Starting phenix.real_space_refine on Fri Jun 6 15:10:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u5q_41930/06_2025/8u5q_41930.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u5q_41930/06_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_41930/06_2025/8u5q_41930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u5q_41930/06_2025/8u5q_41930.map" model { file = "/net/cci-nas-00/data/ceres_data/8u5q_41930/06_2025/8u5q_41930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u5q_41930/06_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-5710/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: 5.37, per 1000 atoms: 0.68 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: 2.05 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: 0.69 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: 2.18 Time building geometry restraints manager: 2.42 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.390 Find NCS groups from input model: 0.250 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:11.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.180 ------------------------------------------------------------------------------- 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 : 0.922 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: 1.0754 time to fit residues: 214.3384 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 : 0.920 ------------------------------------------------------------------------------- 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 = 0.099148 restraints weight = 14337.853| |-----------------------------------------------------------------------------| 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: 0.7671 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 : 0.912 Fit side-chains REVERT: A 164 GLU cc_start: 0.8752 (pm20) cc_final: 0.8514 (pm20) REVERT: A 288 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8336 (mp) REVERT: A 319 LEU cc_start: 0.8813 (mm) cc_final: 0.8187 (tp) REVERT: A 347 MET cc_start: 0.8436 (tmm) cc_final: 0.8087 (tmm) REVERT: A 447 PHE cc_start: 0.8063 (t80) cc_final: 0.7844 (t80) REVERT: A 455 TYR cc_start: 0.4338 (m-10) cc_final: 0.3537 (t80) REVERT: A 677 LEU cc_start: 0.8083 (tm) cc_final: 0.7836 (pp) REVERT: A 691 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7352 (tt0) REVERT: C 41 ARG cc_start: 0.8572 (mtm-85) cc_final: 0.8304 (mtm110) REVERT: C 90 MET cc_start: 0.9264 (tpp) cc_final: 0.9037 (mmm) REVERT: C 164 GLU cc_start: 0.8735 (pm20) cc_final: 0.8498 (pm20) REVERT: C 288 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8324 (mp) REVERT: C 347 MET cc_start: 0.8436 (tmm) cc_final: 0.8085 (tmm) REVERT: C 358 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8433 (mtm) REVERT: C 455 TYR cc_start: 0.4356 (m-10) cc_final: 0.3537 (t80) REVERT: C 677 LEU cc_start: 0.8067 (tm) cc_final: 0.7665 (pp) REVERT: C 691 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7412 (tt0) outliers start: 27 outliers final: 4 residues processed: 169 average time/residue: 1.0161 time to fit residues: 184.2649 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 : 0.916 ------------------------------------------------------------------------------- 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: 0.6980 chunk 37 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.130883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.099293 restraints weight = 14586.899| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.51 r_work: 0.3310 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3536 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= 0.170 Angle : 0.664 12.983 10996 Z= 0.324 Chirality : 0.043 0.220 1310 Planarity : 0.004 0.033 1324 Dihedral : 4.821 31.867 1058 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.23 % Allowed : 12.36 % Favored : 84.41 % 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: 1.74 (0.27), residues: 984 helix: 1.51 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -0.24 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 679 HIS 0.010 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 A 295 Details of bonding type rmsd hydrogen bonds : bond 0.05190 ( 635) hydrogen bonds : angle 4.61077 ( 1881) covalent geometry : bond 0.00385 ( 8092) covalent geometry : angle 0.66442 (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 170 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.884 Fit side-chains REVERT: A 41 ARG cc_start: 0.8341 (mtm110) cc_final: 0.7890 (mtm180) REVERT: A 164 GLU cc_start: 0.8788 (pm20) cc_final: 0.8457 (pm20) REVERT: A 255 SER cc_start: 0.8989 (t) cc_final: 0.8729 (m) REVERT: A 288 LEU cc_start: 0.8669 (tp) cc_final: 0.8332 (mp) REVERT: A 299 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8357 (mt-10) REVERT: A 319 LEU cc_start: 0.8814 (mm) cc_final: 0.8155 (tp) REVERT: A 347 MET cc_start: 0.8484 (tmm) cc_final: 0.8181 (tmm) REVERT: A 381 ASN cc_start: 0.7905 (t0) cc_final: 0.7641 (t0) REVERT: A 677 LEU cc_start: 0.8126 (tm) cc_final: 0.7859 (pp) REVERT: A 691 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7493 (tt0) REVERT: C 41 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.8198 (mtm110) REVERT: C 143 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7744 (mp10) REVERT: C 164 GLU cc_start: 0.8803 (pm20) cc_final: 0.8470 (pm20) REVERT: C 255 SER cc_start: 0.8989 (t) cc_final: 0.8741 (m) REVERT: C 288 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8338 (mp) REVERT: C 299 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8410 (mt-10) REVERT: C 347 MET cc_start: 0.8498 (tmm) cc_final: 0.8201 (tmm) REVERT: C 358 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8332 (mtm) REVERT: C 677 LEU cc_start: 0.7921 (tm) cc_final: 0.7505 (pp) REVERT: C 691 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7501 (tt0) outliers start: 28 outliers final: 13 residues processed: 153 average time/residue: 1.0606 time to fit residues: 173.1969 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 : 0.836 ------------------------------------------------------------------------------- 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: 0.6980 chunk 46 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.0570 chunk 16 optimal weight: 7.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.132549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.101246 restraints weight = 14335.005| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.50 r_work: 0.3342 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3976 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= 0.149 Angle : 0.649 11.996 10996 Z= 0.310 Chirality : 0.042 0.201 1310 Planarity : 0.004 0.033 1324 Dihedral : 4.546 27.530 1058 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.35 % Allowed : 14.67 % Favored : 81.99 % 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: 2.03 (0.27), residues: 984 helix: 1.73 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -0.27 (0.51), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 679 HIS 0.004 0.001 HIS A 505 PHE 0.028 0.002 PHE A 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 0.04793 ( 635) hydrogen bonds : angle 4.42190 ( 1881) covalent geometry : bond 0.00332 ( 8092) covalent geometry : angle 0.64926 (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 162 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.832 Fit side-chains REVERT: A 41 ARG cc_start: 0.8347 (mtm110) cc_final: 0.7972 (mtm180) REVERT: A 164 GLU cc_start: 0.8843 (pm20) cc_final: 0.8401 (pm20) REVERT: A 255 SER cc_start: 0.8964 (t) cc_final: 0.8730 (m) REVERT: A 288 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8300 (mp) REVERT: A 299 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8342 (mt-10) REVERT: A 319 LEU cc_start: 0.8821 (mm) cc_final: 0.8128 (tp) REVERT: A 337 ASN cc_start: 0.8996 (t0) cc_final: 0.8762 (p0) REVERT: A 347 MET cc_start: 0.8510 (tmm) cc_final: 0.8160 (tmm) REVERT: A 677 LEU cc_start: 0.8106 (tm) cc_final: 0.7803 (pp) REVERT: A 688 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6938 (tm) REVERT: A 691 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: C 41 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.8124 (mtm110) REVERT: C 164 GLU cc_start: 0.8831 (pm20) cc_final: 0.8422 (pm20) REVERT: C 255 SER cc_start: 0.8957 (t) cc_final: 0.8725 (m) REVERT: C 288 LEU cc_start: 0.8615 (tp) cc_final: 0.8308 (mp) REVERT: C 299 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8373 (mt-10) REVERT: C 337 ASN cc_start: 0.8992 (t0) cc_final: 0.8676 (p0) REVERT: C 347 MET cc_start: 0.8518 (tmm) cc_final: 0.8173 (tmm) REVERT: C 677 LEU cc_start: 0.7741 (tm) cc_final: 0.7416 (pp) REVERT: C 688 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7055 (tm) REVERT: C 691 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7471 (tt0) outliers start: 29 outliers final: 5 residues processed: 149 average time/residue: 1.1241 time to fit residues: 178.2024 Evaluate side-chains 128 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 688 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU 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: 1.9990 chunk 34 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.131870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.100588 restraints weight = 14491.186| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.47 r_work: 0.3327 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4085 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= 0.166 Angle : 0.667 12.908 10996 Z= 0.319 Chirality : 0.042 0.219 1310 Planarity : 0.004 0.033 1324 Dihedral : 4.506 26.659 1058 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 3.00 % Allowed : 14.78 % Favored : 82.22 % 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: 2.13 (0.27), residues: 984 helix: 1.80 (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 0.023 0.002 TRP A 679 HIS 0.003 0.001 HIS A 505 PHE 0.029 0.002 PHE C 221 TYR 0.022 0.002 TYR A 451 ARG 0.005 0.000 ARG A 295 Details of bonding type rmsd hydrogen bonds : bond 0.04804 ( 635) hydrogen bonds : angle 4.44478 ( 1881) covalent geometry : bond 0.00380 ( 8092) covalent geometry : angle 0.66749 (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 153 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.922 Fit side-chains REVERT: A 41 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8010 (mtm180) REVERT: A 164 GLU cc_start: 0.8851 (pm20) cc_final: 0.8431 (pm20) REVERT: A 255 SER cc_start: 0.9025 (t) cc_final: 0.8773 (m) REVERT: A 288 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8335 (mp) REVERT: A 299 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8365 (mt-10) REVERT: A 319 LEU cc_start: 0.8859 (mm) cc_final: 0.8156 (tp) REVERT: A 337 ASN cc_start: 0.8986 (t0) cc_final: 0.8765 (p0) REVERT: A 347 MET cc_start: 0.8586 (tmm) cc_final: 0.8288 (tmm) REVERT: A 677 LEU cc_start: 0.8112 (tm) cc_final: 0.7836 (pp) REVERT: A 688 LEU cc_start: 0.7242 (mm) cc_final: 0.6988 (tm) REVERT: A 691 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7500 (tt0) REVERT: C 41 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.8017 (mtm110) REVERT: C 155 GLU cc_start: 0.8935 (tt0) cc_final: 0.8706 (pt0) REVERT: C 164 GLU cc_start: 0.8862 (pm20) cc_final: 0.8433 (pm20) REVERT: C 255 SER cc_start: 0.9019 (t) cc_final: 0.8771 (m) REVERT: C 288 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8339 (mp) REVERT: C 299 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8361 (mt-10) REVERT: C 337 ASN cc_start: 0.8983 (t0) cc_final: 0.8684 (p0) REVERT: C 347 MET cc_start: 0.8580 (tmm) cc_final: 0.8277 (tmm) REVERT: C 677 LEU cc_start: 0.7762 (tm) cc_final: 0.7475 (pp) REVERT: C 688 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7041 (tm) REVERT: C 691 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7475 (tt0) outliers start: 26 outliers final: 12 residues processed: 137 average time/residue: 1.1215 time to fit residues: 163.6670 Evaluate side-chains 135 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG 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 204 ILE Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU 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: 10.0000 chunk 92 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 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 = 0.3926 r_free = 0.3926 target = 0.131643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.100186 restraints weight = 14387.933| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.49 r_work: 0.3323 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4221 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= 0.165 Angle : 0.664 13.636 10996 Z= 0.315 Chirality : 0.042 0.228 1310 Planarity : 0.004 0.033 1324 Dihedral : 4.467 26.875 1058 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 3.23 % Allowed : 14.67 % 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: 2.17 (0.27), residues: 984 helix: 1.84 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -0.31 (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 0.029 0.002 PHE A 221 TYR 0.025 0.002 TYR C 451 ARG 0.005 0.000 ARG A 295 Details of bonding type rmsd hydrogen bonds : bond 0.04772 ( 635) hydrogen bonds : angle 4.44812 ( 1881) covalent geometry : bond 0.00377 ( 8092) covalent geometry : angle 0.66427 (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 155 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.922 Fit side-chains REVERT: A 41 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7984 (mtm180) REVERT: A 146 ASP cc_start: 0.8885 (m-30) cc_final: 0.8455 (m-30) REVERT: A 164 GLU cc_start: 0.8855 (pm20) cc_final: 0.8408 (pm20) REVERT: A 255 SER cc_start: 0.9016 (t) cc_final: 0.8753 (m) REVERT: A 288 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8333 (mp) REVERT: A 299 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8327 (mt-10) REVERT: A 319 LEU cc_start: 0.8824 (mm) cc_final: 0.8087 (tp) REVERT: A 337 ASN cc_start: 0.9007 (t0) cc_final: 0.8794 (p0) REVERT: A 341 GLU cc_start: 0.8627 (pm20) cc_final: 0.8331 (pm20) REVERT: A 347 MET cc_start: 0.8589 (tmm) cc_final: 0.8287 (tmm) REVERT: A 677 LEU cc_start: 0.8070 (tm) cc_final: 0.7848 (pp) REVERT: A 688 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6893 (tm) REVERT: A 691 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7531 (tt0) REVERT: C 41 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.7992 (mtm110) REVERT: C 146 ASP cc_start: 0.8915 (m-30) cc_final: 0.8518 (m-30) REVERT: C 155 GLU cc_start: 0.8914 (tt0) cc_final: 0.8667 (pt0) REVERT: C 164 GLU cc_start: 0.8875 (pm20) cc_final: 0.8426 (pm20) REVERT: C 255 SER cc_start: 0.9012 (t) cc_final: 0.8751 (m) REVERT: C 288 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8321 (mp) REVERT: C 299 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8352 (mt-10) REVERT: C 337 ASN cc_start: 0.9006 (t0) cc_final: 0.8721 (p0) REVERT: C 341 GLU cc_start: 0.8656 (pm20) cc_final: 0.8361 (pm20) REVERT: C 347 MET cc_start: 0.8600 (tmm) cc_final: 0.8290 (tmm) REVERT: C 447 PHE cc_start: 0.8085 (t80) cc_final: 0.7777 (t80) REVERT: C 451 TYR cc_start: 0.7826 (m-80) cc_final: 0.7583 (m-80) REVERT: C 677 LEU cc_start: 0.7796 (tm) cc_final: 0.7535 (pp) REVERT: C 688 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7034 (tm) REVERT: C 691 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7434 (tt0) outliers start: 28 outliers final: 15 residues processed: 138 average time/residue: 1.1334 time to fit residues: 166.3304 Evaluate side-chains 142 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 425 VAL Chi-restraints excluded: chain A residue 688 LEU 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 377 TYR 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 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: 0.8980 chunk 39 optimal weight: 0.1980 chunk 63 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 23 optimal weight: 0.0030 chunk 53 optimal weight: 0.7980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.133189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.101910 restraints weight = 14575.698| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.51 r_work: 0.3351 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4443 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= 0.146 Angle : 0.639 12.249 10996 Z= 0.304 Chirality : 0.041 0.227 1310 Planarity : 0.004 0.034 1324 Dihedral : 4.353 27.575 1058 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 3.12 % Allowed : 14.55 % Favored : 82.33 % 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: 2.21 (0.27), residues: 984 helix: 1.91 (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 505 PHE 0.029 0.001 PHE C 221 TYR 0.021 0.002 TYR C 451 ARG 0.005 0.000 ARG A 295 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 635) hydrogen bonds : angle 4.33876 ( 1881) covalent geometry : bond 0.00329 ( 8092) covalent geometry : angle 0.63867 (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 153 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.896 Fit side-chains REVERT: A 146 ASP cc_start: 0.8932 (m-30) cc_final: 0.8511 (m-30) REVERT: A 164 GLU cc_start: 0.8887 (pm20) cc_final: 0.8519 (pm20) REVERT: A 255 SER cc_start: 0.8997 (t) cc_final: 0.8772 (m) REVERT: A 288 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8328 (mp) REVERT: A 299 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8350 (mt-10) REVERT: A 319 LEU cc_start: 0.8839 (mm) cc_final: 0.8096 (tp) REVERT: A 341 GLU cc_start: 0.8699 (pm20) cc_final: 0.8434 (pm20) REVERT: A 347 MET cc_start: 0.8634 (tmm) cc_final: 0.8333 (tmm) REVERT: A 691 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: C 41 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.8030 (mtm110) REVERT: C 146 ASP cc_start: 0.8952 (m-30) cc_final: 0.8567 (m-30) REVERT: C 155 GLU cc_start: 0.8935 (tt0) cc_final: 0.8726 (pt0) REVERT: C 164 GLU cc_start: 0.8911 (pm20) cc_final: 0.8356 (pm20) REVERT: C 288 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8335 (mp) REVERT: C 299 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8376 (mt-10) REVERT: C 337 ASN cc_start: 0.8998 (t0) cc_final: 0.8755 (p0) REVERT: C 341 GLU cc_start: 0.8710 (pm20) cc_final: 0.8440 (pm20) REVERT: C 347 MET cc_start: 0.8640 (tmm) cc_final: 0.8327 (tmm) REVERT: C 677 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7620 (pp) REVERT: C 691 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7515 (tt0) outliers start: 27 outliers final: 12 residues processed: 134 average time/residue: 1.1178 time to fit residues: 159.3584 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 : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 425 VAL 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: 0.5980 chunk 48 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 99 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: A 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.132334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.100825 restraints weight = 14537.966| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.51 r_work: 0.3338 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4478 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= 0.159 Angle : 0.651 12.172 10996 Z= 0.311 Chirality : 0.042 0.275 1310 Planarity : 0.004 0.033 1324 Dihedral : 4.352 26.429 1058 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.89 % Allowed : 15.36 % Favored : 81.76 % 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: 2.22 (0.27), residues: 984 helix: 1.92 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -0.86 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 679 HIS 0.002 0.001 HIS A 658 PHE 0.030 0.002 PHE A 221 TYR 0.022 0.002 TYR C 451 ARG 0.006 0.001 ARG A 295 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 635) hydrogen bonds : angle 4.33952 ( 1881) covalent geometry : bond 0.00362 ( 8092) covalent geometry : angle 0.65139 (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 146 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.859 Fit side-chains REVERT: A 41 ARG cc_start: 0.8437 (mtm180) cc_final: 0.8123 (mtm180) REVERT: A 146 ASP cc_start: 0.8928 (m-30) cc_final: 0.8480 (m-30) REVERT: A 164 GLU cc_start: 0.8877 (pm20) cc_final: 0.8436 (pm20) REVERT: A 255 SER cc_start: 0.9020 (t) cc_final: 0.8785 (m) REVERT: A 288 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8341 (mp) REVERT: A 299 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8325 (mt-10) REVERT: A 319 LEU cc_start: 0.8823 (mm) cc_final: 0.8066 (tp) REVERT: A 341 GLU cc_start: 0.8742 (pm20) cc_final: 0.8503 (pm20) REVERT: A 347 MET cc_start: 0.8627 (tmm) cc_final: 0.8313 (tmm) REVERT: A 691 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: C 41 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.8021 (mtm110) REVERT: C 146 ASP cc_start: 0.8994 (m-30) cc_final: 0.8616 (m-30) REVERT: C 155 GLU cc_start: 0.8939 (tt0) cc_final: 0.8716 (pt0) REVERT: C 164 GLU cc_start: 0.8939 (pm20) cc_final: 0.8490 (pm20) REVERT: C 288 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8341 (mp) REVERT: C 299 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8366 (mt-10) REVERT: C 337 ASN cc_start: 0.8960 (t0) cc_final: 0.8759 (p0) REVERT: C 341 GLU cc_start: 0.8763 (pm20) cc_final: 0.8524 (pm20) REVERT: C 347 MET cc_start: 0.8667 (tmm) cc_final: 0.8333 (tmm) REVERT: C 677 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7708 (pp) REVERT: C 691 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7442 (tt0) outliers start: 25 outliers final: 12 residues processed: 131 average time/residue: 1.1706 time to fit residues: 164.3190 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 : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 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 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 425 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.132438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.100968 restraints weight = 14677.745| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.47 r_work: 0.3335 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4505 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= 0.163 Angle : 0.665 12.478 10996 Z= 0.319 Chirality : 0.043 0.309 1310 Planarity : 0.004 0.033 1324 Dihedral : 4.360 26.661 1058 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.00 % Allowed : 15.36 % 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: 2.23 (0.27), residues: 984 helix: 1.93 (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 0.029 0.002 TRP A 679 HIS 0.002 0.001 HIS A 658 PHE 0.029 0.002 PHE C 221 TYR 0.023 0.002 TYR C 689 ARG 0.006 0.001 ARG C 295 Details of bonding type rmsd hydrogen bonds : bond 0.04600 ( 635) hydrogen bonds : angle 4.35486 ( 1881) covalent geometry : bond 0.00373 ( 8092) covalent geometry : angle 0.66522 (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 146 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.889 Fit side-chains REVERT: A 41 ARG cc_start: 0.8380 (mtm180) cc_final: 0.8063 (mtm180) REVERT: A 146 ASP cc_start: 0.8800 (m-30) cc_final: 0.8365 (m-30) REVERT: A 164 GLU cc_start: 0.8931 (pm20) cc_final: 0.8483 (pm20) REVERT: A 255 SER cc_start: 0.9052 (t) cc_final: 0.8780 (m) REVERT: A 288 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8353 (mp) REVERT: A 299 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8348 (mt-10) REVERT: A 319 LEU cc_start: 0.8828 (mm) cc_final: 0.8070 (tp) REVERT: A 341 GLU cc_start: 0.8696 (pm20) cc_final: 0.8457 (pm20) REVERT: A 347 MET cc_start: 0.8623 (tmm) cc_final: 0.8305 (tmm) REVERT: A 691 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7636 (tt0) REVERT: C 41 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.8016 (mtm110) REVERT: C 146 ASP cc_start: 0.8845 (m-30) cc_final: 0.8444 (m-30) REVERT: C 155 GLU cc_start: 0.8944 (tt0) cc_final: 0.8717 (pt0) REVERT: C 164 GLU cc_start: 0.8945 (pm20) cc_final: 0.8492 (pm20) REVERT: C 288 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8358 (mp) REVERT: C 299 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8353 (mt-10) REVERT: C 341 GLU cc_start: 0.8756 (pm20) cc_final: 0.8497 (pm20) REVERT: C 347 MET cc_start: 0.8645 (tmm) cc_final: 0.8321 (tmm) REVERT: C 691 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7490 (tt0) outliers start: 26 outliers final: 10 residues processed: 131 average time/residue: 1.1544 time to fit residues: 160.7984 Evaluate side-chains 130 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.0040 chunk 83 optimal weight: 0.0010 chunk 84 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 28 optimal weight: 0.0470 chunk 80 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 81 optimal weight: 0.6980 overall best weight: 0.1896 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.136392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.105601 restraints weight = 14328.093| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.46 r_work: 0.3415 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8092 Z= 0.132 Angle : 0.674 14.301 10996 Z= 0.316 Chirality : 0.042 0.315 1310 Planarity : 0.004 0.034 1324 Dihedral : 4.223 27.771 1058 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.50 % Allowed : 16.97 % Favored : 81.52 % 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: 2.47 (0.28), residues: 984 helix: 2.09 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -0.84 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 432 HIS 0.003 0.001 HIS A 658 PHE 0.028 0.001 PHE A 221 TYR 0.024 0.001 TYR C 451 ARG 0.008 0.001 ARG A 295 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 635) hydrogen bonds : angle 4.21718 ( 1881) covalent geometry : bond 0.00281 ( 8092) covalent geometry : angle 0.67428 (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 148 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.922 Fit side-chains REVERT: A 146 ASP cc_start: 0.8897 (m-30) cc_final: 0.8692 (m-30) REVERT: A 164 GLU cc_start: 0.8927 (pm20) cc_final: 0.8431 (pm20) REVERT: A 167 GLN cc_start: 0.8777 (mt0) cc_final: 0.8341 (pt0) REVERT: A 212 LEU cc_start: 0.8877 (tp) cc_final: 0.8501 (mm) REVERT: A 288 LEU cc_start: 0.8497 (tp) cc_final: 0.8258 (mp) REVERT: A 299 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8316 (mt-10) REVERT: A 319 LEU cc_start: 0.8804 (mm) cc_final: 0.8542 (mm) REVERT: A 341 GLU cc_start: 0.8700 (pm20) cc_final: 0.8453 (pm20) REVERT: A 347 MET cc_start: 0.8612 (tmm) cc_final: 0.8308 (tmm) REVERT: A 691 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: C 41 ARG cc_start: 0.8427 (mtm-85) cc_final: 0.8094 (mtm110) REVERT: C 146 ASP cc_start: 0.9010 (m-30) cc_final: 0.8659 (m-30) REVERT: C 164 GLU cc_start: 0.8970 (pm20) cc_final: 0.8583 (pm20) REVERT: C 288 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8270 (mp) REVERT: C 299 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8325 (mt-10) REVERT: C 341 GLU cc_start: 0.8730 (pm20) cc_final: 0.8494 (pm20) REVERT: C 347 MET cc_start: 0.8629 (tmm) cc_final: 0.8316 (tmm) REVERT: C 691 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7461 (tt0) outliers start: 13 outliers final: 7 residues processed: 140 average time/residue: 1.1734 time to fit residues: 175.1575 Evaluate side-chains 133 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.7980 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 3 optimal weight: 0.0870 chunk 1 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.134317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.102897 restraints weight = 14423.592| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.46 r_work: 0.3373 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8092 Z= 0.151 Angle : 0.685 14.867 10996 Z= 0.325 Chirality : 0.043 0.319 1310 Planarity : 0.004 0.035 1324 Dihedral : 4.235 25.270 1058 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.85 % Allowed : 18.13 % Favored : 80.02 % 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: 2.46 (0.27), residues: 984 helix: 2.09 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -0.83 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 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 C 451 ARG 0.006 0.000 ARG C 295 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 635) hydrogen bonds : angle 4.19959 ( 1881) covalent geometry : bond 0.00341 ( 8092) covalent geometry : angle 0.68512 (10996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6613.65 seconds wall clock time: 113 minutes 51.24 seconds (6831.24 seconds total)