Starting phenix.real_space_refine on Thu Jun 5 20:44:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iv2_60918/06_2025/9iv2_60918.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iv2_60918/06_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_60918/06_2025/9iv2_60918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iv2_60918/06_2025/9iv2_60918.map" model { file = "/net/cci-nas-00/data/ceres_data/9iv2_60918/06_2025/9iv2_60918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iv2_60918/06_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 4.25, per 1000 atoms: 0.63 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: 2.36 Conformation dependent library (CDL) restraints added in 1.2 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: 0.68 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: 1.89 Time building geometry restraints manager: 1.68 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: 0.460 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.670 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.550 ------------------------------------------------------------------------------- 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 : 0.769 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: 0.1715 time to fit residues: 22.0355 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 : 0.688 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.066107 restraints weight = 19580.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.067530 restraints weight = 8113.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.068390 restraints weight = 4599.058| |-----------------------------------------------------------------------------| 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 : 0.665 Fit side-chains REVERT: B 13 GLN cc_start: 0.7242 (OUTLIER) cc_final: 0.6545 (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: 0.1629 time to fit residues: 24.7633 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 : 0.709 ------------------------------------------------------------------------------- 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: 3.9990 chunk 58 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.2898 r_free = 0.2898 target = 0.077668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.064545 restraints weight = 20113.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.065946 restraints weight = 8263.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.066833 restraints weight = 4688.176| |-----------------------------------------------------------------------------| r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1311 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= 0.174 Angle : 0.518 5.499 9379 Z= 0.274 Chirality : 0.040 0.144 1109 Planarity : 0.003 0.053 1188 Dihedral : 3.954 40.861 1000 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.04 % Allowed : 31.70 % Favored : 63.26 % 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: -0.37 (0.29), residues: 880 helix: 1.42 (0.28), residues: 366 sheet: 0.46 (0.47), residues: 141 loop : -2.37 (0.28), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 680 HIS 0.002 0.001 HIS A 362 PHE 0.016 0.001 PHE A 340 TYR 0.010 0.001 TYR R 602 ARG 0.002 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 303) hydrogen bonds : angle 4.97387 ( 903) SS BOND : bond 0.00769 ( 1) SS BOND : angle 0.55687 ( 2) covalent geometry : bond 0.00390 ( 6874) covalent geometry : angle 0.51749 ( 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 115 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 80 time to evaluate : 0.689 Fit side-chains REVERT: B 13 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6511 (pm20) REVERT: A 34 LYS cc_start: 0.9189 (tppp) cc_final: 0.8957 (tppt) REVERT: A 391 TYR cc_start: 0.9179 (OUTLIER) cc_final: 0.8899 (t80) REVERT: R 579 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7389 (tt) outliers start: 35 outliers final: 24 residues processed: 105 average time/residue: 0.1463 time to fit residues: 21.8549 Evaluate side-chains 95 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 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 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: 6.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.2895 r_free = 0.2895 target = 0.077612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.064434 restraints weight = 20249.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.065836 restraints weight = 8297.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.066716 restraints weight = 4703.459| |-----------------------------------------------------------------------------| r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1421 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= 0.171 Angle : 0.521 8.032 9379 Z= 0.272 Chirality : 0.040 0.203 1109 Planarity : 0.003 0.047 1188 Dihedral : 3.970 41.586 1000 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 6.34 % Allowed : 31.70 % Favored : 61.96 % 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: -0.36 (0.29), residues: 880 helix: 1.45 (0.28), residues: 363 sheet: 0.40 (0.46), residues: 146 loop : -2.36 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 277 HIS 0.002 0.001 HIS R 605 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 0.03897 ( 303) hydrogen bonds : angle 4.91113 ( 903) SS BOND : bond 0.00684 ( 1) SS BOND : angle 0.48819 ( 2) covalent geometry : bond 0.00382 ( 6874) covalent geometry : angle 0.52124 ( 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: 44 poor density : 72 time to evaluate : 0.780 Fit side-chains REVERT: B 13 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6532 (pm20) REVERT: B 285 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8693 (tp) REVERT: A 391 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.8923 (t80) REVERT: R 579 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7416 (tt) REVERT: R 625 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8415 (tt) REVERT: R 669 ASP cc_start: 0.9469 (OUTLIER) cc_final: 0.8876 (t0) REVERT: R 814 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7059 (mtm-85) outliers start: 44 outliers final: 29 residues processed: 107 average time/residue: 0.1639 time to fit residues: 24.6324 Evaluate side-chains 105 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 69 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 47 THR 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 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 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: 0.0470 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.7482 ------------------------------------------------------------------------------- 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 = 0.2973 r_free = 0.2973 target = 0.081458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.068278 restraints weight = 19582.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.069757 restraints weight = 7928.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.070681 restraints weight = 4452.255| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1374 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= 0.096 Angle : 0.471 5.990 9379 Z= 0.246 Chirality : 0.038 0.135 1109 Planarity : 0.003 0.041 1188 Dihedral : 3.734 40.366 1000 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.47 % Allowed : 33.14 % 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: -0.22 (0.29), residues: 880 helix: 1.81 (0.29), residues: 358 sheet: 0.21 (0.48), residues: 134 loop : -2.29 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 277 HIS 0.001 0.000 HIS A 220 PHE 0.011 0.001 PHE A 340 TYR 0.007 0.001 TYR R 658 ARG 0.002 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 303) hydrogen bonds : angle 4.53799 ( 903) SS BOND : bond 0.00259 ( 1) SS BOND : angle 0.39422 ( 2) covalent geometry : bond 0.00199 ( 6874) covalent geometry : angle 0.47090 ( 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 119 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.773 Fit side-chains REVERT: B 13 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6614 (pm20) REVERT: B 285 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8655 (tp) REVERT: A 34 LYS cc_start: 0.9108 (tppp) cc_final: 0.8861 (tppt) REVERT: A 389 ARG cc_start: 0.9174 (tpm170) cc_final: 0.8850 (tpm170) REVERT: A 391 TYR cc_start: 0.9129 (OUTLIER) cc_final: 0.8916 (t80) REVERT: R 579 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7362 (tt) REVERT: R 601 ARG cc_start: 0.9394 (OUTLIER) cc_final: 0.9174 (ttp-110) REVERT: R 669 ASP cc_start: 0.9435 (OUTLIER) cc_final: 0.8883 (t0) outliers start: 31 outliers final: 14 residues processed: 111 average time/residue: 0.1743 time to fit residues: 26.6936 Evaluate side-chains 98 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 54 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL 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 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: 3.9990 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 0.2980 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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 = 0.2939 r_free = 0.2939 target = 0.080178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.067010 restraints weight = 19839.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.068448 restraints weight = 8125.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.069326 restraints weight = 4599.739| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6875 Z= 0.122 Angle : 0.505 8.701 9379 Z= 0.260 Chirality : 0.039 0.137 1109 Planarity : 0.003 0.038 1188 Dihedral : 3.736 39.949 1000 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.61 % Allowed : 32.85 % Favored : 62.54 % 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: -0.24 (0.29), residues: 880 helix: 1.78 (0.28), residues: 358 sheet: 0.18 (0.48), residues: 134 loop : -2.29 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 277 HIS 0.002 0.001 HIS R 605 PHE 0.014 0.001 PHE A 340 TYR 0.007 0.001 TYR R 789 ARG 0.004 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 303) hydrogen bonds : angle 4.57494 ( 903) SS BOND : bond 0.00473 ( 1) SS BOND : angle 0.41592 ( 2) covalent geometry : bond 0.00268 ( 6874) covalent geometry : angle 0.50521 ( 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 110 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.705 Fit side-chains REVERT: B 13 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6496 (pm20) REVERT: B 285 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8678 (tp) REVERT: A 34 LYS cc_start: 0.9106 (tppp) cc_final: 0.8835 (tppt) REVERT: A 211 LYS cc_start: 0.8801 (mmmm) cc_final: 0.8573 (mmmm) REVERT: A 391 TYR cc_start: 0.9143 (OUTLIER) cc_final: 0.8893 (t80) REVERT: R 579 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7357 (tt) REVERT: R 601 ARG cc_start: 0.9410 (OUTLIER) cc_final: 0.9190 (ttp-110) REVERT: R 669 ASP cc_start: 0.9444 (OUTLIER) cc_final: 0.8896 (t0) REVERT: R 814 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7130 (mtm-85) outliers start: 32 outliers final: 22 residues processed: 102 average time/residue: 0.1714 time to fit residues: 23.8774 Evaluate side-chains 105 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 54 HIS 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 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 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 44 HIS 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 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 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: 4.9990 chunk 68 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.2906 r_free = 0.2906 target = 0.078149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.064982 restraints weight = 19968.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.066389 restraints weight = 8236.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.067246 restraints weight = 4680.555| |-----------------------------------------------------------------------------| r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1559 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= 0.158 Angle : 0.520 8.233 9379 Z= 0.270 Chirality : 0.039 0.137 1109 Planarity : 0.003 0.038 1188 Dihedral : 3.874 40.114 1000 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.62 % Allowed : 31.84 % Favored : 62.54 % 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: 1.55 (0.28), residues: 365 sheet: 0.18 (0.46), residues: 140 loop : -2.28 (0.28), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.002 0.001 HIS R 605 PHE 0.015 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 0.03753 ( 303) hydrogen bonds : angle 4.71042 ( 903) SS BOND : bond 0.00653 ( 1) SS BOND : angle 0.48515 ( 2) covalent geometry : bond 0.00353 ( 6874) covalent geometry : angle 0.52002 ( 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 113 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 74 time to evaluate : 0.792 Fit side-chains REVERT: B 13 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6531 (pm20) REVERT: B 285 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8725 (tp) REVERT: B 292 PHE cc_start: 0.9508 (m-10) cc_final: 0.9266 (m-80) REVERT: A 34 LYS cc_start: 0.9144 (tppp) cc_final: 0.8902 (tppt) REVERT: A 391 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.8937 (t80) REVERT: R 579 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7418 (tt) REVERT: R 625 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8413 (tt) REVERT: R 669 ASP cc_start: 0.9455 (OUTLIER) cc_final: 0.8843 (t0) REVERT: R 814 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7093 (mtm-85) outliers start: 39 outliers final: 28 residues processed: 105 average time/residue: 0.1757 time to fit residues: 25.4270 Evaluate side-chains 106 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 71 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 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 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 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 391 TYR 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: 0.9980 chunk 13 optimal weight: 0.3980 chunk 40 optimal weight: 0.0070 chunk 58 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.2979 r_free = 0.2979 target = 0.082155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.069044 restraints weight = 19567.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.070478 restraints weight = 8116.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.071367 restraints weight = 4612.142| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6875 Z= 0.097 Angle : 0.495 7.454 9379 Z= 0.254 Chirality : 0.038 0.134 1109 Planarity : 0.003 0.036 1188 Dihedral : 3.679 39.388 1000 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.90 % Allowed : 32.56 % Favored : 62.54 % 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: -0.17 (0.29), residues: 880 helix: 1.83 (0.29), residues: 358 sheet: 0.14 (0.47), residues: 134 loop : -2.21 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 R 658 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 303) hydrogen bonds : angle 4.43860 ( 903) SS BOND : bond 0.00317 ( 1) SS BOND : angle 0.30603 ( 2) covalent geometry : bond 0.00203 ( 6874) covalent geometry : angle 0.49492 ( 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 117 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 0.703 Fit side-chains REVERT: B 13 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.6673 (pm20) REVERT: B 285 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8673 (tp) REVERT: A 34 LYS cc_start: 0.9115 (tppp) cc_final: 0.8844 (tppt) REVERT: A 389 ARG cc_start: 0.9177 (tpm170) cc_final: 0.8598 (tpm170) REVERT: R 579 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7425 (tt) REVERT: R 625 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8244 (tt) REVERT: R 669 ASP cc_start: 0.9424 (OUTLIER) cc_final: 0.8921 (t0) REVERT: R 814 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7166 (mtm-85) outliers start: 34 outliers final: 23 residues processed: 109 average time/residue: 0.1770 time to fit residues: 26.1749 Evaluate side-chains 110 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 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 262 MET Chi-restraints excluded: chain B residue 285 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 82 optimal weight: 0.0270 chunk 29 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- 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** ** 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 = 0.2927 r_free = 0.2927 target = 0.078982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.065889 restraints weight = 19931.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.067279 restraints weight = 8323.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.068137 restraints weight = 4771.743| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6875 Z= 0.140 Angle : 0.518 7.909 9379 Z= 0.268 Chirality : 0.039 0.156 1109 Planarity : 0.003 0.036 1188 Dihedral : 3.753 37.886 1000 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.76 % Allowed : 32.71 % Favored : 62.54 % 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: -0.27 (0.29), residues: 880 helix: 1.62 (0.28), residues: 365 sheet: 0.22 (0.48), residues: 132 loop : -2.24 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.002 0.001 HIS R 672 PHE 0.015 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 0.03590 ( 303) hydrogen bonds : angle 4.60180 ( 903) SS BOND : bond 0.00585 ( 1) SS BOND : angle 0.41752 ( 2) covalent geometry : bond 0.00313 ( 6874) covalent geometry : angle 0.51778 ( 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 110 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.780 Fit side-chains REVERT: B 13 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6533 (pm20) REVERT: B 285 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8710 (tp) REVERT: A 34 LYS cc_start: 0.9109 (tppp) cc_final: 0.8849 (tppt) REVERT: A 389 ARG cc_start: 0.9152 (tpm170) cc_final: 0.8742 (tpm170) REVERT: R 579 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7399 (tt) REVERT: R 625 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8360 (tt) REVERT: R 669 ASP cc_start: 0.9452 (OUTLIER) cc_final: 0.8835 (t0) REVERT: R 814 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7148 (mtm-85) outliers start: 33 outliers final: 24 residues processed: 102 average time/residue: 0.1789 time to fit residues: 25.0321 Evaluate side-chains 105 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 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 262 MET Chi-restraints excluded: chain B residue 285 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 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 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: 3.9990 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.2909 r_free = 0.2909 target = 0.078314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.065077 restraints weight = 20250.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.066499 restraints weight = 8294.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.067369 restraints weight = 4683.497| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1629 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= 0.158 Angle : 0.535 8.987 9379 Z= 0.277 Chirality : 0.040 0.181 1109 Planarity : 0.003 0.036 1188 Dihedral : 3.880 39.390 1000 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.32 % Allowed : 33.43 % 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: -0.33 (0.29), residues: 880 helix: 1.51 (0.28), residues: 365 sheet: 0.19 (0.46), residues: 137 loop : -2.23 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.002 0.001 HIS R 672 PHE 0.015 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 0.03756 ( 303) hydrogen bonds : angle 4.71247 ( 903) SS BOND : bond 0.00664 ( 1) SS BOND : angle 0.49589 ( 2) covalent geometry : bond 0.00353 ( 6874) covalent geometry : angle 0.53455 ( 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 103 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.772 Fit side-chains REVERT: B 13 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6533 (pm20) REVERT: B 285 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8709 (tp) REVERT: A 34 LYS cc_start: 0.9126 (tppp) cc_final: 0.8879 (tppt) REVERT: R 579 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7416 (tt) REVERT: R 625 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8423 (tt) REVERT: R 669 ASP cc_start: 0.9456 (OUTLIER) cc_final: 0.8841 (t0) REVERT: R 814 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7069 (mtm-85) outliers start: 30 outliers final: 24 residues processed: 95 average time/residue: 0.1722 time to fit residues: 22.7466 Evaluate side-chains 100 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 262 MET Chi-restraints excluded: chain B residue 285 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 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 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 16 optimal weight: 9.9990 chunk 45 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 57 optimal weight: 0.0870 chunk 64 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 overall best weight: 1.2560 ------------------------------------------------------------------------------- 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 = 0.2947 r_free = 0.2947 target = 0.079913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.066742 restraints weight = 19891.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.068173 restraints weight = 8139.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.069060 restraints weight = 4606.447| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6875 Z= 0.116 Angle : 0.516 9.155 9379 Z= 0.266 Chirality : 0.039 0.172 1109 Planarity : 0.003 0.035 1188 Dihedral : 3.745 38.916 1000 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.32 % Allowed : 33.72 % Favored : 61.96 % 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: -0.27 (0.29), residues: 880 helix: 1.64 (0.28), residues: 364 sheet: 0.03 (0.47), residues: 134 loop : -2.19 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 649 HIS 0.002 0.000 HIS A 362 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 0.03464 ( 303) hydrogen bonds : angle 4.54766 ( 903) SS BOND : bond 0.00468 ( 1) SS BOND : angle 0.40915 ( 2) covalent geometry : bond 0.00254 ( 6874) covalent geometry : angle 0.51611 ( 9377) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2331.76 seconds wall clock time: 41 minutes 33.48 seconds (2493.48 seconds total)