Starting phenix.real_space_refine on Sat Oct 11 07:47:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rlc_19338/10_2025/8rlc_19338_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rlc_19338/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8rlc_19338/10_2025/8rlc_19338_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rlc_19338/10_2025/8rlc_19338_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rlc_19338/10_2025/8rlc_19338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rlc_19338/10_2025/8rlc_19338.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'GLU:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 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: {'ARG:plan': 3, 'GLU:plan': 1} 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: 2.61, per 1000 atoms: 0.20 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: 1.11 Conformation dependent library (CDL) restraints added in 421.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.24 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: 2.81 Time building geometry restraints manager: 1.56 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: 3.340 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: 0.090 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.140 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.160 ------------------------------------------------------------------------------- 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 : 6.32 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG C 53 TYR 0.021 0.001 TYR A 449 PHE 0.011 0.001 PHE A 151 TRP 0.013 0.001 TRP A 178 HIS 0.004 0.000 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6729) covalent geometry : angle 0.49461 ( 9143) SS BOND : bond 0.00221 ( 3) SS BOND : angle 0.58014 ( 6) hydrogen bonds : bond 0.09893 ( 437) hydrogen bonds : angle 5.32657 ( 1242) *********************** 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 : 0.308 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: 0.1567 time to fit residues: 33.1966 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 : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.1980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.204894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.169710 restraints weight = 27321.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.175251 restraints weight = 13930.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.178720 restraints weight = 8643.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.180865 restraints weight = 6147.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.182103 restraints weight = 4814.522| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6732 Z= 0.139 Angle : 0.491 5.101 9149 Z= 0.265 Chirality : 0.039 0.140 1037 Planarity : 0.003 0.050 1165 Dihedral : 4.463 47.463 971 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.51 % Allowed : 6.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.29), residues: 854 helix: 2.30 (0.26), residues: 394 sheet: 0.21 (0.34), residues: 211 loop : 0.14 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 98 TYR 0.016 0.001 TYR A 116 PHE 0.018 0.001 PHE B 71 TRP 0.015 0.001 TRP A 178 HIS 0.008 0.002 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6729) covalent geometry : angle 0.49097 ( 9143) SS BOND : bond 0.00249 ( 3) SS BOND : angle 0.50279 ( 6) hydrogen bonds : bond 0.04104 ( 437) hydrogen bonds : angle 4.73842 ( 1242) *********************** 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 143 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.328 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: D 86 ASP cc_start: 0.7597 (m-30) cc_final: 0.7359 (m-30) REVERT: C 13 LYS cc_start: 0.6365 (pttt) cc_final: 0.6126 (pttp) REVERT: A 472 ASP cc_start: 0.8417 (t70) cc_final: 0.8189 (t0) outliers start: 17 outliers final: 14 residues processed: 134 average time/residue: 0.1519 time to fit residues: 28.6696 Evaluate side-chains 128 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 489 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 59 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 ASN B 198 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.202656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.167462 restraints weight = 27893.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.173100 restraints weight = 14108.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.176569 restraints weight = 8783.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.178732 restraints weight = 6317.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.180212 restraints weight = 4984.367| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6732 Z= 0.159 Angle : 0.516 6.022 9149 Z= 0.279 Chirality : 0.040 0.223 1037 Planarity : 0.004 0.036 1165 Dihedral : 4.558 42.846 971 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.37 % Allowed : 8.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.29), residues: 854 helix: 2.33 (0.26), residues: 393 sheet: 0.19 (0.34), residues: 211 loop : -0.06 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 38 TYR 0.029 0.001 TYR A 449 PHE 0.012 0.002 PHE A 151 TRP 0.018 0.001 TRP A 178 HIS 0.011 0.002 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 6729) covalent geometry : angle 0.51618 ( 9143) SS BOND : bond 0.00235 ( 3) SS BOND : angle 0.64782 ( 6) hydrogen bonds : bond 0.04400 ( 437) hydrogen bonds : angle 4.72505 ( 1242) *********************** 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 134 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.374 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: 0.6493 (pttt) cc_final: 0.6253 (pttp) REVERT: A 472 ASP cc_start: 0.8406 (t70) cc_final: 0.8197 (t0) outliers start: 16 outliers final: 12 residues processed: 127 average time/residue: 0.1483 time to fit residues: 26.5975 Evaluate side-chains 121 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 63 THR 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 Chi-restraints excluded: chain A residue 489 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 65 optimal weight: 0.0980 chunk 29 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.4341 r_free = 0.4341 target = 0.201283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.165553 restraints weight = 27605.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.171261 restraints weight = 14044.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.174706 restraints weight = 8723.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.176963 restraints weight = 6272.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.178213 restraints weight = 4981.476| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6732 Z= 0.142 Angle : 0.491 5.764 9149 Z= 0.266 Chirality : 0.039 0.186 1037 Planarity : 0.004 0.037 1165 Dihedral : 4.290 47.087 971 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.11 % Allowed : 8.58 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.29), residues: 854 helix: 2.38 (0.26), residues: 394 sheet: 0.16 (0.35), residues: 211 loop : -0.10 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.013 0.001 TYR A 116 PHE 0.012 0.001 PHE C 47 TRP 0.019 0.001 TRP A 178 HIS 0.004 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6729) covalent geometry : angle 0.49081 ( 9143) SS BOND : bond 0.00265 ( 3) SS BOND : angle 0.53064 ( 6) hydrogen bonds : bond 0.04258 ( 437) hydrogen bonds : angle 4.64777 ( 1242) *********************** 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 140 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.6579 (pttt) cc_final: 0.6331 (pttp) REVERT: A 472 ASP cc_start: 0.8448 (t70) cc_final: 0.8199 (t0) outliers start: 21 outliers final: 17 residues processed: 130 average time/residue: 0.1557 time to fit residues: 27.9705 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 : 0.341 ------------------------------------------------------------------------------- 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 50 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 242 SER Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 489 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4329 r_free = 0.4329 target = 0.199757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.163929 restraints weight = 27712.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.169732 restraints weight = 14070.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.173260 restraints weight = 8779.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.175485 restraints weight = 6301.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.176757 restraints weight = 5000.017| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.2703 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 : 0.481 5.482 9149 Z= 0.261 Chirality : 0.038 0.180 1037 Planarity : 0.004 0.037 1165 Dihedral : 4.290 47.907 971 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.96 % Allowed : 10.80 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.29), residues: 854 helix: 2.43 (0.26), residues: 394 sheet: 0.24 (0.35), residues: 211 loop : -0.06 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 164 TYR 0.014 0.001 TYR A 449 PHE 0.022 0.002 PHE A 176 TRP 0.019 0.001 TRP A 178 HIS 0.004 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6729) covalent geometry : angle 0.48067 ( 9143) SS BOND : bond 0.00205 ( 3) SS BOND : angle 0.51503 ( 6) hydrogen bonds : bond 0.04247 ( 437) hydrogen bonds : angle 4.60310 ( 1242) *********************** 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 133 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.347 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: 0.6608 (pttt) cc_final: 0.6371 (pttp) REVERT: A 472 ASP cc_start: 0.8388 (t70) cc_final: 0.8165 (t0) outliers start: 20 outliers final: 17 residues processed: 126 average time/residue: 0.1628 time to fit residues: 28.3017 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 : 0.374 ------------------------------------------------------------------------------- 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 50 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 18 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 56 LEU 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 364 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 18 optimal weight: 20.0000 overall best weight: 0.9988 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.195135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.158285 restraints weight = 27601.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.163955 restraints weight = 14296.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.167473 restraints weight = 8984.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.169628 restraints weight = 6495.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.170767 restraints weight = 5196.349| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6732 Z= 0.171 Angle : 0.521 6.543 9149 Z= 0.289 Chirality : 0.039 0.169 1037 Planarity : 0.004 0.042 1165 Dihedral : 4.607 52.258 971 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.55 % Allowed : 11.39 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.29), residues: 854 helix: 2.25 (0.26), residues: 399 sheet: 0.29 (0.35), residues: 211 loop : -0.32 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 530 TYR 0.018 0.001 TYR A 246 PHE 0.026 0.002 PHE C 47 TRP 0.018 0.001 TRP A 178 HIS 0.003 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 6729) covalent geometry : angle 0.52093 ( 9143) SS BOND : bond 0.00145 ( 3) SS BOND : angle 0.73178 ( 6) hydrogen bonds : bond 0.04613 ( 437) hydrogen bonds : angle 4.76275 ( 1242) *********************** 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 143 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.406 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 outliers start: 24 outliers final: 21 residues processed: 135 average time/residue: 0.1596 time to fit residues: 29.9853 Evaluate side-chains 130 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 50 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 56 LEU 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 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 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 82 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.0870 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.197011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.160653 restraints weight = 27671.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.166218 restraints weight = 14317.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.169771 restraints weight = 9036.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.171822 restraints weight = 6532.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.173372 restraints weight = 5243.267| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6732 Z= 0.124 Angle : 0.486 5.550 9149 Z= 0.265 Chirality : 0.039 0.186 1037 Planarity : 0.004 0.040 1165 Dihedral : 4.499 54.846 971 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.25 % Allowed : 13.31 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.29), residues: 854 helix: 2.35 (0.26), residues: 400 sheet: 0.21 (0.34), residues: 222 loop : -0.07 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 138 TYR 0.013 0.001 TYR A 246 PHE 0.048 0.002 PHE C 47 TRP 0.021 0.001 TRP A 178 HIS 0.003 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6729) covalent geometry : angle 0.48582 ( 9143) SS BOND : bond 0.00054 ( 3) SS BOND : angle 0.59397 ( 6) hydrogen bonds : bond 0.04329 ( 437) hydrogen bonds : angle 4.59984 ( 1242) *********************** 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 137 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.350 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: A 142 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.8013 (tt) outliers start: 22 outliers final: 19 residues processed: 127 average time/residue: 0.1544 time to fit residues: 27.2409 Evaluate side-chains 130 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 50 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 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 56 LEU Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 364 LEU 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 78 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 8 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.195613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.159171 restraints weight = 27656.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.164773 restraints weight = 14213.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.168332 restraints weight = 8956.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.170398 restraints weight = 6460.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.171969 restraints weight = 5185.813| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.3450 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= 0.144 Angle : 0.499 5.791 9149 Z= 0.274 Chirality : 0.039 0.225 1037 Planarity : 0.004 0.041 1165 Dihedral : 4.562 57.682 971 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.40 % Allowed : 13.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.29), residues: 854 helix: 2.35 (0.26), residues: 400 sheet: 0.17 (0.34), residues: 228 loop : -0.03 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 200 TYR 0.013 0.001 TYR A 116 PHE 0.031 0.002 PHE C 47 TRP 0.019 0.001 TRP A 178 HIS 0.034 0.003 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6729) covalent geometry : angle 0.49867 ( 9143) SS BOND : bond 0.00043 ( 3) SS BOND : angle 0.71599 ( 6) hydrogen bonds : bond 0.04401 ( 437) hydrogen bonds : angle 4.67706 ( 1242) *********************** 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 136 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.347 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 outliers start: 23 outliers final: 20 residues processed: 127 average time/residue: 0.1545 time to fit residues: 27.1426 Evaluate side-chains 133 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 50 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 B residue 208 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 364 LEU 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 11 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 = 0.4270 r_free = 0.4270 target = 0.193992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.157366 restraints weight = 27725.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.162825 restraints weight = 14412.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.166337 restraints weight = 9216.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.168106 restraints weight = 6699.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.169799 restraints weight = 5519.630| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 6732 Z= 0.160 Angle : 0.512 6.067 9149 Z= 0.284 Chirality : 0.039 0.237 1037 Planarity : 0.004 0.041 1165 Dihedral : 4.709 59.193 971 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.40 % Allowed : 13.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.29), residues: 854 helix: 2.28 (0.26), residues: 393 sheet: 0.16 (0.34), residues: 228 loop : -0.15 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 200 TYR 0.013 0.001 TYR A 246 PHE 0.029 0.002 PHE C 47 TRP 0.018 0.001 TRP A 178 HIS 0.028 0.002 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6729) covalent geometry : angle 0.51243 ( 9143) SS BOND : bond 0.00084 ( 3) SS BOND : angle 0.55688 ( 6) hydrogen bonds : bond 0.04559 ( 437) hydrogen bonds : angle 4.76409 ( 1242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 11 is missing expected H atoms. Skipping. Residue VAL 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue MET 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue LYS 285 is missing expected H atoms. Skipping. Residue LYS 348 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 MET cc_start: 0.6604 (mmm) cc_final: 0.6352 (mmm) outliers start: 23 outliers final: 18 residues processed: 130 average time/residue: 0.1518 time to fit residues: 27.6913 Evaluate side-chains 127 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 50 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 B residue 208 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 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 4 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.194149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.157556 restraints weight = 27842.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.163009 restraints weight = 14462.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.166503 restraints weight = 9192.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.168759 restraints weight = 6696.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.169442 restraints weight = 5369.732| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6732 Z= 0.148 Angle : 0.511 5.784 9149 Z= 0.281 Chirality : 0.039 0.222 1037 Planarity : 0.004 0.041 1165 Dihedral : 4.710 59.986 971 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.66 % Allowed : 14.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.29), residues: 854 helix: 2.26 (0.26), residues: 393 sheet: 0.18 (0.34), residues: 228 loop : -0.14 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 530 TYR 0.012 0.001 TYR A 246 PHE 0.026 0.002 PHE C 47 TRP 0.020 0.001 TRP A 178 HIS 0.027 0.002 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6729) covalent geometry : angle 0.51144 ( 9143) SS BOND : bond 0.00062 ( 3) SS BOND : angle 0.55804 ( 6) hydrogen bonds : bond 0.04498 ( 437) hydrogen bonds : angle 4.74439 ( 1242) ********************** 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 132 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 MET cc_start: 0.6638 (mmm) cc_final: 0.6369 (mmm) outliers start: 18 outliers final: 18 residues processed: 126 average time/residue: 0.1655 time to fit residues: 28.9472 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 : 0.340 ------------------------------------------------------------------------------- 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 50 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 B residue 208 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 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 66 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 14 optimal weight: 0.0770 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.4272 r_free = 0.4272 target = 0.194520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.157979 restraints weight = 27725.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.163495 restraints weight = 14617.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.166979 restraints weight = 9190.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.169237 restraints weight = 6668.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.170398 restraints weight = 5334.537| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6732 Z= 0.138 Angle : 0.503 5.669 9149 Z= 0.275 Chirality : 0.039 0.222 1037 Planarity : 0.004 0.041 1165 Dihedral : 4.684 59.466 971 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.81 % Allowed : 14.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.29), residues: 854 helix: 2.30 (0.26), residues: 393 sheet: 0.19 (0.34), residues: 228 loop : -0.08 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.013 0.001 TYR A 246 PHE 0.026 0.002 PHE C 47 TRP 0.020 0.001 TRP A 178 HIS 0.026 0.002 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6729) covalent geometry : angle 0.50277 ( 9143) SS BOND : bond 0.00062 ( 3) SS BOND : angle 0.49984 ( 6) hydrogen bonds : bond 0.04423 ( 437) hydrogen bonds : angle 4.70617 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2549.72 seconds wall clock time: 44 minutes 7.93 seconds (2647.93 seconds total)