Starting phenix.real_space_refine on Sun May 11 10:08:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u5q_41930/05_2025/8u5q_41930.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u5q_41930/05_2025/8u5q_41930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u5q_41930/05_2025/8u5q_41930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u5q_41930/05_2025/8u5q_41930.map" model { file = "/net/cci-nas-00/data/ceres_data/8u5q_41930/05_2025/8u5q_41930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u5q_41930/05_2025/8u5q_41930.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 5298 2.51 5 N 1218 2.21 5 O 1334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7896 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3935 Classifications: {'peptide': 502} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 482} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 3935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3935 Classifications: {'peptide': 502} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 482} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.87, per 1000 atoms: 0.74 Number of scatterers: 7896 At special positions: 0 Unit cell: (122.999, 100.837, 76.4589, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1334 8.00 N 1218 7.00 C 5298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 1.1 seconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1884 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 89.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 41 through 62 Processing helix chain 'A' and resid 66 through 80 removed outlier: 3.695A pdb=" N LYS A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.662A pdb=" N VAL A 98 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 125 removed outlier: 3.599A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 143 Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.660A pdb=" N ILE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 165 Processing helix chain 'A' and resid 166 through 196 removed outlier: 4.299A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Proline residue: A 174 - end of helix Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.999A pdb=" N ILE A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 238 through 264 removed outlier: 4.180A pdb=" N ASN A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLY A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 288 Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 326 through 337 removed outlier: 4.190A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.654A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 404 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 411 through 433 removed outlier: 3.871A pdb=" N ASN A 417 " --> pdb=" O MET A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 472 Processing helix chain 'A' and resid 655 through 680 removed outlier: 4.265A pdb=" N PHE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA A 671 " --> pdb=" O ILE A 667 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASN A 672 " --> pdb=" O GLY A 668 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS A 676 " --> pdb=" O ASN A 672 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 711 removed outlier: 5.676A pdb=" N GLY A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 706 " --> pdb=" O GLY A 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 41 through 62 Processing helix chain 'C' and resid 66 through 80 removed outlier: 3.688A pdb=" N LYS C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLY C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU C 73 " --> pdb=" O GLN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 93 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.666A pdb=" N VAL C 98 " --> pdb=" O PHE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 125 removed outlier: 3.608A pdb=" N LEU C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 143 Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 149 through 159 removed outlier: 3.660A pdb=" N ILE C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 165 Processing helix chain 'C' and resid 166 through 196 removed outlier: 4.295A pdb=" N TYR C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Proline residue: C 174 - end of helix Proline residue: C 182 - end of helix Processing helix chain 'C' and resid 202 through 216 removed outlier: 4.000A pdb=" N ILE C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 234 Processing helix chain 'C' and resid 238 through 264 removed outlier: 4.180A pdb=" N ASN C 243 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE C 244 " --> pdb=" O TYR C 240 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLY C 254 " --> pdb=" O ASN C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 288 Processing helix chain 'C' and resid 288 through 302 Processing helix chain 'C' and resid 306 through 322 Processing helix chain 'C' and resid 326 through 337 removed outlier: 4.195A pdb=" N ALA C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 367 removed outlier: 3.659A pdb=" N ALA C 355 " --> pdb=" O THR C 351 " (cutoff:3.500A) Proline residue: C 356 - end of helix Processing helix chain 'C' and resid 368 through 370 No H-bonds generated for 'chain 'C' and resid 368 through 370' Processing helix chain 'C' and resid 371 through 404 Processing helix chain 'C' and resid 405 through 409 Processing helix chain 'C' and resid 411 through 433 removed outlier: 3.871A pdb=" N ASN C 417 " --> pdb=" O MET C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 472 Processing helix chain 'C' and resid 655 through 680 removed outlier: 4.294A pdb=" N ILE C 667 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 711 removed outlier: 5.691A pdb=" N GLY C 704 " --> pdb=" O ASN C 700 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N PHE C 705 " --> pdb=" O PHE C 701 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 706 " --> pdb=" O GLY C 702 " (cutoff:3.500A) 635 hydrogen bonds defined for protein. 1881 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: 2.49 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2314 1.34 - 1.46: 1845 1.46 - 1.58: 3859 1.58 - 1.70: 0 1.70 - 1.81: 74 Bond restraints: 8092 Sorted by residual: bond pdb=" C1 IAC A 901 " pdb=" C7 IAC A 901 " ideal model delta sigma weight residual 1.433 1.364 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C1 IAC C 901 " pdb=" C7 IAC C 901 " ideal model delta sigma weight residual 1.433 1.364 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C IAC A 901 " pdb=" C1 IAC A 901 " ideal model delta sigma weight residual 1.414 1.363 0.051 2.00e-02 2.50e+03 6.49e+00 bond pdb=" C IAC C 901 " pdb=" C1 IAC C 901 " ideal model delta sigma weight residual 1.414 1.365 0.049 2.00e-02 2.50e+03 5.99e+00 bond pdb=" C17 IAC C 901 " pdb=" C7 IAC C 901 " ideal model delta sigma weight residual 1.487 1.530 -0.043 2.00e-02 2.50e+03 4.68e+00 ... (remaining 8087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 10782 2.71 - 5.42: 186 5.42 - 8.12: 21 8.12 - 10.83: 3 10.83 - 13.54: 4 Bond angle restraints: 10996 Sorted by residual: angle pdb=" C SER A 675 " pdb=" N CYS A 676 " pdb=" CA CYS A 676 " ideal model delta sigma weight residual 121.52 112.76 8.76 1.84e+00 2.95e-01 2.27e+01 angle pdb=" C17 IAC C 901 " pdb=" C7 IAC C 901 " pdb=" C8 IAC C 901 " ideal model delta sigma weight residual 127.34 113.80 13.54 3.00e+00 1.11e-01 2.04e+01 angle pdb=" C17 IAC A 901 " pdb=" C7 IAC A 901 " pdb=" C8 IAC A 901 " ideal model delta sigma weight residual 127.34 113.87 13.47 3.00e+00 1.11e-01 2.02e+01 angle pdb=" C SER C 675 " pdb=" N CYS C 676 " pdb=" CA CYS C 676 " ideal model delta sigma weight residual 120.29 114.59 5.70 1.42e+00 4.96e-01 1.61e+01 angle pdb=" C1 IAC C 901 " pdb=" C7 IAC C 901 " pdb=" C17 IAC C 901 " ideal model delta sigma weight residual 126.92 138.66 -11.74 3.00e+00 1.11e-01 1.53e+01 ... (remaining 10991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 4368 16.99 - 33.98: 270 33.98 - 50.98: 37 50.98 - 67.97: 11 67.97 - 84.96: 6 Dihedral angle restraints: 4692 sinusoidal: 1776 harmonic: 2916 Sorted by residual: dihedral pdb=" CA PHE A 670 " pdb=" C PHE A 670 " pdb=" N ALA A 671 " pdb=" CA ALA A 671 " ideal model delta harmonic sigma weight residual -180.00 -151.18 -28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LEU A 233 " pdb=" C LEU A 233 " pdb=" N ASP A 234 " pdb=" CA ASP A 234 " ideal model delta harmonic sigma weight residual -180.00 -153.16 -26.84 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA LEU C 233 " pdb=" C LEU C 233 " pdb=" N ASP C 234 " pdb=" CA ASP C 234 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 4689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 893 0.043 - 0.086: 322 0.086 - 0.128: 79 0.128 - 0.171: 9 0.171 - 0.214: 7 Chirality restraints: 1310 Sorted by residual: chirality pdb=" CA CYS A 676 " pdb=" N CYS A 676 " pdb=" C CYS A 676 " pdb=" CB CYS A 676 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB VAL A 214 " pdb=" CA VAL A 214 " pdb=" CG1 VAL A 214 " pdb=" CG2 VAL A 214 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL C 214 " pdb=" CA VAL C 214 " pdb=" CG1 VAL C 214 " pdb=" CG2 VAL C 214 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1307 not shown) Planarity restraints: 1324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 320 " 0.038 2.00e-02 2.50e+03 2.01e-02 8.10e+00 pdb=" CG TYR A 320 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 320 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 320 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 320 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 320 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 320 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 320 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 320 " 0.038 2.00e-02 2.50e+03 2.00e-02 7.98e+00 pdb=" CG TYR C 320 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR C 320 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR C 320 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 320 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 320 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 320 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 320 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 221 " 0.025 2.00e-02 2.50e+03 2.13e-02 7.91e+00 pdb=" CG PHE C 221 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE C 221 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 221 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 221 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 221 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 221 " 0.004 2.00e-02 2.50e+03 ... (remaining 1321 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 3119 2.90 - 3.40: 8592 3.40 - 3.90: 14012 3.90 - 4.40: 16360 4.40 - 4.90: 26391 Nonbonded interactions: 68474 Sorted by model distance: nonbonded pdb=" OD1 ASN A 672 " pdb=" ND2 ASN A 700 " model vdw 2.402 3.120 nonbonded pdb=" O LEU C 454 " pdb=" OG1 THR C 457 " model vdw 2.415 3.040 nonbonded pdb=" O LEU A 454 " pdb=" OG1 THR A 457 " model vdw 2.417 3.040 nonbonded pdb=" OH TYR C 359 " pdb=" OD2 ASP C 385 " model vdw 2.417 3.040 nonbonded pdb=" OH TYR A 359 " pdb=" OD2 ASP A 385 " model vdw 2.417 3.040 ... (remaining 68469 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.920 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 8092 Z= 0.240 Angle : 0.896 13.539 10996 Z= 0.477 Chirality : 0.048 0.214 1310 Planarity : 0.006 0.066 1324 Dihedral : 12.123 84.962 2808 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.23 % Allowed : 1.39 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.24), residues: 984 helix: -0.82 (0.16), residues: 804 sheet: None (None), residues: 0 loop : -0.67 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP A 193 HIS 0.014 0.004 HIS A 505 PHE 0.049 0.004 PHE C 221 TYR 0.038 0.004 TYR A 320 ARG 0.004 0.001 ARG C 130 Details of bonding type rmsd hydrogen bonds : bond 0.16795 ( 635) hydrogen bonds : angle 7.10308 ( 1881) covalent geometry : bond 0.00562 ( 8092) covalent geometry : angle 0.89617 (10996) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.906 Fit side-chains REVERT: A 41 ARG cc_start: 0.7917 (mtp180) cc_final: 0.7714 (mmm-85) REVERT: A 319 LEU cc_start: 0.8660 (mm) cc_final: 0.8379 (tm) REVERT: A 347 MET cc_start: 0.8783 (tmm) cc_final: 0.8572 (tmm) REVERT: A 455 TYR cc_start: 0.4591 (m-10) cc_final: 0.3607 (t80) REVERT: C 347 MET cc_start: 0.8753 (tmm) cc_final: 0.8533 (tmm) REVERT: C 455 TYR cc_start: 0.4980 (m-10) cc_final: 0.3961 (t80) outliers start: 2 outliers final: 2 residues processed: 187 average time/residue: 1.1233 time to fit residues: 223.6794 Evaluate side-chains 123 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 90 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 505 HIS A 672 ASN C 505 HIS C 672 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.130613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.099149 restraints weight = 14337.847| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.48 r_work: 0.3309 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8092 Z= 0.185 Angle : 0.673 9.273 10996 Z= 0.348 Chirality : 0.045 0.241 1310 Planarity : 0.005 0.034 1324 Dihedral : 5.601 48.418 1060 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.12 % Allowed : 9.47 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 984 helix: 0.93 (0.17), residues: 802 sheet: None (None), residues: 0 loop : -0.29 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 679 HIS 0.008 0.002 HIS A 658 PHE 0.029 0.002 PHE C 221 TYR 0.025 0.002 TYR C 451 ARG 0.004 0.000 ARG A 295 Details of bonding type rmsd hydrogen bonds : bond 0.05731 ( 635) hydrogen bonds : angle 4.94810 ( 1881) covalent geometry : bond 0.00412 ( 8092) covalent geometry : angle 0.67322 (10996) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.847 Fit side-chains REVERT: A 164 GLU cc_start: 0.8753 (pm20) cc_final: 0.8514 (pm20) REVERT: A 288 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8334 (mp) REVERT: A 319 LEU cc_start: 0.8812 (mm) cc_final: 0.8185 (tp) REVERT: A 347 MET cc_start: 0.8437 (tmm) cc_final: 0.8089 (tmm) REVERT: A 447 PHE cc_start: 0.8069 (t80) cc_final: 0.7850 (t80) REVERT: A 455 TYR cc_start: 0.4344 (m-10) cc_final: 0.3540 (t80) REVERT: A 677 LEU cc_start: 0.8080 (tm) cc_final: 0.7835 (pp) REVERT: A 691 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7353 (tt0) REVERT: C 41 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.8306 (mtm110) REVERT: C 90 MET cc_start: 0.9263 (tpp) cc_final: 0.9035 (mmm) REVERT: C 164 GLU cc_start: 0.8735 (pm20) cc_final: 0.8498 (pm20) REVERT: C 288 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8322 (mp) REVERT: C 347 MET cc_start: 0.8436 (tmm) cc_final: 0.8085 (tmm) REVERT: C 358 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8431 (mtm) REVERT: C 455 TYR cc_start: 0.4362 (m-10) cc_final: 0.3540 (t80) REVERT: C 677 LEU cc_start: 0.8064 (tm) cc_final: 0.7664 (pp) REVERT: C 691 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7414 (tt0) outliers start: 27 outliers final: 4 residues processed: 169 average time/residue: 0.9369 time to fit residues: 170.2303 Evaluate side-chains 139 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 691 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.131070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.099587 restraints weight = 14585.873| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.51 r_work: 0.3312 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8092 Z= 0.168 Angle : 0.661 12.992 10996 Z= 0.323 Chirality : 0.042 0.212 1310 Planarity : 0.004 0.033 1324 Dihedral : 4.786 31.340 1058 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.23 % Allowed : 12.47 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.27), residues: 984 helix: 1.53 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -0.25 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 679 HIS 0.009 0.002 HIS A 658 PHE 0.028 0.002 PHE A 221 TYR 0.024 0.002 TYR A 451 ARG 0.004 0.001 ARG C 295 Details of bonding type rmsd hydrogen bonds : bond 0.05135 ( 635) hydrogen bonds : angle 4.59124 ( 1881) covalent geometry : bond 0.00378 ( 8092) covalent geometry : angle 0.66085 (10996) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.865 Fit side-chains REVERT: A 41 ARG cc_start: 0.8361 (mtm110) cc_final: 0.7935 (mtm180) REVERT: A 164 GLU cc_start: 0.8796 (pm20) cc_final: 0.8454 (pm20) REVERT: A 255 SER cc_start: 0.8996 (t) cc_final: 0.8746 (m) REVERT: A 288 LEU cc_start: 0.8677 (tp) cc_final: 0.8323 (mp) REVERT: A 299 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8356 (mt-10) REVERT: A 319 LEU cc_start: 0.8817 (mm) cc_final: 0.8159 (tp) REVERT: A 347 MET cc_start: 0.8485 (tmm) cc_final: 0.8184 (tmm) REVERT: A 381 ASN cc_start: 0.7904 (t0) cc_final: 0.7630 (t0) REVERT: A 677 LEU cc_start: 0.8113 (tm) cc_final: 0.7844 (pp) REVERT: A 691 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: C 41 ARG cc_start: 0.8495 (mtm-85) cc_final: 0.8194 (mtm110) REVERT: C 143 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: C 164 GLU cc_start: 0.8803 (pm20) cc_final: 0.8462 (pm20) REVERT: C 255 SER cc_start: 0.8988 (t) cc_final: 0.8744 (m) REVERT: C 288 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8326 (mp) REVERT: C 299 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8435 (mt-10) REVERT: C 347 MET cc_start: 0.8499 (tmm) cc_final: 0.8202 (tmm) REVERT: C 358 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8313 (mtm) REVERT: C 677 LEU cc_start: 0.7929 (tm) cc_final: 0.7511 (pp) REVERT: C 691 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7489 (tt0) outliers start: 28 outliers final: 13 residues processed: 155 average time/residue: 1.0218 time to fit residues: 169.3979 Evaluate side-chains 137 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 691 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN C 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.131509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.100124 restraints weight = 14358.462| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.47 r_work: 0.3322 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8092 Z= 0.163 Angle : 0.654 11.396 10996 Z= 0.313 Chirality : 0.042 0.203 1310 Planarity : 0.004 0.033 1324 Dihedral : 4.579 26.975 1058 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 3.70 % Allowed : 14.67 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.27), residues: 984 helix: 1.72 (0.18), residues: 802 sheet: None (None), residues: 0 loop : -0.28 (0.50), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 679 HIS 0.004 0.001 HIS A 505 PHE 0.028 0.002 PHE C 221 TYR 0.021 0.002 TYR A 451 ARG 0.005 0.000 ARG A 295 Details of bonding type rmsd hydrogen bonds : bond 0.04916 ( 635) hydrogen bonds : angle 4.47016 ( 1881) covalent geometry : bond 0.00372 ( 8092) covalent geometry : angle 0.65371 (10996) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.826 Fit side-chains REVERT: A 41 ARG cc_start: 0.8342 (mtm110) cc_final: 0.7955 (mtm180) REVERT: A 164 GLU cc_start: 0.8841 (pm20) cc_final: 0.8442 (pm20) REVERT: A 255 SER cc_start: 0.9001 (t) cc_final: 0.8739 (m) REVERT: A 288 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8314 (mp) REVERT: A 299 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8337 (mt-10) REVERT: A 319 LEU cc_start: 0.8831 (mm) cc_final: 0.8141 (tp) REVERT: A 337 ASN cc_start: 0.9008 (t0) cc_final: 0.8759 (p0) REVERT: A 347 MET cc_start: 0.8524 (tmm) cc_final: 0.8238 (tmm) REVERT: A 677 LEU cc_start: 0.8118 (tm) cc_final: 0.7827 (pp) REVERT: A 691 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7506 (tt0) REVERT: C 41 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.8013 (mtm110) REVERT: C 164 GLU cc_start: 0.8831 (pm20) cc_final: 0.8423 (pm20) REVERT: C 255 SER cc_start: 0.8996 (t) cc_final: 0.8738 (m) REVERT: C 288 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8310 (mp) REVERT: C 299 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8365 (mt-10) REVERT: C 337 ASN cc_start: 0.9000 (t0) cc_final: 0.8679 (p0) REVERT: C 347 MET cc_start: 0.8542 (tmm) cc_final: 0.8195 (tmm) REVERT: C 358 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8439 (ttm) REVERT: C 381 ASN cc_start: 0.7833 (t0) cc_final: 0.7590 (t0) REVERT: C 677 LEU cc_start: 0.7855 (tm) cc_final: 0.7489 (pp) REVERT: C 688 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7031 (tm) REVERT: C 691 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7472 (tt0) outliers start: 32 outliers final: 11 residues processed: 149 average time/residue: 1.0419 time to fit residues: 165.5164 Evaluate side-chains 133 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 691 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN C 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.131905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.100491 restraints weight = 14432.925| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.48 r_work: 0.3330 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8092 Z= 0.160 Angle : 0.663 12.919 10996 Z= 0.317 Chirality : 0.042 0.217 1310 Planarity : 0.004 0.033 1324 Dihedral : 4.507 27.181 1058 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 3.35 % Allowed : 14.09 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.27), residues: 984 helix: 1.81 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -0.23 (0.53), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 679 HIS 0.003 0.001 HIS A 505 PHE 0.029 0.002 PHE C 221 TYR 0.023 0.002 TYR A 451 ARG 0.005 0.000 ARG A 295 Details of bonding type rmsd hydrogen bonds : bond 0.04775 ( 635) hydrogen bonds : angle 4.43569 ( 1881) covalent geometry : bond 0.00365 ( 8092) covalent geometry : angle 0.66283 (10996) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.813 Fit side-chains REVERT: A 41 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7980 (mtm180) REVERT: A 164 GLU cc_start: 0.8871 (pm20) cc_final: 0.8446 (pm20) REVERT: A 255 SER cc_start: 0.9012 (t) cc_final: 0.8759 (m) REVERT: A 288 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8330 (mp) REVERT: A 299 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8368 (mt-10) REVERT: A 319 LEU cc_start: 0.8827 (mm) cc_final: 0.8114 (tp) REVERT: A 337 ASN cc_start: 0.8985 (t0) cc_final: 0.8762 (p0) REVERT: A 347 MET cc_start: 0.8590 (tmm) cc_final: 0.8295 (tmm) REVERT: A 677 LEU cc_start: 0.8102 (tm) cc_final: 0.7826 (pp) REVERT: A 688 LEU cc_start: 0.7315 (mm) cc_final: 0.7042 (tm) REVERT: A 691 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: C 41 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.8013 (mtm110) REVERT: C 164 GLU cc_start: 0.8863 (pm20) cc_final: 0.8430 (pm20) REVERT: C 255 SER cc_start: 0.9015 (t) cc_final: 0.8764 (m) REVERT: C 288 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8334 (mp) REVERT: C 299 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8357 (mt-10) REVERT: C 337 ASN cc_start: 0.8996 (t0) cc_final: 0.8690 (p0) REVERT: C 347 MET cc_start: 0.8579 (tmm) cc_final: 0.8279 (tmm) REVERT: C 677 LEU cc_start: 0.7755 (tm) cc_final: 0.7471 (pp) REVERT: C 688 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7038 (tm) REVERT: C 691 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7474 (tt0) outliers start: 29 outliers final: 11 residues processed: 140 average time/residue: 1.0844 time to fit residues: 161.6945 Evaluate side-chains 136 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 691 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN C 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.131402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.099927 restraints weight = 14396.247| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.47 r_work: 0.3319 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8092 Z= 0.168 Angle : 0.671 13.466 10996 Z= 0.318 Chirality : 0.042 0.223 1310 Planarity : 0.004 0.033 1324 Dihedral : 4.488 26.708 1058 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 3.00 % Allowed : 14.90 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.27), residues: 984 helix: 1.84 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -0.27 (0.52), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 679 HIS 0.002 0.001 HIS A 658 PHE 0.027 0.002 PHE C 221 TYR 0.020 0.002 TYR C 451 ARG 0.005 0.000 ARG C 295 Details of bonding type rmsd hydrogen bonds : bond 0.04775 ( 635) hydrogen bonds : angle 4.46310 ( 1881) covalent geometry : bond 0.00384 ( 8092) covalent geometry : angle 0.67122 (10996) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.889 Fit side-chains REVERT: A 164 GLU cc_start: 0.8868 (pm20) cc_final: 0.8416 (pm20) REVERT: A 255 SER cc_start: 0.9023 (t) cc_final: 0.8752 (m) REVERT: A 288 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8331 (mp) REVERT: A 299 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8334 (mt-10) REVERT: A 319 LEU cc_start: 0.8825 (mm) cc_final: 0.8087 (tp) REVERT: A 337 ASN cc_start: 0.9008 (t0) cc_final: 0.8794 (p0) REVERT: A 341 GLU cc_start: 0.8639 (pm20) cc_final: 0.8349 (pm20) REVERT: A 347 MET cc_start: 0.8589 (tmm) cc_final: 0.8283 (tmm) REVERT: A 677 LEU cc_start: 0.8068 (tm) cc_final: 0.7829 (pp) REVERT: A 691 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: C 41 ARG cc_start: 0.8358 (mtm-85) cc_final: 0.8004 (mtm180) REVERT: C 164 GLU cc_start: 0.8871 (pm20) cc_final: 0.8419 (pm20) REVERT: C 255 SER cc_start: 0.9024 (t) cc_final: 0.8754 (m) REVERT: C 288 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8320 (mp) REVERT: C 299 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8348 (mt-10) REVERT: C 337 ASN cc_start: 0.9026 (t0) cc_final: 0.8732 (p0) REVERT: C 341 GLU cc_start: 0.8646 (pm20) cc_final: 0.8337 (pm20) REVERT: C 347 MET cc_start: 0.8594 (tmm) cc_final: 0.8281 (tmm) REVERT: C 451 TYR cc_start: 0.7915 (m-80) cc_final: 0.7698 (m-80) REVERT: C 677 LEU cc_start: 0.7779 (tm) cc_final: 0.7525 (pp) REVERT: C 688 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6987 (tm) REVERT: C 691 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7453 (tt0) outliers start: 26 outliers final: 12 residues processed: 132 average time/residue: 1.1852 time to fit residues: 165.9783 Evaluate side-chains 134 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 691 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 87 optimal weight: 0.0970 chunk 93 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.132112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.100597 restraints weight = 14613.553| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.49 r_work: 0.3330 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8092 Z= 0.159 Angle : 0.655 12.237 10996 Z= 0.313 Chirality : 0.042 0.235 1310 Planarity : 0.004 0.033 1324 Dihedral : 4.423 27.252 1058 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 3.12 % Allowed : 15.24 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.27), residues: 984 helix: 1.87 (0.18), residues: 816 sheet: None (None), residues: 0 loop : -0.95 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 679 HIS 0.002 0.001 HIS A 505 PHE 0.029 0.002 PHE A 221 TYR 0.020 0.002 TYR A 451 ARG 0.005 0.000 ARG A 295 Details of bonding type rmsd hydrogen bonds : bond 0.04650 ( 635) hydrogen bonds : angle 4.41565 ( 1881) covalent geometry : bond 0.00364 ( 8092) covalent geometry : angle 0.65470 (10996) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.823 Fit side-chains REVERT: A 41 ARG cc_start: 0.8412 (mtm180) cc_final: 0.8176 (mtp180) REVERT: A 146 ASP cc_start: 0.8843 (m-30) cc_final: 0.8396 (m-30) REVERT: A 164 GLU cc_start: 0.8891 (pm20) cc_final: 0.8438 (pm20) REVERT: A 255 SER cc_start: 0.9034 (t) cc_final: 0.8780 (m) REVERT: A 288 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8342 (mp) REVERT: A 299 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8346 (mt-10) REVERT: A 319 LEU cc_start: 0.8837 (mm) cc_final: 0.8086 (tp) REVERT: A 341 GLU cc_start: 0.8722 (pm20) cc_final: 0.8450 (pm20) REVERT: A 347 MET cc_start: 0.8634 (tmm) cc_final: 0.8327 (tmm) REVERT: A 511 ASP cc_start: 0.7693 (p0) cc_final: 0.7447 (p0) REVERT: A 691 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7591 (tt0) REVERT: C 41 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.8043 (mtm180) REVERT: C 146 ASP cc_start: 0.8840 (m-30) cc_final: 0.8432 (m-30) REVERT: C 164 GLU cc_start: 0.8895 (pm20) cc_final: 0.8443 (pm20) REVERT: C 255 SER cc_start: 0.9034 (t) cc_final: 0.8785 (m) REVERT: C 288 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8342 (mp) REVERT: C 299 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8387 (mt-10) REVERT: C 337 ASN cc_start: 0.9041 (t0) cc_final: 0.8780 (p0) REVERT: C 341 GLU cc_start: 0.8718 (pm20) cc_final: 0.8424 (pm20) REVERT: C 347 MET cc_start: 0.8629 (tmm) cc_final: 0.8315 (tmm) REVERT: C 677 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7648 (pp) REVERT: C 691 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7490 (tt0) outliers start: 27 outliers final: 13 residues processed: 133 average time/residue: 1.0494 time to fit residues: 148.7137 Evaluate side-chains 138 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 691 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.131859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.100194 restraints weight = 14582.126| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.50 r_work: 0.3325 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8092 Z= 0.166 Angle : 0.662 12.234 10996 Z= 0.316 Chirality : 0.042 0.274 1310 Planarity : 0.004 0.033 1324 Dihedral : 4.402 26.799 1058 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.77 % Allowed : 15.94 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.27), residues: 984 helix: 1.89 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -0.85 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 679 HIS 0.002 0.001 HIS A 658 PHE 0.027 0.002 PHE A 221 TYR 0.023 0.002 TYR C 689 ARG 0.006 0.000 ARG C 295 Details of bonding type rmsd hydrogen bonds : bond 0.04654 ( 635) hydrogen bonds : angle 4.41784 ( 1881) covalent geometry : bond 0.00378 ( 8092) covalent geometry : angle 0.66210 (10996) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 1.029 Fit side-chains REVERT: A 41 ARG cc_start: 0.8379 (mtm180) cc_final: 0.7989 (mtm180) REVERT: A 146 ASP cc_start: 0.8881 (m-30) cc_final: 0.8446 (m-30) REVERT: A 164 GLU cc_start: 0.8931 (pm20) cc_final: 0.8458 (pm20) REVERT: A 255 SER cc_start: 0.9043 (t) cc_final: 0.8784 (m) REVERT: A 288 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8357 (mp) REVERT: A 299 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8334 (mt-10) REVERT: A 319 LEU cc_start: 0.8826 (mm) cc_final: 0.8051 (tp) REVERT: A 341 GLU cc_start: 0.8740 (pm20) cc_final: 0.8484 (pm20) REVERT: A 347 MET cc_start: 0.8621 (tmm) cc_final: 0.8307 (tmm) REVERT: A 511 ASP cc_start: 0.7729 (p0) cc_final: 0.7454 (p0) REVERT: A 691 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7625 (tt0) REVERT: C 41 ARG cc_start: 0.8375 (mtm-85) cc_final: 0.8031 (mtm180) REVERT: C 146 ASP cc_start: 0.8883 (m-30) cc_final: 0.8501 (m-30) REVERT: C 164 GLU cc_start: 0.8930 (pm20) cc_final: 0.8455 (pm20) REVERT: C 255 SER cc_start: 0.9040 (t) cc_final: 0.8780 (m) REVERT: C 288 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8362 (mp) REVERT: C 299 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8351 (mt-10) REVERT: C 341 GLU cc_start: 0.8742 (pm20) cc_final: 0.8472 (pm20) REVERT: C 347 MET cc_start: 0.8642 (tmm) cc_final: 0.8323 (tmm) REVERT: C 691 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7565 (tt0) outliers start: 24 outliers final: 10 residues processed: 128 average time/residue: 1.2090 time to fit residues: 164.1288 Evaluate side-chains 126 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 691 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.132548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.101218 restraints weight = 14668.986| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.48 r_work: 0.3343 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8092 Z= 0.158 Angle : 0.673 12.477 10996 Z= 0.322 Chirality : 0.043 0.304 1310 Planarity : 0.004 0.034 1324 Dihedral : 4.371 27.315 1058 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.89 % Allowed : 15.82 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.27), residues: 984 helix: 1.97 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -0.84 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 679 HIS 0.002 0.001 HIS A 658 PHE 0.029 0.002 PHE A 221 TYR 0.023 0.002 TYR C 689 ARG 0.006 0.000 ARG C 295 Details of bonding type rmsd hydrogen bonds : bond 0.04533 ( 635) hydrogen bonds : angle 4.37441 ( 1881) covalent geometry : bond 0.00358 ( 8092) covalent geometry : angle 0.67273 (10996) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.912 Fit side-chains REVERT: A 41 ARG cc_start: 0.8377 (mtm180) cc_final: 0.8053 (mtm180) REVERT: A 146 ASP cc_start: 0.8896 (m-30) cc_final: 0.8458 (m-30) REVERT: A 164 GLU cc_start: 0.8922 (pm20) cc_final: 0.8369 (pm20) REVERT: A 255 SER cc_start: 0.9029 (t) cc_final: 0.8784 (m) REVERT: A 288 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8351 (mp) REVERT: A 299 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8354 (mt-10) REVERT: A 319 LEU cc_start: 0.8828 (mm) cc_final: 0.8071 (tp) REVERT: A 341 GLU cc_start: 0.8712 (pm20) cc_final: 0.8477 (pm20) REVERT: A 347 MET cc_start: 0.8642 (tmm) cc_final: 0.8332 (tmm) REVERT: A 511 ASP cc_start: 0.7806 (p0) cc_final: 0.7517 (p0) REVERT: A 691 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: C 41 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.8007 (mtm110) REVERT: C 146 ASP cc_start: 0.8883 (m-30) cc_final: 0.8508 (m-30) REVERT: C 164 GLU cc_start: 0.8935 (pm20) cc_final: 0.8456 (pm20) REVERT: C 255 SER cc_start: 0.9028 (t) cc_final: 0.8785 (m) REVERT: C 288 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8348 (mp) REVERT: C 299 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8366 (mt-10) REVERT: C 341 GLU cc_start: 0.8747 (pm20) cc_final: 0.8491 (pm20) REVERT: C 347 MET cc_start: 0.8652 (tmm) cc_final: 0.8338 (tmm) REVERT: C 691 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7542 (tt0) outliers start: 25 outliers final: 12 residues processed: 135 average time/residue: 1.1604 time to fit residues: 166.7956 Evaluate side-chains 136 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 691 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 83 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN C 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.133233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.101849 restraints weight = 14362.306| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.46 r_work: 0.3356 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8092 Z= 0.152 Angle : 0.689 14.676 10996 Z= 0.325 Chirality : 0.043 0.322 1310 Planarity : 0.004 0.034 1324 Dihedral : 4.327 27.034 1058 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.96 % Allowed : 16.63 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.27), residues: 984 helix: 2.02 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -0.86 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 432 HIS 0.002 0.001 HIS A 658 PHE 0.026 0.001 PHE C 221 TYR 0.020 0.002 TYR C 689 ARG 0.007 0.001 ARG A 295 Details of bonding type rmsd hydrogen bonds : bond 0.04466 ( 635) hydrogen bonds : angle 4.32785 ( 1881) covalent geometry : bond 0.00340 ( 8092) covalent geometry : angle 0.68902 (10996) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.858 Fit side-chains REVERT: A 41 ARG cc_start: 0.8370 (mtm180) cc_final: 0.8052 (mtm180) REVERT: A 164 GLU cc_start: 0.8938 (pm20) cc_final: 0.8484 (pm20) REVERT: A 255 SER cc_start: 0.9007 (t) cc_final: 0.8773 (m) REVERT: A 288 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8320 (mp) REVERT: A 299 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8349 (mt-10) REVERT: A 319 LEU cc_start: 0.8821 (mm) cc_final: 0.8058 (tp) REVERT: A 341 GLU cc_start: 0.8720 (pm20) cc_final: 0.8473 (pm20) REVERT: A 347 MET cc_start: 0.8641 (tmm) cc_final: 0.8331 (tmm) REVERT: A 691 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: C 41 ARG cc_start: 0.8377 (mtm-85) cc_final: 0.8009 (mtm110) REVERT: C 146 ASP cc_start: 0.8874 (m-30) cc_final: 0.8493 (m-30) REVERT: C 164 GLU cc_start: 0.8928 (pm20) cc_final: 0.8367 (pm20) REVERT: C 255 SER cc_start: 0.8996 (t) cc_final: 0.8785 (m) REVERT: C 288 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8320 (mp) REVERT: C 299 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8358 (mt-10) REVERT: C 341 GLU cc_start: 0.8719 (pm20) cc_final: 0.8473 (pm20) REVERT: C 347 MET cc_start: 0.8649 (tmm) cc_final: 0.8329 (tmm) REVERT: C 691 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7453 (tt0) outliers start: 17 outliers final: 11 residues processed: 128 average time/residue: 1.1623 time to fit residues: 158.0323 Evaluate side-chains 134 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 691 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.0570 chunk 7 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.133915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.102696 restraints weight = 14450.053| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.47 r_work: 0.3363 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8092 Z= 0.150 Angle : 0.687 14.702 10996 Z= 0.324 Chirality : 0.043 0.316 1310 Planarity : 0.004 0.034 1324 Dihedral : 4.281 26.745 1058 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.08 % Allowed : 16.63 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.27), residues: 984 helix: 2.04 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -0.86 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 432 HIS 0.002 0.001 HIS A 658 PHE 0.029 0.001 PHE C 221 TYR 0.021 0.002 TYR A 451 ARG 0.006 0.000 ARG C 295 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 635) hydrogen bonds : angle 4.27081 ( 1881) covalent geometry : bond 0.00336 ( 8092) covalent geometry : angle 0.68732 (10996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6255.38 seconds wall clock time: 108 minutes 13.04 seconds (6493.04 seconds total)