Starting phenix.real_space_refine on Tue May 13 12:08:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fps_29369/05_2025/8fps_29369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fps_29369/05_2025/8fps_29369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fps_29369/05_2025/8fps_29369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fps_29369/05_2025/8fps_29369.map" model { file = "/net/cci-nas-00/data/ceres_data/8fps_29369/05_2025/8fps_29369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fps_29369/05_2025/8fps_29369.cif" } resolution = 2.38 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= 0.005 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 S 74 5.16 5 Cl 4 4.86 5 C 6884 2.51 5 N 1662 2.21 5 O 1978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10602 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1159 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1147 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 146, 1147 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1165 Chain: "B" Number of atoms: 1190 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 151, 1184 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 151, 1184 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1209 Chain: "C" Number of atoms: 1159 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 146, 1147 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 146, 1147 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1165 Chain: "D" Number of atoms: 1190 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 151, 1184 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 151, 1184 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 1209 Chain: "E" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1435 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1435 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1439 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1439 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "G" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ACYS A 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 589 " occ=0.50 residue: pdb=" N ASER A 615 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 615 " occ=0.50 residue: pdb=" N ACYS B 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 589 " occ=0.50 residue: pdb=" N ACYS C 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 589 " occ=0.50 residue: pdb=" N ASER C 615 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 615 " occ=0.50 residue: pdb=" N ACYS D 589 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 589 " occ=0.50 Time building chain proxies: 9.85, per 1000 atoms: 0.93 Number of scatterers: 10602 At special positions: 0 Unit cell: (112.203, 110.565, 86.814, 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) Cl 4 17.00 S 74 16.00 O 1978 8.00 N 1662 7.00 C 6884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 2.0 seconds 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 74.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 625 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 826 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 624 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 826 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 625 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 826 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 624 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 826 Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 70 through 74 removed outlier: 4.170A pdb=" N PHE E 73 " --> pdb=" O GLU E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 105 removed outlier: 3.611A pdb=" N TYR E 96 " --> pdb=" O ASP E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 128 Processing helix chain 'E' and resid 132 through 160 removed outlier: 3.699A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 211 Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 70 through 74 removed outlier: 4.159A pdb=" N PHE G 73 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 105 removed outlier: 3.570A pdb=" N TYR G 96 " --> pdb=" O ASP G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 128 removed outlier: 3.842A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 160 removed outlier: 3.713A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 212 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 Processing helix chain 'F' and resid 105 through 129 removed outlier: 3.524A pdb=" N ILE F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.633A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 212 Processing helix chain 'H' and resid 6 through 30 Processing helix chain 'H' and resid 92 through 105 Processing helix chain 'H' and resid 105 through 129 removed outlier: 3.508A pdb=" N ILE H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.651A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 212 Processing sheet with id=AA1, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AA2, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AA3, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AA4, first strand: chain 'H' and resid 77 through 79 855 hydrogen bonds defined for protein. 2468 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: 3.37 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3146 1.34 - 1.46: 2871 1.46 - 1.58: 4583 1.58 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 10712 Sorted by residual: bond pdb=" N GLY B 588 " pdb=" CA GLY B 588 " ideal model delta sigma weight residual 1.447 1.454 -0.008 1.09e-02 8.42e+03 5.19e-01 bond pdb=" C VAL C 792 " pdb=" O VAL C 792 " ideal model delta sigma weight residual 1.231 1.241 -0.010 1.51e-02 4.39e+03 3.97e-01 bond pdb=" N GLY D 588 " pdb=" CA GLY D 588 " ideal model delta sigma weight residual 1.447 1.453 -0.007 1.09e-02 8.42e+03 3.96e-01 bond pdb=" C PHE D 607 " pdb=" O PHE D 607 " ideal model delta sigma weight residual 1.236 1.244 -0.007 1.15e-02 7.56e+03 3.80e-01 bond pdb=" C VAL A 792 " pdb=" O VAL A 792 " ideal model delta sigma weight residual 1.235 1.244 -0.008 1.45e-02 4.76e+03 3.42e-01 ... (remaining 10707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 14102 0.94 - 1.88: 334 1.88 - 2.82: 45 2.82 - 3.76: 15 3.76 - 4.70: 10 Bond angle restraints: 14506 Sorted by residual: angle pdb=" CA TYR C 523 " pdb=" CB TYR C 523 " pdb=" CG TYR C 523 " ideal model delta sigma weight residual 113.90 117.55 -3.65 1.80e+00 3.09e-01 4.12e+00 angle pdb=" CA TYR A 523 " pdb=" CB TYR A 523 " pdb=" CG TYR A 523 " ideal model delta sigma weight residual 113.90 117.19 -3.29 1.80e+00 3.09e-01 3.35e+00 angle pdb=" CA GLU A 550 " pdb=" CB GLU A 550 " pdb=" CG GLU A 550 " ideal model delta sigma weight residual 114.10 117.72 -3.62 2.00e+00 2.50e-01 3.27e+00 angle pdb=" CA GLU C 550 " pdb=" CB GLU C 550 " pdb=" CG GLU C 550 " ideal model delta sigma weight residual 114.10 117.42 -3.32 2.00e+00 2.50e-01 2.76e+00 angle pdb=" N PHE F 107 " pdb=" CA PHE F 107 " pdb=" C PHE F 107 " ideal model delta sigma weight residual 109.81 113.32 -3.51 2.21e+00 2.05e-01 2.52e+00 ... (remaining 14501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5356 17.93 - 35.86: 551 35.86 - 53.79: 144 53.79 - 71.72: 36 71.72 - 89.65: 9 Dihedral angle restraints: 6096 sinusoidal: 2246 harmonic: 3850 Sorted by residual: dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual -86.00 -131.23 45.23 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual -86.00 -131.16 45.16 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" CB GLU E 90 " pdb=" CG GLU E 90 " pdb=" CD GLU E 90 " pdb=" OE1 GLU E 90 " ideal model delta sinusoidal sigma weight residual 0.00 89.65 -89.65 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 969 0.021 - 0.043: 327 0.043 - 0.064: 223 0.064 - 0.085: 90 0.085 - 0.107: 29 Chirality restraints: 1638 Sorted by residual: chirality pdb=" CA PHE H 107 " pdb=" N PHE H 107 " pdb=" C PHE H 107 " pdb=" CB PHE H 107 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.84e-01 chirality pdb=" CA PRO A 520 " pdb=" N PRO A 520 " pdb=" C PRO A 520 " pdb=" CB PRO A 520 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.82e-01 chirality pdb=" CA PRO D 520 " pdb=" N PRO D 520 " pdb=" C PRO D 520 " pdb=" CB PRO D 520 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.81e-01 ... (remaining 1635 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE G 107 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO G 108 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO G 108 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 108 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 60 " -0.008 2.00e-02 2.50e+03 1.01e-02 1.53e+00 pdb=" CG HIS E 60 " 0.022 2.00e-02 2.50e+03 pdb=" ND1 HIS E 60 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS E 60 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS E 60 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS E 60 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 107 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO E 108 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 108 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 108 " 0.017 5.00e-02 4.00e+02 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1396 2.75 - 3.29: 10427 3.29 - 3.83: 19341 3.83 - 4.36: 20648 4.36 - 4.90: 36556 Nonbonded interactions: 88368 Sorted by model distance: nonbonded pdb=" OG1 THR G 30 " pdb=" OG SER G 179 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR E 30 " pdb=" OG SER E 179 " model vdw 2.223 3.040 nonbonded pdb=" O SER E 105 " pdb=" OG SER E 105 " model vdw 2.232 3.040 nonbonded pdb=" O SER G 105 " pdb=" OG SER G 105 " model vdw 2.233 3.040 nonbonded pdb=" O HOH B 926 " pdb=" O HOH D 925 " model vdw 2.243 3.040 ... (remaining 88363 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 511 or (resid 512 and (name N or name CA or name C or name \ O or name CB )) or resid 513 through 588 or resid 590 through 614 or resid 616 \ through 625 or resid 784 through 826)) selection = (chain 'B' and (resid 511 through 552 or resid 566 through 588 or resid 590 thro \ ugh 614 or resid 616 through 824 or (resid 825 and (name N or name CA or name C \ or name O or name CB )) or resid 826)) selection = (chain 'C' and (resid 511 or (resid 512 and (name N or name CA or name C or name \ O or name CB )) or resid 513 through 588 or resid 590 through 614 or resid 616 \ through 625 or resid 784 through 826)) selection = (chain 'D' and (resid 511 through 552 or resid 566 through 588 or resid 590 thro \ ugh 614 or resid 616 through 824 or (resid 825 and (name N or name CA or name C \ or name O or name CB )) or resid 826)) } ncs_group { reference = (chain 'E' and (resid 5 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 212 or resid 401)) selection = (chain 'F' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 212 or resid 401)) selection = (chain 'G' and (resid 5 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 212 or resid 401)) selection = (chain 'H' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 212 or resid 401)) } 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=0.50 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: 2.890 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: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.170 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10720 Z= 0.096 Angle : 0.370 4.700 14522 Z= 0.209 Chirality : 0.033 0.107 1638 Planarity : 0.002 0.031 1766 Dihedral : 16.267 89.649 3608 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.01 % Allowed : 19.20 % Favored : 79.80 % 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: 4.11 (0.23), residues: 1308 helix: 3.82 (0.15), residues: 930 sheet: 1.09 (0.82), residues: 40 loop : -0.50 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 64 HIS 0.012 0.001 HIS E 60 PHE 0.010 0.001 PHE G 107 TYR 0.021 0.001 TYR A 523 ARG 0.001 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.13870 ( 855) hydrogen bonds : angle 3.96125 ( 2468) SS BOND : bond 0.00084 ( 8) SS BOND : angle 0.21353 ( 16) covalent geometry : bond 0.00179 (10712) covalent geometry : angle 0.37055 (14506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 1.079 Fit side-chains REVERT: E 11 LEU cc_start: 0.7891 (tm) cc_final: 0.7600 (tp) REVERT: E 97 PHE cc_start: 0.6303 (t80) cc_final: 0.6001 (t80) REVERT: G 97 PHE cc_start: 0.6345 (t80) cc_final: 0.6012 (t80) outliers start: 10 outliers final: 9 residues processed: 155 average time/residue: 1.0464 time to fit residues: 177.0183 Evaluate side-chains 154 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 120 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 60 HIS E 132 HIS G 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.178215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.130462 restraints weight = 35278.571| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.49 r_work: 0.2993 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10720 Z= 0.156 Angle : 0.465 4.603 14522 Z= 0.263 Chirality : 0.037 0.121 1638 Planarity : 0.003 0.035 1766 Dihedral : 4.752 51.862 1447 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.37 % Allowed : 18.28 % Favored : 80.35 % 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: 4.03 (0.23), residues: 1308 helix: 3.78 (0.16), residues: 928 sheet: 0.03 (0.68), residues: 60 loop : -0.44 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 578 HIS 0.009 0.001 HIS E 60 PHE 0.014 0.002 PHE G 107 TYR 0.016 0.002 TYR C 523 ARG 0.004 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.05994 ( 855) hydrogen bonds : angle 3.43178 ( 2468) SS BOND : bond 0.00201 ( 8) SS BOND : angle 0.40150 ( 16) covalent geometry : bond 0.00329 (10712) covalent geometry : angle 0.46535 (14506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 1.160 Fit side-chains REVERT: G 58 MET cc_start: 0.6482 (OUTLIER) cc_final: 0.6276 (tpt) outliers start: 14 outliers final: 5 residues processed: 164 average time/residue: 1.1304 time to fit residues: 201.0551 Evaluate side-chains 153 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 124 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN D 586 GLN E 132 HIS G 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.175290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.120661 restraints weight = 27367.099| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.55 r_work: 0.2908 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10720 Z= 0.187 Angle : 0.505 4.536 14522 Z= 0.285 Chirality : 0.038 0.127 1638 Planarity : 0.004 0.037 1766 Dihedral : 4.284 44.397 1437 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.10 % Allowed : 17.64 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.23), residues: 1308 helix: 3.46 (0.16), residues: 928 sheet: 0.58 (0.78), residues: 40 loop : -0.76 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 578 HIS 0.007 0.001 HIS E 205 PHE 0.016 0.002 PHE G 107 TYR 0.019 0.002 TYR A 523 ARG 0.005 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.06338 ( 855) hydrogen bonds : angle 3.53976 ( 2468) SS BOND : bond 0.00263 ( 8) SS BOND : angle 0.45244 ( 16) covalent geometry : bond 0.00412 (10712) covalent geometry : angle 0.50503 (14506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.332 Fit side-chains REVERT: E 58 MET cc_start: 0.6674 (tpt) cc_final: 0.6244 (tpt) outliers start: 22 outliers final: 13 residues processed: 172 average time/residue: 1.1288 time to fit residues: 210.6789 Evaluate side-chains 168 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 4 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.179826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.129558 restraints weight = 34656.039| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.66 r_work: 0.3013 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10720 Z= 0.109 Angle : 0.397 4.608 14522 Z= 0.226 Chirality : 0.035 0.108 1638 Planarity : 0.003 0.036 1766 Dihedral : 3.663 28.698 1437 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.10 % Allowed : 17.55 % Favored : 80.35 % 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: 4.09 (0.23), residues: 1308 helix: 3.87 (0.16), residues: 930 sheet: 0.71 (0.80), residues: 40 loop : -0.69 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 178 HIS 0.004 0.001 HIS E 205 PHE 0.009 0.001 PHE G 107 TYR 0.019 0.001 TYR A 523 ARG 0.002 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.04764 ( 855) hydrogen bonds : angle 3.19707 ( 2468) SS BOND : bond 0.00138 ( 8) SS BOND : angle 0.20833 ( 16) covalent geometry : bond 0.00201 (10712) covalent geometry : angle 0.39702 (14506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 1.054 Fit side-chains REVERT: B 514 VAL cc_start: 0.7309 (OUTLIER) cc_final: 0.7030 (p) REVERT: D 825 MET cc_start: 0.3349 (OUTLIER) cc_final: 0.2903 (tpp) REVERT: E 11 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7415 (tp) REVERT: E 58 MET cc_start: 0.6644 (tpt) cc_final: 0.6216 (tpt) REVERT: E 90 GLU cc_start: 0.0977 (OUTLIER) cc_final: -0.0238 (pm20) REVERT: E 97 PHE cc_start: 0.6326 (t80) cc_final: 0.5852 (t80) REVERT: E 127 PHE cc_start: 0.5556 (OUTLIER) cc_final: 0.5320 (t80) REVERT: G 58 MET cc_start: 0.6382 (OUTLIER) cc_final: 0.6160 (tpt) REVERT: G 90 GLU cc_start: 0.1106 (OUTLIER) cc_final: -0.0204 (pm20) REVERT: G 97 PHE cc_start: 0.6339 (t80) cc_final: 0.5858 (t80) outliers start: 23 outliers final: 4 residues processed: 184 average time/residue: 1.1097 time to fit residues: 221.4063 Evaluate side-chains 170 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain D residue 825 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 88 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.176422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124939 restraints weight = 31223.001| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.64 r_work: 0.2958 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10720 Z= 0.196 Angle : 0.512 4.543 14522 Z= 0.289 Chirality : 0.039 0.128 1638 Planarity : 0.004 0.038 1766 Dihedral : 3.969 22.793 1435 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.92 % Allowed : 19.10 % Favored : 78.98 % 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: 3.49 (0.23), residues: 1308 helix: 3.39 (0.16), residues: 932 sheet: 0.49 (0.82), residues: 40 loop : -0.80 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 578 HIS 0.007 0.001 HIS E 205 PHE 0.016 0.002 PHE E 107 TYR 0.020 0.002 TYR A 523 ARG 0.005 0.001 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.06354 ( 855) hydrogen bonds : angle 3.52216 ( 2468) SS BOND : bond 0.00265 ( 8) SS BOND : angle 0.45884 ( 16) covalent geometry : bond 0.00436 (10712) covalent geometry : angle 0.51223 (14506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 1.367 Fit side-chains REVERT: A 550 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.6179 (pm20) REVERT: C 550 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6249 (pm20) REVERT: D 825 MET cc_start: 0.3320 (OUTLIER) cc_final: 0.2840 (tpp) REVERT: E 58 MET cc_start: 0.6698 (tpt) cc_final: 0.6243 (tpt) REVERT: E 90 GLU cc_start: 0.1107 (OUTLIER) cc_final: -0.0209 (pm20) REVERT: G 90 GLU cc_start: 0.1023 (OUTLIER) cc_final: -0.0215 (pm20) outliers start: 21 outliers final: 8 residues processed: 169 average time/residue: 1.1237 time to fit residues: 206.4271 Evaluate side-chains 169 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain C residue 550 GLU Chi-restraints excluded: chain D residue 825 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 129 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.177958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.127124 restraints weight = 33050.743| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.68 r_work: 0.2983 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10720 Z= 0.134 Angle : 0.437 5.546 14522 Z= 0.247 Chirality : 0.036 0.113 1638 Planarity : 0.003 0.039 1766 Dihedral : 3.711 16.125 1434 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.55 % Allowed : 19.29 % Favored : 79.16 % 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: 3.79 (0.23), residues: 1308 helix: 3.62 (0.16), residues: 932 sheet: 0.62 (0.83), residues: 40 loop : -0.73 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 578 HIS 0.005 0.001 HIS E 205 PHE 0.015 0.001 PHE G 107 TYR 0.022 0.002 TYR C 523 ARG 0.003 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.05353 ( 855) hydrogen bonds : angle 3.32480 ( 2468) SS BOND : bond 0.00173 ( 8) SS BOND : angle 0.31279 ( 16) covalent geometry : bond 0.00273 (10712) covalent geometry : angle 0.43691 (14506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 1.128 Fit side-chains REVERT: D 825 MET cc_start: 0.3312 (OUTLIER) cc_final: 0.2858 (tpp) REVERT: E 58 MET cc_start: 0.6701 (tpt) cc_final: 0.6362 (tpt) REVERT: E 90 GLU cc_start: 0.0866 (OUTLIER) cc_final: -0.0329 (pm20) REVERT: G 58 MET cc_start: 0.6409 (OUTLIER) cc_final: 0.6180 (tpt) REVERT: G 90 GLU cc_start: 0.1017 (OUTLIER) cc_final: -0.0137 (pm20) outliers start: 17 outliers final: 8 residues processed: 168 average time/residue: 1.1895 time to fit residues: 216.5734 Evaluate side-chains 168 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 825 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 111 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.178734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.127720 restraints weight = 33944.067| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.68 r_work: 0.2994 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10720 Z= 0.122 Angle : 0.420 5.164 14522 Z= 0.237 Chirality : 0.035 0.126 1638 Planarity : 0.003 0.039 1766 Dihedral : 3.619 15.895 1434 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.37 % Allowed : 19.47 % Favored : 79.16 % 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: 3.98 (0.23), residues: 1308 helix: 3.76 (0.16), residues: 934 sheet: 0.65 (0.84), residues: 40 loop : -0.69 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 178 HIS 0.004 0.001 HIS E 205 PHE 0.015 0.001 PHE C 546 TYR 0.020 0.001 TYR A 523 ARG 0.003 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.05046 ( 855) hydrogen bonds : angle 3.24206 ( 2468) SS BOND : bond 0.00132 ( 8) SS BOND : angle 0.27452 ( 16) covalent geometry : bond 0.00239 (10712) covalent geometry : angle 0.41984 (14506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 1.145 Fit side-chains REVERT: D 825 MET cc_start: 0.3419 (OUTLIER) cc_final: 0.2951 (tpp) REVERT: E 11 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7431 (tp) REVERT: E 58 MET cc_start: 0.6600 (tpt) cc_final: 0.6286 (tpt) REVERT: E 90 GLU cc_start: 0.0843 (OUTLIER) cc_final: -0.0351 (pm20) REVERT: E 97 PHE cc_start: 0.6349 (t80) cc_final: 0.5826 (t80) REVERT: E 120 LEU cc_start: 0.7793 (tp) cc_final: 0.7505 (mt) REVERT: E 127 PHE cc_start: 0.5654 (OUTLIER) cc_final: 0.5324 (t80) REVERT: G 58 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.6161 (tpt) REVERT: G 90 GLU cc_start: 0.0939 (OUTLIER) cc_final: -0.0205 (pm20) REVERT: G 97 PHE cc_start: 0.6345 (t80) cc_final: 0.5821 (t80) outliers start: 15 outliers final: 7 residues processed: 169 average time/residue: 1.0996 time to fit residues: 201.8222 Evaluate side-chains 171 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 825 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 71 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.178614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.127761 restraints weight = 29510.040| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.44 r_work: 0.3012 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10720 Z= 0.123 Angle : 0.423 5.265 14522 Z= 0.239 Chirality : 0.035 0.126 1638 Planarity : 0.003 0.039 1766 Dihedral : 3.620 15.895 1434 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.37 % Allowed : 19.29 % Favored : 79.34 % 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: 4.01 (0.23), residues: 1308 helix: 3.79 (0.16), residues: 934 sheet: 0.66 (0.84), residues: 40 loop : -0.67 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 178 HIS 0.005 0.001 HIS E 205 PHE 0.017 0.001 PHE A 546 TYR 0.022 0.001 TYR C 523 ARG 0.002 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.05086 ( 855) hydrogen bonds : angle 3.25033 ( 2468) SS BOND : bond 0.00120 ( 8) SS BOND : angle 0.26887 ( 16) covalent geometry : bond 0.00242 (10712) covalent geometry : angle 0.42348 (14506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 1.091 Fit side-chains REVERT: D 825 MET cc_start: 0.3415 (OUTLIER) cc_final: 0.2935 (tpp) REVERT: E 11 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7462 (tp) REVERT: E 58 MET cc_start: 0.6606 (tpt) cc_final: 0.6292 (tpt) REVERT: E 90 GLU cc_start: 0.0924 (OUTLIER) cc_final: -0.0309 (pm20) REVERT: E 97 PHE cc_start: 0.6339 (t80) cc_final: 0.5816 (t80) REVERT: E 120 LEU cc_start: 0.7821 (tp) cc_final: 0.7533 (mt) REVERT: E 127 PHE cc_start: 0.5679 (OUTLIER) cc_final: 0.5352 (t80) REVERT: G 58 MET cc_start: 0.6421 (OUTLIER) cc_final: 0.6187 (tpt) REVERT: G 97 PHE cc_start: 0.6313 (t80) cc_final: 0.5786 (t80) outliers start: 15 outliers final: 7 residues processed: 166 average time/residue: 1.1666 time to fit residues: 209.8832 Evaluate side-chains 168 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 825 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 96 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.176734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.125378 restraints weight = 34428.389| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.67 r_work: 0.2976 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10720 Z= 0.178 Angle : 0.500 6.271 14522 Z= 0.281 Chirality : 0.038 0.123 1638 Planarity : 0.003 0.038 1766 Dihedral : 3.901 18.574 1434 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.01 % Allowed : 19.93 % Favored : 79.07 % 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: 3.58 (0.23), residues: 1308 helix: 3.44 (0.16), residues: 932 sheet: 0.50 (0.85), residues: 40 loop : -0.72 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 578 HIS 0.006 0.001 HIS E 205 PHE 0.019 0.002 PHE C 546 TYR 0.017 0.002 TYR A 549 ARG 0.003 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.06090 ( 855) hydrogen bonds : angle 3.47686 ( 2468) SS BOND : bond 0.00246 ( 8) SS BOND : angle 0.40405 ( 16) covalent geometry : bond 0.00388 (10712) covalent geometry : angle 0.50050 (14506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 1.085 Fit side-chains REVERT: D 825 MET cc_start: 0.3243 (OUTLIER) cc_final: 0.2750 (tpp) REVERT: E 58 MET cc_start: 0.6554 (tpt) cc_final: 0.6267 (tpt) REVERT: E 90 GLU cc_start: 0.1029 (OUTLIER) cc_final: -0.0322 (pm20) REVERT: E 127 PHE cc_start: 0.5822 (OUTLIER) cc_final: 0.5411 (t80) outliers start: 11 outliers final: 8 residues processed: 167 average time/residue: 1.1033 time to fit residues: 200.2201 Evaluate side-chains 170 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 825 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 69 optimal weight: 0.0010 chunk 56 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 65 optimal weight: 0.0870 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 0.2980 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 overall best weight: 0.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.180732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.130546 restraints weight = 32289.749| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.45 r_work: 0.3044 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10720 Z= 0.101 Angle : 0.396 6.215 14522 Z= 0.224 Chirality : 0.035 0.136 1638 Planarity : 0.003 0.040 1766 Dihedral : 3.551 19.756 1434 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.64 % Allowed : 20.02 % Favored : 79.34 % 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: 4.21 (0.23), residues: 1308 helix: 3.96 (0.16), residues: 934 sheet: 0.64 (0.84), residues: 40 loop : -0.65 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 178 HIS 0.004 0.001 HIS F 205 PHE 0.016 0.001 PHE C 546 TYR 0.012 0.001 TYR B 523 ARG 0.001 0.000 ARG B 599 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 855) hydrogen bonds : angle 3.12085 ( 2468) SS BOND : bond 0.00076 ( 8) SS BOND : angle 0.21056 ( 16) covalent geometry : bond 0.00182 (10712) covalent geometry : angle 0.39633 (14506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 1.079 Fit side-chains REVERT: E 11 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7446 (tp) REVERT: E 58 MET cc_start: 0.6536 (tpt) cc_final: 0.6237 (tpt) REVERT: E 90 GLU cc_start: 0.0951 (OUTLIER) cc_final: -0.0277 (pm20) REVERT: E 97 PHE cc_start: 0.6343 (t80) cc_final: 0.5816 (t80) REVERT: E 127 PHE cc_start: 0.5533 (OUTLIER) cc_final: 0.5241 (t80) REVERT: G 97 PHE cc_start: 0.6303 (t80) cc_final: 0.5758 (t80) outliers start: 7 outliers final: 4 residues processed: 167 average time/residue: 1.2134 time to fit residues: 219.5394 Evaluate side-chains 161 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 117 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 122 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS G 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.178439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.127029 restraints weight = 35403.479| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.71 r_work: 0.2990 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10720 Z= 0.131 Angle : 0.435 6.441 14522 Z= 0.245 Chirality : 0.036 0.127 1638 Planarity : 0.003 0.039 1766 Dihedral : 3.652 19.210 1434 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.64 % Allowed : 20.29 % Favored : 79.07 % 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: 4.03 (0.23), residues: 1308 helix: 3.79 (0.16), residues: 934 sheet: 0.62 (0.84), residues: 40 loop : -0.61 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 178 HIS 0.005 0.001 HIS E 205 PHE 0.015 0.001 PHE A 546 TYR 0.016 0.002 TYR C 523 ARG 0.002 0.000 ARG G 209 Details of bonding type rmsd hydrogen bonds : bond 0.05183 ( 855) hydrogen bonds : angle 3.27099 ( 2468) SS BOND : bond 0.00142 ( 8) SS BOND : angle 0.29808 ( 16) covalent geometry : bond 0.00265 (10712) covalent geometry : angle 0.43552 (14506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8662.02 seconds wall clock time: 149 minutes 35.62 seconds (8975.62 seconds total)