Starting phenix.real_space_refine on Sat May 10 18:10:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iv2_60918/05_2025/9iv2_60918.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iv2_60918/05_2025/9iv2_60918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iv2_60918/05_2025/9iv2_60918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iv2_60918/05_2025/9iv2_60918.map" model { file = "/net/cci-nas-00/data/ceres_data/9iv2_60918/05_2025/9iv2_60918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iv2_60918/05_2025/9iv2_60918.cif" } resolution = 3.53 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= 0.001 sd= 0.014 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 41 5.16 5 C 4300 2.51 5 N 1134 2.21 5 O 1257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6732 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2493 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 8, 'PHE:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 85 Chain: "G" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 417 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1756 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 10, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 83 Chain: "R" Number of atoms: 2045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2045 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'DHT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.37, per 1000 atoms: 0.65 Number of scatterers: 6732 At special positions: 0 Unit cell: (76.36, 103.96, 124.2, 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 41 16.00 O 1257 8.00 N 1134 7.00 C 4300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 632 " - pdb=" SG CYS R 704 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 1.0 seconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 9 sheets defined 42.7% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 12 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.563A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.568A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 38 removed outlier: 3.583A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 233 through 239 removed outlier: 4.119A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.561A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.159A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.672A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'R' and resid 566 through 591 Processing helix chain 'R' and resid 599 through 624 removed outlier: 3.736A pdb=" N HIS R 603 " --> pdb=" O ASN R 599 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG R 624 " --> pdb=" O LEU R 620 " (cutoff:3.500A) Processing helix chain 'R' and resid 629 through 662 removed outlier: 3.681A pdb=" N GLN R 633 " --> pdb=" O THR R 629 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL R 637 " --> pdb=" O GLN R 633 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU R 638 " --> pdb=" O VAL R 634 " (cutoff:3.500A) Processing helix chain 'R' and resid 671 through 681 Processing helix chain 'R' and resid 681 through 694 removed outlier: 3.983A pdb=" N PHE R 693 " --> pdb=" O ILE R 689 " (cutoff:3.500A) Processing helix chain 'R' and resid 713 through 743 removed outlier: 3.797A pdb=" N ALA R 718 " --> pdb=" O TRP R 714 " (cutoff:3.500A) Proline residue: R 719 - end of helix Processing helix chain 'R' and resid 756 through 770 Proline residue: R 767 - end of helix Processing helix chain 'R' and resid 774 through 781 removed outlier: 3.932A pdb=" N LEU R 778 " --> pdb=" O VAL R 774 " (cutoff:3.500A) Processing helix chain 'R' and resid 788 through 797 removed outlier: 3.862A pdb=" N LEU R 797 " --> pdb=" O THR R 793 " (cutoff:3.500A) Processing helix chain 'R' and resid 797 through 809 removed outlier: 3.756A pdb=" N PHE R 801 " --> pdb=" O LEU R 797 " (cutoff:3.500A) Processing helix chain 'R' and resid 810 through 827 removed outlier: 3.592A pdb=" N THR R 827 " --> pdb=" O VAL R 823 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.425A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.461A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS B 62 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.510A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.510A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.647A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG B 150 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL B 158 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 removed outlier: 3.597A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.372A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.989A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 286 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.662A pdb=" N ASP A 223 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 219 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 214 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 903 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: 1.90 Time building geometry restraints manager: 2.01 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: 2185 1.34 - 1.46: 1150 1.46 - 1.58: 3483 1.58 - 1.70: 0 1.70 - 1.81: 56 Bond restraints: 6874 Sorted by residual: bond pdb=" C10 DHT R 901 " pdb=" C9 DHT R 901 " ideal model delta sigma weight residual 1.551 1.523 0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C13 DHT R 901 " pdb=" C14 DHT R 901 " ideal model delta sigma weight residual 1.534 1.511 0.023 2.00e-02 2.50e+03 1.33e+00 bond pdb=" C17 DHT R 901 " pdb=" O17 DHT R 901 " ideal model delta sigma weight residual 1.407 1.430 -0.023 2.00e-02 2.50e+03 1.27e+00 bond pdb=" C10 DHT R 901 " pdb=" C5 DHT R 901 " ideal model delta sigma weight residual 1.546 1.524 0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" CB PRO R 767 " pdb=" CG PRO R 767 " ideal model delta sigma weight residual 1.492 1.545 -0.053 5.00e-02 4.00e+02 1.14e+00 ... (remaining 6869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 9277 2.19 - 4.39: 82 4.39 - 6.58: 13 6.58 - 8.78: 3 8.78 - 10.97: 2 Bond angle restraints: 9377 Sorted by residual: angle pdb=" CA LEU R 769 " pdb=" CB LEU R 769 " pdb=" CG LEU R 769 " ideal model delta sigma weight residual 116.30 127.27 -10.97 3.50e+00 8.16e-02 9.83e+00 angle pdb=" CB MET B 101 " pdb=" CG MET B 101 " pdb=" SD MET B 101 " ideal model delta sigma weight residual 112.70 121.13 -8.43 3.00e+00 1.11e-01 7.90e+00 angle pdb=" C TRP R 649 " pdb=" N MET R 650 " pdb=" CA MET R 650 " ideal model delta sigma weight residual 120.31 116.28 4.03 1.52e+00 4.33e-01 7.03e+00 angle pdb=" CA LEU G 15 " pdb=" CB LEU G 15 " pdb=" CG LEU G 15 " ideal model delta sigma weight residual 116.30 125.56 -9.26 3.50e+00 8.16e-02 7.00e+00 angle pdb=" N ILE R 713 " pdb=" CA ILE R 713 " pdb=" C ILE R 713 " ideal model delta sigma weight residual 112.98 109.72 3.26 1.25e+00 6.40e-01 6.82e+00 ... (remaining 9372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3466 18.00 - 35.99: 449 35.99 - 53.99: 125 53.99 - 71.98: 11 71.98 - 89.98: 11 Dihedral angle restraints: 4062 sinusoidal: 1466 harmonic: 2596 Sorted by residual: dihedral pdb=" CB CYS R 632 " pdb=" SG CYS R 632 " pdb=" SG CYS R 704 " pdb=" CB CYS R 704 " ideal model delta sinusoidal sigma weight residual 93.00 144.51 -51.51 1 1.00e+01 1.00e-02 3.62e+01 dihedral pdb=" CB GLU B 3 " pdb=" CG GLU B 3 " pdb=" CD GLU B 3 " pdb=" OE1 GLU B 3 " ideal model delta sinusoidal sigma weight residual 0.00 -89.98 89.98 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU R 653 " pdb=" CG GLU R 653 " pdb=" CD GLU R 653 " pdb=" OE1 GLU R 653 " ideal model delta sinusoidal sigma weight residual 0.00 -84.77 84.77 1 3.00e+01 1.11e-03 9.69e+00 ... (remaining 4059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 935 0.054 - 0.108: 155 0.108 - 0.163: 16 0.163 - 0.217: 2 0.217 - 0.271: 1 Chirality restraints: 1109 Sorted by residual: chirality pdb=" C10 DHT R 901 " pdb=" C1 DHT R 901 " pdb=" C5 DHT R 901 " pdb=" C9 DHT R 901 " both_signs ideal model delta sigma weight residual False -2.97 -2.70 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C13 DHT R 901 " pdb=" C12 DHT R 901 " pdb=" C14 DHT R 901 " pdb=" C17 DHT R 901 " both_signs ideal model delta sigma weight residual False -2.87 -2.67 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA PRO R 767 " pdb=" N PRO R 767 " pdb=" C PRO R 767 " pdb=" CB PRO R 767 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 1106 not shown) Planarity restraints: 1188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 360 " -0.059 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO A 361 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C2 DHT R 901 " 0.017 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C3 DHT R 901 " -0.055 2.00e-02 2.50e+03 pdb=" C4 DHT R 901 " 0.017 2.00e-02 2.50e+03 pdb=" O3 DHT R 901 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 766 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.61e+00 pdb=" N PRO R 767 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO R 767 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 767 " -0.041 5.00e-02 4.00e+02 ... (remaining 1185 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 391 2.73 - 3.27: 6889 3.27 - 3.81: 10887 3.81 - 4.36: 11181 4.36 - 4.90: 20012 Nonbonded interactions: 49360 Sorted by model distance: nonbonded pdb=" O LEU R 566 " pdb=" OG SER R 570 " model vdw 2.186 3.040 nonbonded pdb=" OG1 THR B 165 " pdb=" O PHE B 180 " model vdw 2.263 3.040 nonbonded pdb=" O ALA A 48 " pdb=" OG SER A 51 " model vdw 2.269 3.040 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.307 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.307 3.040 ... (remaining 49355 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.120 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 : 0.002 0.053 6875 Z= 0.105 Angle : 0.539 10.974 9379 Z= 0.268 Chirality : 0.040 0.271 1109 Planarity : 0.004 0.089 1188 Dihedral : 17.472 89.977 2375 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 37.75 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.29), residues: 880 helix: 1.74 (0.29), residues: 354 sheet: 0.81 (0.53), residues: 118 loop : -2.16 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 277 HIS 0.002 0.000 HIS B 54 PHE 0.012 0.001 PHE A 340 TYR 0.005 0.001 TYR A 263 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.15353 ( 303) hydrogen bonds : angle 6.17547 ( 903) SS BOND : bond 0.00411 ( 1) SS BOND : angle 0.61197 ( 2) covalent geometry : bond 0.00222 ( 6874) covalent geometry : angle 0.53887 ( 9377) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.723 Fit side-chains REVERT: A 34 LYS cc_start: 0.9241 (tppp) cc_final: 0.8965 (tppt) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1725 time to fit residues: 22.2133 Evaluate side-chains 85 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 40 optimal weight: 0.5980 chunk 50 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.079114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.066108 restraints weight = 19580.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.067530 restraints weight = 8112.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.068391 restraints weight = 4604.463| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6875 Z= 0.150 Angle : 0.512 7.402 9379 Z= 0.269 Chirality : 0.040 0.146 1109 Planarity : 0.004 0.064 1188 Dihedral : 3.806 36.583 1000 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.04 % Allowed : 32.56 % Favored : 62.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.29), residues: 880 helix: 1.59 (0.28), residues: 364 sheet: 0.52 (0.48), residues: 136 loop : -2.29 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.002 0.001 HIS R 672 PHE 0.014 0.001 PHE A 340 TYR 0.009 0.001 TYR R 602 ARG 0.002 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 303) hydrogen bonds : angle 5.01107 ( 903) SS BOND : bond 0.00636 ( 1) SS BOND : angle 0.51441 ( 2) covalent geometry : bond 0.00332 ( 6874) covalent geometry : angle 0.51162 ( 9377) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.710 Fit side-chains REVERT: B 13 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6546 (pm20) REVERT: B 285 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8656 (tp) REVERT: A 391 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.8877 (t80) outliers start: 35 outliers final: 20 residues processed: 110 average time/residue: 0.1561 time to fit residues: 23.8650 Evaluate side-chains 100 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain R residue 564 VAL Chi-restraints excluded: chain R residue 567 SER Chi-restraints excluded: chain R residue 582 VAL Chi-restraints excluded: chain R residue 644 LEU Chi-restraints excluded: chain R residue 652 VAL Chi-restraints excluded: chain R residue 726 VAL Chi-restraints excluded: chain R residue 768 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.078149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.065030 restraints weight = 20053.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.066451 restraints weight = 8219.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.067335 restraints weight = 4657.150| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6875 Z= 0.159 Angle : 0.507 5.559 9379 Z= 0.268 Chirality : 0.039 0.142 1109 Planarity : 0.003 0.052 1188 Dihedral : 3.886 39.997 1000 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.19 % Allowed : 31.84 % Favored : 62.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.29), residues: 880 helix: 1.52 (0.28), residues: 364 sheet: 0.44 (0.47), residues: 136 loop : -2.31 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 680 HIS 0.002 0.001 HIS A 362 PHE 0.015 0.001 PHE A 340 TYR 0.009 0.001 TYR R 602 ARG 0.002 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 303) hydrogen bonds : angle 4.92259 ( 903) SS BOND : bond 0.00687 ( 1) SS BOND : angle 0.50896 ( 2) covalent geometry : bond 0.00353 ( 6874) covalent geometry : angle 0.50715 ( 9377) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 82 time to evaluate : 0.709 Fit side-chains REVERT: B 13 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.6532 (pm20) REVERT: B 285 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8685 (tp) REVERT: A 34 LYS cc_start: 0.9176 (tppp) cc_final: 0.8933 (tppt) REVERT: A 391 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.8877 (t80) REVERT: R 579 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7404 (tt) outliers start: 36 outliers final: 25 residues processed: 108 average time/residue: 0.1693 time to fit residues: 25.6482 Evaluate side-chains 100 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain R residue 564 VAL Chi-restraints excluded: chain R residue 567 SER Chi-restraints excluded: chain R residue 579 LEU Chi-restraints excluded: chain R residue 582 VAL Chi-restraints excluded: chain R residue 601 ARG Chi-restraints excluded: chain R residue 644 LEU Chi-restraints excluded: chain R residue 652 VAL Chi-restraints excluded: chain R residue 726 VAL Chi-restraints excluded: chain R residue 768 ILE Chi-restraints excluded: chain R residue 802 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 34 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.078062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.064890 restraints weight = 20198.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.066313 restraints weight = 8271.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.067192 restraints weight = 4675.970| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6875 Z= 0.159 Angle : 0.515 7.884 9379 Z= 0.268 Chirality : 0.040 0.187 1109 Planarity : 0.003 0.046 1188 Dihedral : 3.924 42.275 1000 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.76 % Allowed : 31.27 % Favored : 62.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.29), residues: 880 helix: 1.48 (0.28), residues: 364 sheet: 0.39 (0.46), residues: 141 loop : -2.31 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 277 HIS 0.002 0.001 HIS A 362 PHE 0.015 0.001 PHE A 340 TYR 0.009 0.001 TYR R 602 ARG 0.002 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 303) hydrogen bonds : angle 4.85995 ( 903) SS BOND : bond 0.00630 ( 1) SS BOND : angle 0.48392 ( 2) covalent geometry : bond 0.00355 ( 6874) covalent geometry : angle 0.51471 ( 9377) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 76 time to evaluate : 0.745 Fit side-chains REVERT: B 13 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6539 (pm20) REVERT: A 34 LYS cc_start: 0.9165 (tppp) cc_final: 0.8910 (tppt) REVERT: A 391 TYR cc_start: 0.9180 (OUTLIER) cc_final: 0.8913 (t80) REVERT: R 579 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7415 (tt) REVERT: R 625 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8409 (tt) REVERT: R 669 ASP cc_start: 0.9461 (OUTLIER) cc_final: 0.8865 (t0) REVERT: R 814 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7064 (mtm-85) outliers start: 40 outliers final: 28 residues processed: 106 average time/residue: 0.1588 time to fit residues: 23.7515 Evaluate side-chains 105 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 71 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain R residue 564 VAL Chi-restraints excluded: chain R residue 567 SER Chi-restraints excluded: chain R residue 579 LEU Chi-restraints excluded: chain R residue 582 VAL Chi-restraints excluded: chain R residue 625 LEU Chi-restraints excluded: chain R residue 644 LEU Chi-restraints excluded: chain R residue 645 SER Chi-restraints excluded: chain R residue 652 VAL Chi-restraints excluded: chain R residue 669 ASP Chi-restraints excluded: chain R residue 726 VAL Chi-restraints excluded: chain R residue 768 ILE Chi-restraints excluded: chain R residue 802 ILE Chi-restraints excluded: chain R residue 814 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 10 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 0.0870 chunk 76 optimal weight: 0.8980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.082204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.069034 restraints weight = 19555.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.070530 restraints weight = 7915.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.071467 restraints weight = 4428.508| |-----------------------------------------------------------------------------| r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6875 Z= 0.094 Angle : 0.468 6.053 9379 Z= 0.244 Chirality : 0.038 0.134 1109 Planarity : 0.003 0.041 1188 Dihedral : 3.685 40.563 1000 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.04 % Allowed : 32.56 % Favored : 62.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.29), residues: 880 helix: 1.85 (0.29), residues: 358 sheet: 0.31 (0.48), residues: 136 loop : -2.30 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 649 HIS 0.002 0.000 HIS A 220 PHE 0.011 0.001 PHE A 340 TYR 0.007 0.001 TYR A 263 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03247 ( 303) hydrogen bonds : angle 4.49839 ( 903) SS BOND : bond 0.00223 ( 1) SS BOND : angle 0.39929 ( 2) covalent geometry : bond 0.00193 ( 6874) covalent geometry : angle 0.46775 ( 9377) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.790 Fit side-chains REVERT: B 13 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6653 (pm20) REVERT: B 285 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8625 (tp) REVERT: A 34 LYS cc_start: 0.9102 (tppp) cc_final: 0.8849 (tppt) REVERT: A 389 ARG cc_start: 0.9175 (tpm170) cc_final: 0.8852 (tpm170) REVERT: A 391 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.8901 (t80) REVERT: R 579 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7344 (tt) REVERT: R 601 ARG cc_start: 0.9381 (OUTLIER) cc_final: 0.9165 (ttp-110) REVERT: R 669 ASP cc_start: 0.9431 (OUTLIER) cc_final: 0.8944 (t0) outliers start: 35 outliers final: 16 residues processed: 117 average time/residue: 0.1684 time to fit residues: 27.0639 Evaluate side-chains 101 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain R residue 579 LEU Chi-restraints excluded: chain R residue 601 ARG Chi-restraints excluded: chain R residue 644 LEU Chi-restraints excluded: chain R residue 669 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 75 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.081026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.067866 restraints weight = 19514.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.069335 restraints weight = 7924.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.070253 restraints weight = 4453.201| |-----------------------------------------------------------------------------| r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6875 Z= 0.109 Angle : 0.498 8.508 9379 Z= 0.257 Chirality : 0.038 0.137 1109 Planarity : 0.003 0.038 1188 Dihedral : 3.645 38.526 1000 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.18 % Allowed : 33.14 % Favored : 62.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.29), residues: 880 helix: 1.86 (0.28), residues: 358 sheet: 0.18 (0.47), residues: 134 loop : -2.25 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 277 HIS 0.004 0.001 HIS B 225 PHE 0.013 0.001 PHE A 340 TYR 0.007 0.001 TYR R 658 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 303) hydrogen bonds : angle 4.49467 ( 903) SS BOND : bond 0.00392 ( 1) SS BOND : angle 0.35542 ( 2) covalent geometry : bond 0.00236 ( 6874) covalent geometry : angle 0.49810 ( 9377) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.736 Fit side-chains REVERT: B 13 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6606 (pm20) REVERT: B 285 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8666 (tp) REVERT: A 34 LYS cc_start: 0.9107 (tppp) cc_final: 0.8868 (tppt) REVERT: A 211 LYS cc_start: 0.8796 (mmmm) cc_final: 0.8570 (mmmm) REVERT: A 389 ARG cc_start: 0.9170 (tpm170) cc_final: 0.8774 (tpm170) REVERT: R 579 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7347 (tt) REVERT: R 601 ARG cc_start: 0.9403 (OUTLIER) cc_final: 0.9201 (ttp-110) REVERT: R 669 ASP cc_start: 0.9431 (OUTLIER) cc_final: 0.8946 (t0) REVERT: R 814 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7182 (mtm-85) outliers start: 29 outliers final: 19 residues processed: 101 average time/residue: 0.1842 time to fit residues: 25.0694 Evaluate side-chains 105 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain R residue 579 LEU Chi-restraints excluded: chain R residue 601 ARG Chi-restraints excluded: chain R residue 644 LEU Chi-restraints excluded: chain R residue 645 SER Chi-restraints excluded: chain R residue 669 ASP Chi-restraints excluded: chain R residue 768 ILE Chi-restraints excluded: chain R residue 814 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.078355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.065160 restraints weight = 19891.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.066564 restraints weight = 8222.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.067431 restraints weight = 4684.883| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6875 Z= 0.162 Angle : 0.520 8.047 9379 Z= 0.272 Chirality : 0.039 0.137 1109 Planarity : 0.003 0.037 1188 Dihedral : 3.842 39.376 1000 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 5.76 % Allowed : 31.41 % Favored : 62.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.29), residues: 880 helix: 1.56 (0.28), residues: 365 sheet: 0.28 (0.46), residues: 138 loop : -2.25 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.004 0.001 HIS B 225 PHE 0.016 0.001 PHE A 340 TYR 0.008 0.001 TYR R 789 ARG 0.002 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 303) hydrogen bonds : angle 4.70661 ( 903) SS BOND : bond 0.00699 ( 1) SS BOND : angle 0.48102 ( 2) covalent geometry : bond 0.00361 ( 6874) covalent geometry : angle 0.52031 ( 9377) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 75 time to evaluate : 0.846 Fit side-chains REVERT: B 13 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6542 (pm20) REVERT: B 285 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8732 (tp) REVERT: A 34 LYS cc_start: 0.9167 (tppp) cc_final: 0.8921 (tppt) REVERT: R 579 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7429 (tt) REVERT: R 625 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8384 (tt) REVERT: R 669 ASP cc_start: 0.9455 (OUTLIER) cc_final: 0.8840 (t0) REVERT: R 814 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7154 (mtm-85) outliers start: 40 outliers final: 27 residues processed: 106 average time/residue: 0.1747 time to fit residues: 25.3958 Evaluate side-chains 106 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain R residue 564 VAL Chi-restraints excluded: chain R residue 579 LEU Chi-restraints excluded: chain R residue 582 VAL Chi-restraints excluded: chain R residue 601 ARG Chi-restraints excluded: chain R residue 625 LEU Chi-restraints excluded: chain R residue 644 LEU Chi-restraints excluded: chain R residue 645 SER Chi-restraints excluded: chain R residue 669 ASP Chi-restraints excluded: chain R residue 768 ILE Chi-restraints excluded: chain R residue 814 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.8980 chunk 13 optimal weight: 0.0050 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.078811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.065609 restraints weight = 20014.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.067027 restraints weight = 8203.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.067906 restraints weight = 4647.637| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6875 Z= 0.141 Angle : 0.520 7.461 9379 Z= 0.269 Chirality : 0.039 0.138 1109 Planarity : 0.003 0.036 1188 Dihedral : 3.844 39.809 1000 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 5.19 % Allowed : 32.13 % Favored : 62.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.29), residues: 880 helix: 1.57 (0.28), residues: 364 sheet: 0.24 (0.46), residues: 137 loop : -2.29 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS B 225 PHE 0.015 0.001 PHE A 340 TYR 0.007 0.001 TYR R 658 ARG 0.002 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 303) hydrogen bonds : angle 4.64881 ( 903) SS BOND : bond 0.00575 ( 1) SS BOND : angle 0.45855 ( 2) covalent geometry : bond 0.00314 ( 6874) covalent geometry : angle 0.51958 ( 9377) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.713 Fit side-chains REVERT: B 13 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6540 (pm20) REVERT: B 285 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8693 (tp) REVERT: A 34 LYS cc_start: 0.9152 (tppp) cc_final: 0.8898 (tppt) REVERT: R 579 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7412 (tt) REVERT: R 669 ASP cc_start: 0.9458 (OUTLIER) cc_final: 0.8840 (t0) REVERT: R 814 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7096 (mtm-85) outliers start: 36 outliers final: 29 residues processed: 101 average time/residue: 0.1694 time to fit residues: 23.4507 Evaluate side-chains 106 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain R residue 564 VAL Chi-restraints excluded: chain R residue 579 LEU Chi-restraints excluded: chain R residue 582 VAL Chi-restraints excluded: chain R residue 601 ARG Chi-restraints excluded: chain R residue 644 LEU Chi-restraints excluded: chain R residue 645 SER Chi-restraints excluded: chain R residue 652 VAL Chi-restraints excluded: chain R residue 669 ASP Chi-restraints excluded: chain R residue 768 ILE Chi-restraints excluded: chain R residue 814 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 33 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 82 optimal weight: 0.1980 chunk 29 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.077415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.064210 restraints weight = 20096.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.065604 restraints weight = 8292.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.066462 restraints weight = 4723.843| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6875 Z= 0.179 Angle : 0.544 9.028 9379 Z= 0.283 Chirality : 0.040 0.162 1109 Planarity : 0.003 0.037 1188 Dihedral : 3.972 40.314 1000 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 5.76 % Allowed : 31.56 % Favored : 62.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.29), residues: 880 helix: 1.42 (0.28), residues: 365 sheet: 0.14 (0.47), residues: 138 loop : -2.26 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.004 0.001 HIS B 225 PHE 0.016 0.001 PHE A 340 TYR 0.008 0.001 TYR R 789 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 303) hydrogen bonds : angle 4.80570 ( 903) SS BOND : bond 0.00774 ( 1) SS BOND : angle 0.55781 ( 2) covalent geometry : bond 0.00401 ( 6874) covalent geometry : angle 0.54377 ( 9377) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 72 time to evaluate : 0.720 Fit side-chains REVERT: B 13 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6521 (pm20) REVERT: B 285 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8721 (tp) REVERT: A 34 LYS cc_start: 0.9161 (tppp) cc_final: 0.8902 (tppt) REVERT: R 579 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7349 (tt) REVERT: R 625 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8433 (tt) REVERT: R 669 ASP cc_start: 0.9466 (OUTLIER) cc_final: 0.8856 (t0) REVERT: R 814 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7071 (mtm-85) outliers start: 40 outliers final: 31 residues processed: 104 average time/residue: 0.1672 time to fit residues: 24.0183 Evaluate side-chains 107 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 70 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain R residue 564 VAL Chi-restraints excluded: chain R residue 579 LEU Chi-restraints excluded: chain R residue 582 VAL Chi-restraints excluded: chain R residue 601 ARG Chi-restraints excluded: chain R residue 625 LEU Chi-restraints excluded: chain R residue 644 LEU Chi-restraints excluded: chain R residue 645 SER Chi-restraints excluded: chain R residue 652 VAL Chi-restraints excluded: chain R residue 669 ASP Chi-restraints excluded: chain R residue 768 ILE Chi-restraints excluded: chain R residue 814 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 8 optimal weight: 0.0050 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.079421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.066237 restraints weight = 20127.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.067676 restraints weight = 8202.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.068568 restraints weight = 4620.207| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6875 Z= 0.120 Angle : 0.519 9.208 9379 Z= 0.268 Chirality : 0.039 0.155 1109 Planarity : 0.003 0.036 1188 Dihedral : 3.816 40.240 1000 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.76 % Allowed : 32.56 % Favored : 62.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.29), residues: 880 helix: 1.61 (0.28), residues: 364 sheet: 0.10 (0.48), residues: 132 loop : -2.24 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 649 HIS 0.003 0.001 HIS B 225 PHE 0.013 0.001 PHE A 340 TYR 0.007 0.001 TYR R 658 ARG 0.002 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 303) hydrogen bonds : angle 4.59171 ( 903) SS BOND : bond 0.00468 ( 1) SS BOND : angle 0.45878 ( 2) covalent geometry : bond 0.00262 ( 6874) covalent geometry : angle 0.51926 ( 9377) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.801 Fit side-chains REVERT: B 13 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6514 (pm20) REVERT: B 285 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8702 (tp) REVERT: A 34 LYS cc_start: 0.9090 (tppp) cc_final: 0.8837 (tppt) REVERT: A 389 ARG cc_start: 0.9190 (tpm170) cc_final: 0.8800 (tpm170) REVERT: R 579 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7355 (tt) REVERT: R 625 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8338 (tt) REVERT: R 669 ASP cc_start: 0.9454 (OUTLIER) cc_final: 0.8844 (t0) REVERT: R 814 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7100 (mtm-85) outliers start: 33 outliers final: 24 residues processed: 106 average time/residue: 0.1944 time to fit residues: 27.8530 Evaluate side-chains 106 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain R residue 564 VAL Chi-restraints excluded: chain R residue 579 LEU Chi-restraints excluded: chain R residue 582 VAL Chi-restraints excluded: chain R residue 625 LEU Chi-restraints excluded: chain R residue 644 LEU Chi-restraints excluded: chain R residue 645 SER Chi-restraints excluded: chain R residue 669 ASP Chi-restraints excluded: chain R residue 768 ILE Chi-restraints excluded: chain R residue 814 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 16 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 67 optimal weight: 0.4980 chunk 29 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.076296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.063203 restraints weight = 20313.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.064520 restraints weight = 8618.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.065339 restraints weight = 4988.907| |-----------------------------------------------------------------------------| r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6875 Z= 0.229 Angle : 0.584 8.845 9379 Z= 0.307 Chirality : 0.041 0.197 1109 Planarity : 0.003 0.036 1188 Dihedral : 4.119 41.797 1000 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 5.04 % Allowed : 32.28 % Favored : 62.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.29), residues: 880 helix: 1.28 (0.28), residues: 365 sheet: 0.07 (0.47), residues: 138 loop : -2.27 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 99 HIS 0.003 0.001 HIS B 225 PHE 0.019 0.002 PHE A 340 TYR 0.013 0.001 TYR A 318 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 303) hydrogen bonds : angle 4.95071 ( 903) SS BOND : bond 0.01014 ( 1) SS BOND : angle 0.62641 ( 2) covalent geometry : bond 0.00515 ( 6874) covalent geometry : angle 0.58429 ( 9377) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2178.16 seconds wall clock time: 38 minutes 53.16 seconds (2333.16 seconds total)