle 0.85236 ( 6) covalent geometry : bond 0.00316 ( 6729) covalent geometry : angle 0.49412 ( 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 134 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.958 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: A 176 PHE cc_start: 0.8469 (m-80) cc_final: 0.8060 (m-80) outliers start: 22 outliers final: 17 residues processed: 124 average time/residue: 0.3601 time to fit residues: 61.7920 Evaluate side-chains 127 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 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 118 ASP 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=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: 0.9980 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.193523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.158208 restraints weight = 27802.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.163087 restraints weight = 15311.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.166277 restraints weight = 10127.561| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6732 Z= 0.167 Angle : 0.528 6.300 9149 Z= 0.292 Chirality : 0.039 0.210 1037 Planarity : 0.004 0.042 1165 Dihedral : 4.759 59.046 971 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.81 % Allowed : 13.61 % Favored : 83.58 % 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: 1.51 (0.29), residues: 854 helix: 2.25 (0.26), residues: 393 sheet: 0.27 (0.35), residues: 221 loop : -0.30 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 178 HIS 0.016 0.002 HIS B 181 PHE 0.017 0.002 PHE C 47 TYR 0.013 0.001 TYR A 246 ARG 0.002 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04679 ( 437) hydrogen bonds : angle 4.79565 ( 1242) SS BOND : bond 0.00161 ( 3) SS BOND : angle 0.76775 ( 6) covalent geometry : bond 0.00364 ( 6729) covalent geometry : angle 0.52801 ( 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 139 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.994 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 176 PHE cc_start: 0.8431 (m-80) cc_final: 0.8029 (m-80) outliers start: 19 outliers final: 18 residues processed: 132 average time/residue: 0.3400 time to fit residues: 62.1655 Evaluate side-chains 130 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 118 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 78 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.0030 chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.195873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.159742 restraints weight = 27665.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.165156 restraints weight = 14157.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.168636 restraints weight = 9000.475| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6732 Z= 0.126 Angle : 0.492 5.478 9149 Z= 0.269 Chirality : 0.039 0.206 1037 Planarity : 0.004 0.041 1165 Dihedral : 4.625 59.965 971 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.51 % Allowed : 14.79 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.68 (0.29), residues: 854 helix: 2.41 (0.27), residues: 394 sheet: 0.27 (0.35), residues: 221 loop : -0.19 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 178 HIS 0.017 0.002 HIS B 181 PHE 0.012 0.001 PHE A 236 TYR 0.014 0.001 TYR A 449 ARG 0.001 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 437) hydrogen bonds : angle 4.64638 ( 1242) SS BOND : bond 0.00064 ( 3) SS BOND : angle 0.49540 ( 6) covalent geometry : bond 0.00272 ( 6729) covalent geometry : angle 0.49229 ( 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 128 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.968 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 176 PHE cc_start: 0.8449 (m-80) cc_final: 0.8023 (m-80) outliers start: 17 outliers final: 17 residues processed: 122 average time/residue: 0.3389 time to fit residues: 57.4344 Evaluate side-chains 127 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 117 VAL Chi-restraints excluded: chain A residue 118 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 83 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 54 optimal weight: 0.0470 chunk 69 optimal weight: 1.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.187412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.149821 restraints weight = 27449.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.154884 restraints weight = 14875.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.158140 restraints weight = 9669.339| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6732 Z= 0.143 Angle : 0.505 5.882 9149 Z= 0.277 Chirality : 0.039 0.208 1037 Planarity : 0.004 0.058 1165 Dihedral : 4.645 59.263 971 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.96 % Allowed : 14.94 % Favored : 82.10 % 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: 1.66 (0.29), residues: 854 helix: 2.36 (0.26), residues: 394 sheet: 0.28 (0.35), residues: 221 loop : -0.16 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 178 HIS 0.014 0.001 HIS B 181 PHE 0.011 0.002 PHE C 47 TYR 0.013 0.001 TYR A 246 ARG 0.002 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.04423 ( 437) hydrogen bonds : angle 4.67560 ( 1242) SS BOND : bond 0.00043 ( 3) SS BOND : angle 0.53757 ( 6) covalent geometry : bond 0.00313 ( 6729) covalent geometry : angle 0.50475 ( 9143) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4499.24 seconds wall clock time: 78 minutes 14.12 seconds (4694.12 seconds total)