Starting phenix.real_space_refine on Sat May 10 11:33:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vwy_43605/05_2025/8vwy_43605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vwy_43605/05_2025/8vwy_43605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vwy_43605/05_2025/8vwy_43605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vwy_43605/05_2025/8vwy_43605.map" model { file = "/net/cci-nas-00/data/ceres_data/8vwy_43605/05_2025/8vwy_43605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vwy_43605/05_2025/8vwy_43605.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 7 9.91 5 S 52 5.16 5 C 4047 2.51 5 N 1016 2.21 5 O 1171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6293 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1058 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain breaks: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "E" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "H" Number of atoms: 1036 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 1031 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 127} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 132, 1031 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 127} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 1052 Chain: "I" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "B" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1058 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain breaks: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "C" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1058 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain breaks: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 5.60, per 1000 atoms: 0.89 Number of scatterers: 6293 At special positions: 0 Unit cell: (99.256, 104.48, 78.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 7 19.99 S 52 16.00 O 1171 8.00 N 1016 7.00 C 4047 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 29 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 29 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS B 172 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 29 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 86 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 172 " distance=2.03 Simple disulfide: pdb=" SG CYS C 152 " - pdb=" SG CYS C 163 " 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: 1.44 Conformation dependent library (CDL) restraints added in 974.2 milliseconds 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 17 sheets defined 10.5% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 68 through 79 Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 68 through 79 Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 68 through 79 Processing helix chain 'C' and resid 138 through 149 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 3.513A pdb=" N THR A 6 " --> pdb=" O THR A 30 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 34 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 62 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 60 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 13 through 17 removed outlier: 3.563A pdb=" N GLY A 14 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE A 126 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 48 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 29 through 34 removed outlier: 5.106A pdb=" N VAL E 30 " --> pdb=" O GLY E 14 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY E 14 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE E 52 " --> pdb=" O ILE E 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 20 through 21 removed outlier: 3.734A pdb=" N GLY E 116 " --> pdb=" O GLY E 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.599A pdb=" N LYS E 44 " --> pdb=" O ASP E 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.599A pdb=" N LYS E 44 " --> pdb=" O ASP E 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 34 removed outlier: 6.379A pdb=" N TYR H 12 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN H 33 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA H 10 " --> pdb=" O ASN H 33 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE H 52 " --> pdb=" O ILE H 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 38 through 39 removed outlier: 3.557A pdb=" N LYS H 44 " --> pdb=" O ASP H 39 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU H 73 " --> pdb=" O ARG H 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 38 through 39 removed outlier: 3.557A pdb=" N LYS H 44 " --> pdb=" O ASP H 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 29 through 34 removed outlier: 5.226A pdb=" N VAL I 30 " --> pdb=" O GLY I 14 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY I 14 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA I 10 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE I 52 " --> pdb=" O ILE I 134 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 19 through 20 Processing sheet with id=AB3, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.552A pdb=" N LYS I 44 " --> pdb=" O ASP I 39 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU I 73 " --> pdb=" O ARG I 80 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.552A pdb=" N LYS I 44 " --> pdb=" O ASP I 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 8 removed outlier: 3.539A pdb=" N THR B 6 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 34 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 62 " --> pdb=" O GLN B 103 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 60 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 13 through 17 removed outlier: 3.660A pdb=" N GLY B 14 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE B 126 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 43 " --> pdb=" O TYR B 97 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 5 through 8 removed outlier: 3.535A pdb=" N THR C 6 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU C 34 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR C 62 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 60 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 13 through 17 removed outlier: 3.645A pdb=" N GLY C 14 " --> pdb=" O PHE C 129 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE C 126 " --> pdb=" O SER C 48 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 731 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: 1.98 Time building geometry restraints manager: 1.70 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: 1966 1.34 - 1.46: 1609 1.46 - 1.58: 2795 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 6438 Sorted by residual: bond pdb=" C PHE E 132 " pdb=" N ILE E 133 " ideal model delta sigma weight residual 1.329 1.304 0.025 1.46e-02 4.69e+03 2.83e+00 bond pdb=" CB VAL H 99 " pdb=" CG1 VAL H 99 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.62e+00 bond pdb=" CB VAL E 99 " pdb=" CG1 VAL E 99 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CB VAL I 99 " pdb=" CG1 VAL I 99 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.39e+00 bond pdb=" C PHE I 132 " pdb=" N ILE I 133 " ideal model delta sigma weight residual 1.329 1.306 0.023 1.96e-02 2.60e+03 1.36e+00 ... (remaining 6433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 8262 1.14 - 2.27: 405 2.27 - 3.41: 58 3.41 - 4.55: 20 4.55 - 5.68: 2 Bond angle restraints: 8747 Sorted by residual: angle pdb=" C ASN E 76 " pdb=" CA ASN E 76 " pdb=" CB ASN E 76 " ideal model delta sigma weight residual 110.42 115.45 -5.03 1.99e+00 2.53e-01 6.39e+00 angle pdb=" CA TYR E 53 " pdb=" CB TYR E 53 " pdb=" CG TYR E 53 " ideal model delta sigma weight residual 113.90 117.88 -3.98 1.80e+00 3.09e-01 4.89e+00 angle pdb=" CA TYR I 53 " pdb=" CB TYR I 53 " pdb=" CG TYR I 53 " ideal model delta sigma weight residual 113.90 117.70 -3.80 1.80e+00 3.09e-01 4.47e+00 angle pdb=" CA TYR H 53 " pdb=" CB TYR H 53 " pdb=" CG TYR H 53 " ideal model delta sigma weight residual 113.90 117.52 -3.62 1.80e+00 3.09e-01 4.04e+00 angle pdb=" N ASN E 76 " pdb=" CA ASN E 76 " pdb=" C ASN E 76 " ideal model delta sigma weight residual 110.80 106.58 4.22 2.13e+00 2.20e-01 3.92e+00 ... (remaining 8742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 3435 16.43 - 32.85: 245 32.85 - 49.27: 64 49.27 - 65.70: 8 65.70 - 82.12: 3 Dihedral angle restraints: 3755 sinusoidal: 1345 harmonic: 2410 Sorted by residual: dihedral pdb=" CA ASP H 29 " pdb=" C ASP H 29 " pdb=" N VAL H 30 " pdb=" CA VAL H 30 " ideal model delta harmonic sigma weight residual -180.00 -164.07 -15.93 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA LYS C 99 " pdb=" C LYS C 99 " pdb=" N ASN C 100 " pdb=" CA ASN C 100 " ideal model delta harmonic sigma weight residual -180.00 -164.42 -15.58 0 5.00e+00 4.00e-02 9.71e+00 dihedral pdb=" CA ASP I 29 " pdb=" C ASP I 29 " pdb=" N VAL I 30 " pdb=" CA VAL I 30 " ideal model delta harmonic sigma weight residual -180.00 -164.60 -15.40 0 5.00e+00 4.00e-02 9.49e+00 ... (remaining 3752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 516 0.027 - 0.053: 280 0.053 - 0.080: 95 0.080 - 0.106: 44 0.106 - 0.132: 29 Chirality restraints: 964 Sorted by residual: chirality pdb=" CA ILE I 49 " pdb=" N ILE I 49 " pdb=" C ILE I 49 " pdb=" CB ILE I 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE H 49 " pdb=" N ILE H 49 " pdb=" C ILE H 49 " pdb=" CB ILE H 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA PRO H 40 " pdb=" N PRO H 40 " pdb=" C PRO H 40 " pdb=" CB PRO H 40 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 961 not shown) Planarity restraints: 1116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR I 32 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C THR I 32 " -0.020 2.00e-02 2.50e+03 pdb=" O THR I 32 " 0.008 2.00e-02 2.50e+03 pdb=" N ASN I 33 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 53 " -0.012 2.00e-02 2.50e+03 8.15e-03 1.33e+00 pdb=" CG TYR H 53 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR H 53 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR H 53 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR H 53 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR H 53 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR H 53 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 53 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 53 " 0.012 2.00e-02 2.50e+03 7.97e-03 1.27e+00 pdb=" CG TYR E 53 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR E 53 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR E 53 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 53 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 53 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E 53 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 53 " 0.002 2.00e-02 2.50e+03 ... (remaining 1113 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 185 2.69 - 3.24: 5793 3.24 - 3.79: 10529 3.79 - 4.35: 14023 4.35 - 4.90: 23755 Nonbonded interactions: 54285 Sorted by model distance: nonbonded pdb=" OH TYR A 62 " pdb=" OE1 GLN A 103 " model vdw 2.133 3.040 nonbonded pdb=" OH TYR C 62 " pdb=" OE1 GLN C 103 " model vdw 2.135 3.040 nonbonded pdb=" OH TYR B 62 " pdb=" OE1 GLN B 103 " model vdw 2.136 3.040 nonbonded pdb=" OD1 ASP H 39 " pdb=" OG1 THR H 41 " model vdw 2.212 3.040 nonbonded pdb=" OD1 ASP I 39 " pdb=" OG1 THR I 41 " model vdw 2.215 3.040 ... (remaining 54280 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 4 through 173) selection = (chain 'C' and resid 4 through 173) } ncs_group { reference = (chain 'E' and (resid 6 through 68 or resid 70 through 122 or (resid 123 and (na \ me N or name CA or name C or name O or name CB )) or resid 124 through 137 or re \ sid 201)) selection = (chain 'H' and (resid 6 through 68 or resid 70 through 137 or resid 201)) selection = (chain 'I' and (resid 6 through 68 or resid 70 through 122 or (resid 123 and (na \ me N or name CA or name C or name O or name CB )) or resid 124 through 137 or re \ sid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.39 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.180 Find NCS groups from input model: 0.320 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:14.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 6453 Z= 0.291 Angle : 0.580 5.682 8777 Z= 0.323 Chirality : 0.042 0.132 964 Planarity : 0.003 0.021 1116 Dihedral : 12.577 82.124 2166 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 6.10 % Allowed : 10.33 % Favored : 83.57 % 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: -1.38 (0.28), residues: 802 helix: -0.16 (0.52), residues: 93 sheet: -0.60 (0.29), residues: 304 loop : -1.29 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 31 HIS 0.003 0.001 HIS I 102 PHE 0.007 0.002 PHE I 55 TYR 0.019 0.002 TYR H 53 ARG 0.002 0.000 ARG E 17 Details of bonding type rmsd hydrogen bonds : bond 0.24366 ( 250) hydrogen bonds : angle 9.76773 ( 731) SS BOND : bond 0.00123 ( 15) SS BOND : angle 0.44138 ( 30) covalent geometry : bond 0.00640 ( 6438) covalent geometry : angle 0.58000 ( 8747) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.7404 (m-30) cc_final: 0.6970 (t70) REVERT: E 39 ASP cc_start: 0.8067 (t0) cc_final: 0.7698 (m-30) REVERT: E 41 THR cc_start: 0.7057 (p) cc_final: 0.6671 (m) REVERT: H 20 GLU cc_start: 0.8512 (tt0) cc_final: 0.7712 (pm20) REVERT: H 39 ASP cc_start: 0.8037 (t0) cc_final: 0.7682 (m-30) REVERT: H 41 THR cc_start: 0.7094 (p) cc_final: 0.6715 (m) REVERT: I 20 GLU cc_start: 0.8458 (tt0) cc_final: 0.7662 (pm20) REVERT: I 39 ASP cc_start: 0.8012 (t0) cc_final: 0.7667 (m-30) REVERT: I 41 THR cc_start: 0.7280 (p) cc_final: 0.6867 (m) REVERT: B 12 ILE cc_start: 0.8023 (mt) cc_final: 0.7748 (mp) REVERT: B 65 ASP cc_start: 0.7189 (m-30) cc_final: 0.6840 (t70) REVERT: B 138 SER cc_start: 0.6019 (p) cc_final: 0.5658 (t) REVERT: C 65 ASP cc_start: 0.7272 (m-30) cc_final: 0.6952 (t70) outliers start: 39 outliers final: 18 residues processed: 176 average time/residue: 0.7241 time to fit residues: 137.3420 Evaluate side-chains 143 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 73 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.198370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.127209 restraints weight = 14161.322| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.28 r_work: 0.3457 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6453 Z= 0.149 Angle : 0.582 6.810 8777 Z= 0.308 Chirality : 0.043 0.150 964 Planarity : 0.003 0.044 1116 Dihedral : 7.023 56.498 905 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.07 % Allowed : 16.90 % Favored : 79.03 % 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: -1.25 (0.29), residues: 802 helix: 0.52 (0.54), residues: 93 sheet: -0.69 (0.28), residues: 334 loop : -1.22 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 31 HIS 0.004 0.001 HIS H 37 PHE 0.015 0.001 PHE C 101 TYR 0.016 0.001 TYR B 13 ARG 0.005 0.001 ARG B 106 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 250) hydrogen bonds : angle 6.50861 ( 731) SS BOND : bond 0.00276 ( 15) SS BOND : angle 1.15523 ( 30) covalent geometry : bond 0.00326 ( 6438) covalent geometry : angle 0.57943 ( 8747) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7184 (tppt) REVERT: A 83 MET cc_start: 0.6491 (tpp) cc_final: 0.6288 (tmm) REVERT: A 96 GLN cc_start: 0.8265 (tt0) cc_final: 0.8002 (tm-30) REVERT: A 99 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7986 (tttp) REVERT: E 39 ASP cc_start: 0.7921 (t0) cc_final: 0.7473 (m-30) REVERT: E 41 THR cc_start: 0.6965 (p) cc_final: 0.6615 (m) REVERT: H 39 ASP cc_start: 0.7916 (t0) cc_final: 0.7482 (m-30) REVERT: H 41 THR cc_start: 0.7103 (p) cc_final: 0.6644 (m) REVERT: I 39 ASP cc_start: 0.7966 (t0) cc_final: 0.7509 (m-30) REVERT: I 41 THR cc_start: 0.7108 (p) cc_final: 0.6755 (m) REVERT: B 12 ILE cc_start: 0.7954 (mt) cc_final: 0.7702 (mp) REVERT: B 65 ASP cc_start: 0.7326 (m-30) cc_final: 0.6564 (t70) REVERT: B 97 TYR cc_start: 0.8469 (m-80) cc_final: 0.8187 (m-80) REVERT: B 138 SER cc_start: 0.4551 (p) cc_final: 0.4321 (t) REVERT: C 65 ASP cc_start: 0.7117 (m-30) cc_final: 0.6420 (t70) outliers start: 26 outliers final: 13 residues processed: 167 average time/residue: 0.7037 time to fit residues: 126.8622 Evaluate side-chains 155 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 77 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 47 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN C 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.197682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125745 restraints weight = 13604.372| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 3.33 r_work: 0.3454 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6453 Z= 0.156 Angle : 0.541 5.587 8777 Z= 0.288 Chirality : 0.043 0.173 964 Planarity : 0.003 0.032 1116 Dihedral : 6.220 57.274 893 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.60 % Allowed : 21.75 % Favored : 74.65 % 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: -1.20 (0.29), residues: 802 helix: 1.08 (0.54), residues: 90 sheet: -0.64 (0.27), residues: 334 loop : -1.33 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 31 HIS 0.004 0.001 HIS I 119 PHE 0.012 0.001 PHE C 101 TYR 0.018 0.001 TYR C 13 ARG 0.003 0.000 ARG E 80 Details of bonding type rmsd hydrogen bonds : bond 0.03127 ( 250) hydrogen bonds : angle 6.00812 ( 731) SS BOND : bond 0.00209 ( 15) SS BOND : angle 0.88761 ( 30) covalent geometry : bond 0.00343 ( 6438) covalent geometry : angle 0.53937 ( 8747) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 39 ASP cc_start: 0.7939 (t0) cc_final: 0.7579 (m-30) REVERT: E 41 THR cc_start: 0.6971 (p) cc_final: 0.6631 (m) REVERT: H 39 ASP cc_start: 0.7880 (t0) cc_final: 0.7466 (m-30) REVERT: H 41 THR cc_start: 0.7072 (p) cc_final: 0.6618 (m) REVERT: I 39 ASP cc_start: 0.7977 (t0) cc_final: 0.7532 (m-30) REVERT: I 41 THR cc_start: 0.7050 (p) cc_final: 0.6696 (m) REVERT: B 12 ILE cc_start: 0.7966 (mt) cc_final: 0.7710 (mp) REVERT: B 34 GLU cc_start: 0.7461 (tt0) cc_final: 0.7191 (tt0) REVERT: B 65 ASP cc_start: 0.7344 (m-30) cc_final: 0.6671 (t70) REVERT: B 97 TYR cc_start: 0.8458 (m-80) cc_final: 0.8225 (m-80) REVERT: B 99 LYS cc_start: 0.8288 (ttmt) cc_final: 0.8033 (ttmt) REVERT: B 138 SER cc_start: 0.4792 (p) cc_final: 0.4568 (t) REVERT: C 34 GLU cc_start: 0.7563 (tt0) cc_final: 0.7348 (tt0) REVERT: C 65 ASP cc_start: 0.7081 (m-30) cc_final: 0.6493 (t70) REVERT: C 138 SER cc_start: 0.5147 (p) cc_final: 0.4840 (t) outliers start: 23 outliers final: 12 residues processed: 164 average time/residue: 0.7179 time to fit residues: 127.2832 Evaluate side-chains 153 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 38 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 96 GLN A 133 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.198802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.126674 restraints weight = 14761.364| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.48 r_work: 0.3467 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6453 Z= 0.133 Angle : 0.516 7.250 8777 Z= 0.272 Chirality : 0.042 0.171 964 Planarity : 0.003 0.025 1116 Dihedral : 5.644 58.476 890 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.54 % Allowed : 22.22 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.28), residues: 802 helix: 1.39 (0.53), residues: 90 sheet: -0.54 (0.28), residues: 331 loop : -1.31 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 31 HIS 0.004 0.001 HIS I 119 PHE 0.012 0.001 PHE C 101 TYR 0.020 0.001 TYR C 13 ARG 0.003 0.000 ARG E 80 Details of bonding type rmsd hydrogen bonds : bond 0.02700 ( 250) hydrogen bonds : angle 5.71334 ( 731) SS BOND : bond 0.00182 ( 15) SS BOND : angle 0.63832 ( 30) covalent geometry : bond 0.00295 ( 6438) covalent geometry : angle 0.51527 ( 8747) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6415 (tpt) cc_final: 0.5797 (tpp) REVERT: E 39 ASP cc_start: 0.7960 (t0) cc_final: 0.7613 (m-30) REVERT: E 41 THR cc_start: 0.6965 (p) cc_final: 0.6659 (m) REVERT: H 39 ASP cc_start: 0.7893 (t0) cc_final: 0.7478 (m-30) REVERT: H 41 THR cc_start: 0.7022 (p) cc_final: 0.6566 (m) REVERT: H 86 GLN cc_start: 0.8549 (tt0) cc_final: 0.8292 (tt0) REVERT: I 39 ASP cc_start: 0.7968 (t0) cc_final: 0.7543 (m-30) REVERT: I 41 THR cc_start: 0.7043 (p) cc_final: 0.6721 (m) REVERT: B 12 ILE cc_start: 0.7966 (mt) cc_final: 0.7687 (mp) REVERT: B 34 GLU cc_start: 0.7493 (tt0) cc_final: 0.7229 (tt0) REVERT: B 65 ASP cc_start: 0.7339 (m-30) cc_final: 0.6636 (t70) REVERT: B 97 TYR cc_start: 0.8456 (m-80) cc_final: 0.8195 (m-80) REVERT: C 7 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6903 (tt) REVERT: C 65 ASP cc_start: 0.7168 (m-30) cc_final: 0.6504 (t70) REVERT: C 138 SER cc_start: 0.5065 (p) cc_final: 0.4801 (t) outliers start: 29 outliers final: 16 residues processed: 169 average time/residue: 0.6785 time to fit residues: 124.0546 Evaluate side-chains 155 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 4 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 96 GLN A 133 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.193085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.120691 restraints weight = 13602.481| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.23 r_work: 0.3382 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 6453 Z= 0.300 Angle : 0.615 5.544 8777 Z= 0.326 Chirality : 0.045 0.162 964 Planarity : 0.003 0.024 1116 Dihedral : 5.975 58.932 888 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 5.63 % Allowed : 21.91 % Favored : 72.46 % 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: -1.20 (0.29), residues: 802 helix: 1.32 (0.55), residues: 93 sheet: -0.73 (0.27), residues: 340 loop : -1.34 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 31 HIS 0.006 0.002 HIS I 119 PHE 0.010 0.002 PHE C 101 TYR 0.022 0.002 TYR C 13 ARG 0.002 0.000 ARG I 80 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 250) hydrogen bonds : angle 6.05831 ( 731) SS BOND : bond 0.00127 ( 15) SS BOND : angle 0.47034 ( 30) covalent geometry : bond 0.00675 ( 6438) covalent geometry : angle 0.61589 ( 8747) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6479 (tpt) cc_final: 0.5895 (tpp) REVERT: E 39 ASP cc_start: 0.7975 (t0) cc_final: 0.7564 (m-30) REVERT: E 41 THR cc_start: 0.7011 (p) cc_final: 0.6682 (m) REVERT: H 20 GLU cc_start: 0.8449 (tt0) cc_final: 0.7794 (pm20) REVERT: H 39 ASP cc_start: 0.7897 (t0) cc_final: 0.7454 (m-30) REVERT: H 41 THR cc_start: 0.7112 (p) cc_final: 0.6660 (m) REVERT: I 20 GLU cc_start: 0.8360 (tt0) cc_final: 0.7650 (pm20) REVERT: I 39 ASP cc_start: 0.7947 (t0) cc_final: 0.7545 (m-30) REVERT: I 41 THR cc_start: 0.7116 (p) cc_final: 0.6741 (m) REVERT: I 44 LYS cc_start: 0.8332 (mttt) cc_final: 0.8058 (mtmt) REVERT: I 62 ARG cc_start: 0.8383 (mtp85) cc_final: 0.8125 (mtp85) REVERT: B 12 ILE cc_start: 0.8022 (mt) cc_final: 0.7642 (mp) REVERT: B 65 ASP cc_start: 0.7293 (m-30) cc_final: 0.6610 (t70) REVERT: B 99 LYS cc_start: 0.8354 (ttmt) cc_final: 0.8073 (ttpt) REVERT: C 7 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6985 (tt) REVERT: C 65 ASP cc_start: 0.7228 (m-30) cc_final: 0.6949 (t70) REVERT: C 99 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7567 (tttp) outliers start: 36 outliers final: 21 residues processed: 148 average time/residue: 0.6356 time to fit residues: 102.2539 Evaluate side-chains 143 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 24 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 96 GLN A 133 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN C 63 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.198337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134984 restraints weight = 7869.035| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 3.07 r_work: 0.3504 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6453 Z= 0.136 Angle : 0.532 8.266 8777 Z= 0.280 Chirality : 0.043 0.170 964 Planarity : 0.003 0.024 1116 Dihedral : 5.509 52.565 888 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.60 % Allowed : 24.57 % Favored : 71.83 % 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: -1.04 (0.29), residues: 802 helix: 1.78 (0.53), residues: 90 sheet: -0.60 (0.28), residues: 331 loop : -1.34 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 31 HIS 0.004 0.001 HIS I 119 PHE 0.012 0.001 PHE C 101 TYR 0.023 0.001 TYR C 13 ARG 0.002 0.000 ARG E 80 Details of bonding type rmsd hydrogen bonds : bond 0.02549 ( 250) hydrogen bonds : angle 5.63781 ( 731) SS BOND : bond 0.00141 ( 15) SS BOND : angle 0.39798 ( 30) covalent geometry : bond 0.00301 ( 6438) covalent geometry : angle 0.53216 ( 8747) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6407 (tpt) cc_final: 0.5818 (tpp) REVERT: A 96 GLN cc_start: 0.8286 (tt0) cc_final: 0.7753 (tm-30) REVERT: A 99 LYS cc_start: 0.8150 (tttp) cc_final: 0.7726 (tttp) REVERT: E 39 ASP cc_start: 0.8061 (t0) cc_final: 0.7665 (m-30) REVERT: E 41 THR cc_start: 0.6983 (p) cc_final: 0.6676 (m) REVERT: H 39 ASP cc_start: 0.7976 (t0) cc_final: 0.7537 (m-30) REVERT: H 41 THR cc_start: 0.7072 (p) cc_final: 0.6638 (m) REVERT: H 128 THR cc_start: 0.7790 (p) cc_final: 0.7474 (p) REVERT: I 39 ASP cc_start: 0.8062 (t0) cc_final: 0.7658 (m-30) REVERT: I 41 THR cc_start: 0.7064 (p) cc_final: 0.6740 (m) REVERT: B 12 ILE cc_start: 0.7999 (mt) cc_final: 0.7726 (mp) REVERT: B 34 GLU cc_start: 0.7500 (tt0) cc_final: 0.7263 (tt0) REVERT: B 65 ASP cc_start: 0.7425 (m-30) cc_final: 0.6784 (t70) REVERT: B 99 LYS cc_start: 0.8261 (ttmt) cc_final: 0.8040 (tttp) REVERT: C 99 LYS cc_start: 0.8154 (ttmt) cc_final: 0.7319 (tttp) outliers start: 23 outliers final: 18 residues processed: 152 average time/residue: 0.7289 time to fit residues: 119.9770 Evaluate side-chains 146 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 12 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 133 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN B 100 ASN ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.196089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.124783 restraints weight = 9665.265| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.85 r_work: 0.3456 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6453 Z= 0.212 Angle : 0.565 7.514 8777 Z= 0.298 Chirality : 0.044 0.161 964 Planarity : 0.004 0.071 1116 Dihedral : 5.765 55.440 888 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.69 % Allowed : 25.20 % Favored : 70.11 % 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: -1.13 (0.29), residues: 802 helix: 1.86 (0.54), residues: 90 sheet: -0.65 (0.28), residues: 331 loop : -1.45 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 31 HIS 0.005 0.001 HIS I 119 PHE 0.017 0.001 PHE A 26 TYR 0.026 0.002 TYR C 13 ARG 0.001 0.000 ARG I 80 Details of bonding type rmsd hydrogen bonds : bond 0.02723 ( 250) hydrogen bonds : angle 5.71135 ( 731) SS BOND : bond 0.00143 ( 15) SS BOND : angle 0.43977 ( 30) covalent geometry : bond 0.00475 ( 6438) covalent geometry : angle 0.56553 ( 8747) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7467 (ttpt) cc_final: 0.6940 (tppt) REVERT: A 83 MET cc_start: 0.6472 (tpt) cc_final: 0.5873 (tpp) REVERT: A 96 GLN cc_start: 0.8307 (tt0) cc_final: 0.7772 (tm-30) REVERT: A 99 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7750 (tttm) REVERT: E 39 ASP cc_start: 0.8092 (t0) cc_final: 0.7662 (m-30) REVERT: E 41 THR cc_start: 0.7028 (p) cc_final: 0.6723 (m) REVERT: H 39 ASP cc_start: 0.8007 (t0) cc_final: 0.7585 (m-30) REVERT: H 41 THR cc_start: 0.7134 (p) cc_final: 0.6699 (m) REVERT: H 128 THR cc_start: 0.7900 (p) cc_final: 0.7679 (p) REVERT: I 20 GLU cc_start: 0.8483 (tt0) cc_final: 0.7649 (pm20) REVERT: I 39 ASP cc_start: 0.8077 (t0) cc_final: 0.7626 (m-30) REVERT: I 41 THR cc_start: 0.7092 (p) cc_final: 0.6749 (m) REVERT: I 44 LYS cc_start: 0.8352 (mttt) cc_final: 0.8080 (mtmt) REVERT: B 12 ILE cc_start: 0.8037 (mt) cc_final: 0.7664 (mp) REVERT: B 65 ASP cc_start: 0.7368 (m-30) cc_final: 0.6718 (t70) outliers start: 30 outliers final: 23 residues processed: 146 average time/residue: 0.6637 time to fit residues: 105.7636 Evaluate side-chains 144 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.2980 chunk 2 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 133 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN I 122 ASN B 63 GLN B 100 ASN C 100 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.198382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127365 restraints weight = 11646.272| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 3.05 r_work: 0.3480 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6453 Z= 0.144 Angle : 0.544 8.522 8777 Z= 0.283 Chirality : 0.043 0.164 964 Planarity : 0.003 0.051 1116 Dihedral : 5.572 51.185 888 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.54 % Allowed : 25.51 % Favored : 69.95 % 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: -1.01 (0.29), residues: 802 helix: 1.99 (0.54), residues: 90 sheet: -0.59 (0.28), residues: 331 loop : -1.36 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 31 HIS 0.004 0.001 HIS I 119 PHE 0.010 0.001 PHE C 140 TYR 0.025 0.002 TYR C 13 ARG 0.002 0.000 ARG H 62 Details of bonding type rmsd hydrogen bonds : bond 0.02505 ( 250) hydrogen bonds : angle 5.56239 ( 731) SS BOND : bond 0.00149 ( 15) SS BOND : angle 0.38885 ( 30) covalent geometry : bond 0.00320 ( 6438) covalent geometry : angle 0.54452 ( 8747) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7383 (ttpt) cc_final: 0.6434 (tptt) REVERT: A 83 MET cc_start: 0.6458 (tpt) cc_final: 0.5909 (tpp) REVERT: A 96 GLN cc_start: 0.8203 (tt0) cc_final: 0.7665 (tm-30) REVERT: A 99 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7561 (tttm) REVERT: E 39 ASP cc_start: 0.7951 (t0) cc_final: 0.7588 (m-30) REVERT: E 41 THR cc_start: 0.6964 (p) cc_final: 0.6685 (m) REVERT: H 39 ASP cc_start: 0.7908 (t0) cc_final: 0.7467 (m-30) REVERT: H 41 THR cc_start: 0.7088 (p) cc_final: 0.6659 (m) REVERT: H 128 THR cc_start: 0.7741 (p) cc_final: 0.7526 (p) REVERT: I 39 ASP cc_start: 0.7948 (t0) cc_final: 0.7525 (m-30) REVERT: I 41 THR cc_start: 0.7019 (p) cc_final: 0.6691 (m) REVERT: B 96 GLN cc_start: 0.8151 (tt0) cc_final: 0.7878 (tm-30) REVERT: B 99 LYS cc_start: 0.8200 (ttmt) cc_final: 0.7671 (tttp) REVERT: C 166 MET cc_start: 0.4226 (mpm) cc_final: 0.4022 (mpm) outliers start: 29 outliers final: 20 residues processed: 150 average time/residue: 0.6716 time to fit residues: 109.5176 Evaluate side-chains 142 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 0.0370 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 80 optimal weight: 30.0000 chunk 56 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN B 100 ASN ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.197733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.125794 restraints weight = 11582.986| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.05 r_work: 0.3459 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6453 Z= 0.180 Angle : 0.580 9.665 8777 Z= 0.300 Chirality : 0.043 0.162 964 Planarity : 0.003 0.049 1116 Dihedral : 5.836 52.323 888 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.23 % Allowed : 25.98 % Favored : 69.80 % 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: -1.07 (0.29), residues: 802 helix: 2.02 (0.54), residues: 90 sheet: -0.65 (0.27), residues: 337 loop : -1.40 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 31 HIS 0.004 0.001 HIS I 119 PHE 0.012 0.001 PHE B 140 TYR 0.026 0.002 TYR C 13 ARG 0.002 0.000 ARG H 62 Details of bonding type rmsd hydrogen bonds : bond 0.02628 ( 250) hydrogen bonds : angle 5.61000 ( 731) SS BOND : bond 0.00128 ( 15) SS BOND : angle 0.50705 ( 30) covalent geometry : bond 0.00403 ( 6438) covalent geometry : angle 0.57992 ( 8747) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7347 (ttpt) cc_final: 0.6381 (tptt) REVERT: A 83 MET cc_start: 0.6467 (tpt) cc_final: 0.5903 (tpp) REVERT: A 96 GLN cc_start: 0.8278 (tt0) cc_final: 0.7783 (tm-30) REVERT: A 99 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7562 (tttp) REVERT: E 39 ASP cc_start: 0.7949 (t0) cc_final: 0.7571 (m-30) REVERT: E 41 THR cc_start: 0.6966 (p) cc_final: 0.6682 (m) REVERT: H 39 ASP cc_start: 0.7884 (t0) cc_final: 0.7467 (m-30) REVERT: H 41 THR cc_start: 0.7077 (p) cc_final: 0.6653 (m) REVERT: I 20 GLU cc_start: 0.8243 (tt0) cc_final: 0.7559 (pm20) REVERT: I 39 ASP cc_start: 0.7924 (t0) cc_final: 0.7511 (m-30) REVERT: I 41 THR cc_start: 0.7021 (p) cc_final: 0.6684 (m) REVERT: I 44 LYS cc_start: 0.8290 (mttt) cc_final: 0.8029 (mtmt) REVERT: B 12 ILE cc_start: 0.7795 (mt) cc_final: 0.7342 (mp) REVERT: C 9 LYS cc_start: 0.7901 (tppt) cc_final: 0.7675 (tppt) REVERT: C 136 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.8358 (p) outliers start: 27 outliers final: 20 residues processed: 141 average time/residue: 0.6766 time to fit residues: 103.5618 Evaluate side-chains 141 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 42 optimal weight: 0.3980 chunk 61 optimal weight: 0.0470 chunk 66 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN I 122 ASN I 124 ASN B 96 GLN B 100 ASN C 100 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.200876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.129328 restraints weight = 13520.676| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.26 r_work: 0.3485 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6453 Z= 0.117 Angle : 0.548 11.152 8777 Z= 0.282 Chirality : 0.043 0.168 964 Planarity : 0.003 0.037 1116 Dihedral : 5.466 44.394 888 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.44 % Allowed : 26.60 % Favored : 69.95 % 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: -0.87 (0.28), residues: 802 helix: 2.12 (0.53), residues: 90 sheet: -0.50 (0.28), residues: 331 loop : -1.27 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 31 HIS 0.003 0.001 HIS I 119 PHE 0.011 0.001 PHE B 140 TYR 0.024 0.001 TYR C 13 ARG 0.001 0.000 ARG H 62 Details of bonding type rmsd hydrogen bonds : bond 0.02467 ( 250) hydrogen bonds : angle 5.42966 ( 731) SS BOND : bond 0.00206 ( 15) SS BOND : angle 0.42326 ( 30) covalent geometry : bond 0.00261 ( 6438) covalent geometry : angle 0.54844 ( 8747) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7254 (ttpt) cc_final: 0.6299 (tptt) REVERT: A 83 MET cc_start: 0.6481 (tpt) cc_final: 0.5889 (tpp) REVERT: A 96 GLN cc_start: 0.8268 (tt0) cc_final: 0.7747 (tm-30) REVERT: E 39 ASP cc_start: 0.7968 (t0) cc_final: 0.7606 (m-30) REVERT: E 41 THR cc_start: 0.6954 (p) cc_final: 0.6694 (m) REVERT: H 39 ASP cc_start: 0.7930 (t0) cc_final: 0.7498 (m-30) REVERT: H 41 THR cc_start: 0.7057 (p) cc_final: 0.6634 (m) REVERT: I 9 ILE cc_start: 0.8377 (mt) cc_final: 0.8134 (mt) REVERT: I 39 ASP cc_start: 0.7988 (t0) cc_final: 0.7539 (m-30) REVERT: I 41 THR cc_start: 0.7002 (p) cc_final: 0.6689 (m) REVERT: B 12 ILE cc_start: 0.7679 (mt) cc_final: 0.7233 (mp) REVERT: C 99 LYS cc_start: 0.7898 (ttmt) cc_final: 0.7526 (tttp) outliers start: 22 outliers final: 14 residues processed: 142 average time/residue: 0.6816 time to fit residues: 104.7522 Evaluate side-chains 137 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 130 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 78 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 80 optimal weight: 30.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN I 122 ASN B 100 ASN C 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.198286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125339 restraints weight = 14472.047| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 3.35 r_work: 0.3447 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6453 Z= 0.174 Angle : 0.570 7.832 8777 Z= 0.297 Chirality : 0.043 0.166 964 Planarity : 0.003 0.040 1116 Dihedral : 5.295 49.235 885 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.13 % Allowed : 27.39 % Favored : 69.48 % 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: -0.94 (0.28), residues: 802 helix: 1.97 (0.55), residues: 93 sheet: -0.58 (0.27), residues: 337 loop : -1.27 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 31 HIS 0.005 0.001 HIS I 119 PHE 0.016 0.001 PHE C 22 TYR 0.026 0.002 TYR B 13 ARG 0.001 0.000 ARG H 62 Details of bonding type rmsd hydrogen bonds : bond 0.02584 ( 250) hydrogen bonds : angle 5.54450 ( 731) SS BOND : bond 0.00189 ( 15) SS BOND : angle 0.37943 ( 30) covalent geometry : bond 0.00392 ( 6438) covalent geometry : angle 0.57063 ( 8747) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5672.65 seconds wall clock time: 98 minutes 10.88 seconds (5890.88 seconds total)