Starting phenix.real_space_refine on Wed May 14 21:07:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vmj_43358/05_2025/8vmj_43358.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vmj_43358/05_2025/8vmj_43358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vmj_43358/05_2025/8vmj_43358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vmj_43358/05_2025/8vmj_43358.map" model { file = "/net/cci-nas-00/data/ceres_data/8vmj_43358/05_2025/8vmj_43358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vmj_43358/05_2025/8vmj_43358.cif" } resolution = 3.1 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= 0.002 sd= 0.060 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 P 314 5.49 5 S 14 5.16 5 C 6889 2.51 5 N 2355 2.21 5 O 2968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 12540 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 3237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3237 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "I" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "J" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "K" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "Q" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 667 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "S" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3202 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Time building chain proxies: 8.55, per 1000 atoms: 0.68 Number of scatterers: 12540 At special positions: 0 Unit cell: (106.05, 141.75, 121.8, 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) S 14 16.00 P 314 15.00 O 2968 8.00 N 2355 7.00 C 6889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.0 seconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 69.7% alpha, 2.6% beta 157 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 6.39 Creating SS restraints... Processing helix chain 'I' and resid 45 through 57 Processing helix chain 'I' and resid 63 through 77 removed outlier: 3.898A pdb=" N ASP I 77 " --> pdb=" O GLU I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 114 removed outlier: 3.614A pdb=" N MET I 90 " --> pdb=" O SER I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 132 Processing helix chain 'J' and resid 30 through 42 Processing helix chain 'J' and resid 49 through 76 removed outlier: 3.554A pdb=" N GLU J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP J 68 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 94 Processing helix chain 'K' and resid 16 through 21 removed outlier: 3.559A pdb=" N ARG K 20 " --> pdb=" O THR K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 45 through 73 removed outlier: 4.348A pdb=" N VAL K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 90 removed outlier: 3.660A pdb=" N ASP K 90 " --> pdb=" O ALA K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 97 removed outlier: 3.521A pdb=" N LEU K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 46 Processing helix chain 'M' and resid 52 through 81 removed outlier: 3.503A pdb=" N ASN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 99 Processing helix chain 'M' and resid 101 through 121 removed outlier: 3.742A pdb=" N SER M 109 " --> pdb=" O LYS M 105 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA M 121 " --> pdb=" O LYS M 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 57 Processing helix chain 'O' and resid 63 through 75 Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 Processing helix chain 'Q' and resid 25 through 29 Processing helix chain 'Q' and resid 30 through 42 Processing helix chain 'Q' and resid 49 through 77 removed outlier: 4.098A pdb=" N GLU Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP Q 68 " --> pdb=" O ASN Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 93 Processing helix chain 'R' and resid 16 through 22 removed outlier: 3.831A pdb=" N ARG R 20 " --> pdb=" O THR R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 37 Processing helix chain 'R' and resid 46 through 73 Processing helix chain 'R' and resid 79 through 90 removed outlier: 3.543A pdb=" N ASP R 90 " --> pdb=" O ALA R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 97 Processing helix chain 'S' and resid 34 through 46 Processing helix chain 'S' and resid 52 through 81 Processing helix chain 'S' and resid 87 through 99 Processing helix chain 'S' and resid 101 through 121 removed outlier: 3.617A pdb=" N LYS S 105 " --> pdb=" O GLY S 101 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA S 121 " --> pdb=" O LYS S 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 83 through 84 removed outlier: 7.168A pdb=" N ARG I 83 " --> pdb=" O VAL J 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'I' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'J' and resid 96 through 98 removed outlier: 6.151A pdb=" N THR J 96 " --> pdb=" O THR R 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'K' and resid 42 through 43 removed outlier: 7.369A pdb=" N ARG K 42 " --> pdb=" O ILE M 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 100 through 102 removed outlier: 6.928A pdb=" N THR K 101 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.754A pdb=" N ARG O 83 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'R' and resid 42 through 43 removed outlier: 7.383A pdb=" N ARG R 42 " --> pdb=" O ILE S 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'R' and resid 77 through 78 394 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 398 hydrogen bonds 756 hydrogen bond angles 0 basepair planarities 157 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 4.52 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1728 1.33 - 1.45: 4924 1.45 - 1.57: 6098 1.57 - 1.69: 629 1.69 - 1.82: 24 Bond restraints: 13403 Sorted by residual: bond pdb=" CG PRO O 38 " pdb=" CD PRO O 38 " ideal model delta sigma weight residual 1.503 1.205 0.298 3.40e-02 8.65e+02 7.70e+01 bond pdb=" N PRO O 38 " pdb=" CD PRO O 38 " ideal model delta sigma weight residual 1.473 1.558 -0.085 1.40e-02 5.10e+03 3.71e+01 bond pdb=" CB PRO O 38 " pdb=" CG PRO O 38 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.26e+00 bond pdb=" CB PRO I 43 " pdb=" CG PRO I 43 " ideal model delta sigma weight residual 1.492 1.617 -0.125 5.00e-02 4.00e+02 6.28e+00 bond pdb=" CE LYS M 105 " pdb=" NZ LYS M 105 " ideal model delta sigma weight residual 1.489 1.431 0.058 3.00e-02 1.11e+03 3.68e+00 ... (remaining 13398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 19397 3.79 - 7.58: 56 7.58 - 11.37: 1 11.37 - 15.16: 4 15.16 - 18.95: 1 Bond angle restraints: 19459 Sorted by residual: angle pdb=" CA PRO O 38 " pdb=" N PRO O 38 " pdb=" CD PRO O 38 " ideal model delta sigma weight residual 112.00 93.05 18.95 1.40e+00 5.10e-01 1.83e+02 angle pdb=" N PRO O 38 " pdb=" CD PRO O 38 " pdb=" CG PRO O 38 " ideal model delta sigma weight residual 103.20 88.45 14.75 1.50e+00 4.44e-01 9.67e+01 angle pdb=" CA PRO I 43 " pdb=" N PRO I 43 " pdb=" CD PRO I 43 " ideal model delta sigma weight residual 112.00 98.62 13.38 1.40e+00 5.10e-01 9.13e+01 angle pdb=" CA PRO O 38 " pdb=" CB PRO O 38 " pdb=" CG PRO O 38 " ideal model delta sigma weight residual 104.50 91.98 12.52 1.90e+00 2.77e-01 4.34e+01 angle pdb=" N VAL O 117 " pdb=" CA VAL O 117 " pdb=" C VAL O 117 " ideal model delta sigma weight residual 111.81 108.16 3.65 8.60e-01 1.35e+00 1.80e+01 ... (remaining 19454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 5729 35.91 - 71.82: 1433 71.82 - 107.73: 28 107.73 - 143.65: 8 143.65 - 179.56: 24 Dihedral angle restraints: 7222 sinusoidal: 4972 harmonic: 2250 Sorted by residual: dihedral pdb=" CA PHE R 25 " pdb=" C PHE R 25 " pdb=" N PRO R 26 " pdb=" CA PRO R 26 " ideal model delta harmonic sigma weight residual -180.00 -159.37 -20.63 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA HIS S 79 " pdb=" C HIS S 79 " pdb=" N TYR S 80 " pdb=" CA TYR S 80 " ideal model delta harmonic sigma weight residual -180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C4' DT D 68 " pdb=" C3' DT D 68 " pdb=" O3' DT D 68 " pdb=" P DT D 69 " ideal model delta sinusoidal sigma weight residual 220.00 40.44 179.56 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1825 0.049 - 0.098: 336 0.098 - 0.146: 49 0.146 - 0.195: 7 0.195 - 0.244: 1 Chirality restraints: 2218 Sorted by residual: chirality pdb=" CB THR S 112 " pdb=" CA THR S 112 " pdb=" OG1 THR S 112 " pdb=" CG2 THR S 112 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA ASN R 38 " pdb=" N ASN R 38 " pdb=" C ASN R 38 " pdb=" CB ASN R 38 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.89e-01 chirality pdb=" P DC D 93 " pdb=" OP1 DC D 93 " pdb=" OP2 DC D 93 " pdb=" O5' DC D 93 " both_signs ideal model delta sigma weight residual True 2.35 -2.52 -0.18 2.00e-01 2.50e+01 7.92e-01 ... (remaining 2215 not shown) Planarity restraints: 1377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 42 " 0.116 5.00e-02 4.00e+02 1.64e-01 4.29e+01 pdb=" N PRO I 43 " -0.283 5.00e-02 4.00e+02 pdb=" CA PRO I 43 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO I 43 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS O 37 " 0.082 5.00e-02 4.00e+02 1.09e-01 1.90e+01 pdb=" N PRO O 38 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO O 38 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO O 38 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 80 " 0.031 2.00e-02 2.50e+03 2.66e-02 1.42e+01 pdb=" CG TYR S 80 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR S 80 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR S 80 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR S 80 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR S 80 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR S 80 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR S 80 " 0.001 2.00e-02 2.50e+03 ... (remaining 1374 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 268 2.65 - 3.21: 10562 3.21 - 3.77: 24047 3.77 - 4.34: 30514 4.34 - 4.90: 43251 Nonbonded interactions: 108642 Sorted by model distance: nonbonded pdb=" O2 DC H 110 " pdb=" N2 DG D 48 " model vdw 2.082 2.496 nonbonded pdb=" N2 DG H 137 " pdb=" O2 DC D 21 " model vdw 2.097 2.496 nonbonded pdb=" OD2 ASP M 65 " pdb=" OH TYR Q 98 " model vdw 2.101 3.040 nonbonded pdb=" N2 DG H 94 " pdb=" O2 DC D 64 " model vdw 2.110 2.496 nonbonded pdb=" O2 DC H 154 " pdb=" N2 DG D 4 " model vdw 2.125 2.496 ... (remaining 108637 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 'I' and resid 37 through 135) selection = chain 'O' } ncs_group { reference = (chain 'J' and ((resid 20 through 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 102)) selection = (chain 'Q' and resid 20 through 102) } ncs_group { reference = chain 'K' selection = (chain 'R' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 119)) } ncs_group { reference = chain 'M' selection = (chain 'S' and resid 28 through 122) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.020 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 35.570 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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 0.298 13403 Z= 0.225 Angle : 0.743 18.945 19459 Z= 0.437 Chirality : 0.039 0.244 2218 Planarity : 0.008 0.164 1377 Dihedral : 31.124 179.557 5770 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.63 % Allowed : 23.58 % Favored : 75.79 % 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: 0.60 (0.30), residues: 760 helix: 1.06 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.11 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS R 31 PHE 0.022 0.003 PHE R 25 TYR 0.064 0.003 TYR S 80 ARG 0.008 0.001 ARG O 40 Details of bonding type rmsd hydrogen bonds : bond 0.10030 ( 792) hydrogen bonds : angle 4.07596 ( 1932) covalent geometry : bond 0.00557 (13403) covalent geometry : angle 0.74269 (19459) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: S 102 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7221 (tm-30) outliers start: 4 outliers final: 3 residues processed: 129 average time/residue: 0.3380 time to fit residues: 57.6523 Evaluate side-chains 124 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain S residue 49 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 ASN M 60 ASN M 81 ASN ** O 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 125 GLN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN S 79 HIS S 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.176684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.130429 restraints weight = 20266.381| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.53 r_work: 0.3643 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13403 Z= 0.233 Angle : 0.718 7.304 19459 Z= 0.408 Chirality : 0.041 0.174 2218 Planarity : 0.006 0.071 1377 Dihedral : 33.487 179.802 4275 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.38 % Allowed : 19.46 % Favored : 75.16 % 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: 0.80 (0.29), residues: 760 helix: 1.25 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -1.23 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS S 79 PHE 0.019 0.003 PHE O 104 TYR 0.058 0.003 TYR S 80 ARG 0.008 0.001 ARG O 83 Details of bonding type rmsd hydrogen bonds : bond 0.07717 ( 792) hydrogen bonds : angle 3.39147 ( 1932) covalent geometry : bond 0.00538 (13403) covalent geometry : angle 0.71782 (19459) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: K 25 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7752 (t80) REVERT: M 96 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7484 (mpp80) REVERT: O 59 GLU cc_start: 0.7704 (pp20) cc_final: 0.7446 (pp20) REVERT: O 97 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7893 (mt-10) REVERT: Q 77 LYS cc_start: 0.7934 (mmmt) cc_final: 0.7639 (mmmt) REVERT: Q 85 ASP cc_start: 0.8609 (m-30) cc_final: 0.8378 (m-30) REVERT: S 59 MET cc_start: 0.8724 (mmm) cc_final: 0.8312 (mmp) REVERT: S 102 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7296 (tp30) outliers start: 34 outliers final: 19 residues processed: 162 average time/residue: 0.3495 time to fit residues: 73.2786 Evaluate side-chains 147 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 96 ARG Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 24 GLN Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 95 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 81 ASN ** O 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 GLN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.168511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.122260 restraints weight = 20214.100| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.53 r_work: 0.3529 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13403 Z= 0.233 Angle : 0.692 7.379 19459 Z= 0.395 Chirality : 0.041 0.211 2218 Planarity : 0.005 0.060 1377 Dihedral : 33.701 179.089 4272 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 5.70 % Allowed : 19.46 % Favored : 74.84 % 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: 0.93 (0.29), residues: 760 helix: 1.29 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -1.02 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS O 113 PHE 0.015 0.002 PHE O 104 TYR 0.056 0.003 TYR S 80 ARG 0.019 0.001 ARG R 32 Details of bonding type rmsd hydrogen bonds : bond 0.06750 ( 792) hydrogen bonds : angle 3.38575 ( 1932) covalent geometry : bond 0.00532 (13403) covalent geometry : angle 0.69223 (19459) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 125 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8196 (mt0) REVERT: J 84 MET cc_start: 0.7844 (mmm) cc_final: 0.7528 (tpp) REVERT: J 91 LYS cc_start: 0.8976 (ttpp) cc_final: 0.8623 (ttpp) REVERT: K 25 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7569 (t80) REVERT: M 30 ARG cc_start: 0.7338 (ptm160) cc_final: 0.6973 (ptm160) REVERT: M 110 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7927 (mm-30) REVERT: Q 77 LYS cc_start: 0.8013 (mmmt) cc_final: 0.7681 (mmmt) outliers start: 36 outliers final: 24 residues processed: 160 average time/residue: 0.3635 time to fit residues: 76.2615 Evaluate side-chains 155 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain R residue 24 GLN Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 63 optimal weight: 0.0980 chunk 59 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 ASN R 24 GLN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.168749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.122741 restraints weight = 19959.624| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.52 r_work: 0.3538 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13403 Z= 0.190 Angle : 0.643 6.861 19459 Z= 0.371 Chirality : 0.038 0.163 2218 Planarity : 0.004 0.051 1377 Dihedral : 33.487 178.559 4272 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.22 % Allowed : 19.30 % Favored : 75.47 % 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: 1.35 (0.29), residues: 760 helix: 1.62 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.93 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS S 106 PHE 0.012 0.002 PHE O 67 TYR 0.053 0.002 TYR S 80 ARG 0.005 0.000 ARG O 129 Details of bonding type rmsd hydrogen bonds : bond 0.06724 ( 792) hydrogen bonds : angle 3.14942 ( 1932) covalent geometry : bond 0.00433 (13403) covalent geometry : angle 0.64301 (19459) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: I 125 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8201 (mt0) REVERT: J 27 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7578 (tm-30) REVERT: J 84 MET cc_start: 0.7844 (mmm) cc_final: 0.7627 (mmt) REVERT: K 25 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7570 (t80) REVERT: M 30 ARG cc_start: 0.7377 (ptm160) cc_final: 0.7074 (ptm160) REVERT: M 110 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7763 (mm-30) REVERT: Q 77 LYS cc_start: 0.7997 (mmmt) cc_final: 0.7633 (mmmt) outliers start: 33 outliers final: 20 residues processed: 161 average time/residue: 0.3495 time to fit residues: 73.6178 Evaluate side-chains 155 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 27 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 68 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 25 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.165772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.119871 restraints weight = 19883.127| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.52 r_work: 0.3493 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13403 Z= 0.205 Angle : 0.660 7.720 19459 Z= 0.379 Chirality : 0.039 0.167 2218 Planarity : 0.005 0.049 1377 Dihedral : 33.505 178.399 4271 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.06 % Allowed : 19.62 % Favored : 75.32 % 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: 1.28 (0.29), residues: 760 helix: 1.57 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.97 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS I 113 PHE 0.012 0.002 PHE O 67 TYR 0.053 0.002 TYR S 80 ARG 0.009 0.001 ARG R 32 Details of bonding type rmsd hydrogen bonds : bond 0.06532 ( 792) hydrogen bonds : angle 3.20548 ( 1932) covalent geometry : bond 0.00470 (13403) covalent geometry : angle 0.66041 (19459) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: I 125 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8272 (mt0) REVERT: J 27 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7508 (tm-30) REVERT: J 91 LYS cc_start: 0.9048 (ttpp) cc_final: 0.8704 (ttpp) REVERT: K 25 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7652 (t80) REVERT: M 90 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: M 110 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7833 (mm-30) REVERT: O 97 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7963 (mt-10) REVERT: Q 77 LYS cc_start: 0.8144 (mmmt) cc_final: 0.7784 (mmmt) outliers start: 32 outliers final: 23 residues processed: 159 average time/residue: 0.3374 time to fit residues: 70.8251 Evaluate side-chains 154 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain Q residue 25 ASN Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 76 ARG Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 67 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 82 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.164441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.118529 restraints weight = 20026.354| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.62 r_work: 0.3436 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13403 Z= 0.187 Angle : 0.638 8.070 19459 Z= 0.369 Chirality : 0.038 0.172 2218 Planarity : 0.004 0.047 1377 Dihedral : 33.400 179.714 4271 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.43 % Allowed : 21.36 % Favored : 74.21 % 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: 1.55 (0.29), residues: 760 helix: 1.79 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.91 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 113 PHE 0.012 0.002 PHE O 67 TYR 0.051 0.002 TYR S 80 ARG 0.003 0.000 ARG Q 78 Details of bonding type rmsd hydrogen bonds : bond 0.06600 ( 792) hydrogen bonds : angle 3.09593 ( 1932) covalent geometry : bond 0.00426 (13403) covalent geometry : angle 0.63780 (19459) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: I 125 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8129 (mt0) REVERT: J 27 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7446 (tm-30) REVERT: J 88 TYR cc_start: 0.8896 (m-10) cc_final: 0.8682 (m-10) REVERT: K 25 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7588 (t80) REVERT: M 106 HIS cc_start: 0.8468 (OUTLIER) cc_final: 0.8149 (m170) REVERT: M 110 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7776 (mm-30) REVERT: O 97 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7983 (mt-10) REVERT: Q 77 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7697 (mmmt) outliers start: 28 outliers final: 22 residues processed: 150 average time/residue: 0.3274 time to fit residues: 65.2865 Evaluate side-chains 158 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 106 HIS Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.161968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.115726 restraints weight = 19839.270| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.61 r_work: 0.3409 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13403 Z= 0.203 Angle : 0.655 7.173 19459 Z= 0.376 Chirality : 0.039 0.192 2218 Planarity : 0.004 0.045 1377 Dihedral : 33.450 179.859 4271 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 5.22 % Allowed : 20.57 % Favored : 74.21 % 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: 1.50 (0.29), residues: 760 helix: 1.73 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.88 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 113 PHE 0.014 0.002 PHE O 67 TYR 0.053 0.002 TYR S 80 ARG 0.003 0.000 ARG Q 78 Details of bonding type rmsd hydrogen bonds : bond 0.06562 ( 792) hydrogen bonds : angle 3.15417 ( 1932) covalent geometry : bond 0.00464 (13403) covalent geometry : angle 0.65486 (19459) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: I 125 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: J 27 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7496 (tm-30) REVERT: J 59 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8163 (ttmt) REVERT: K 25 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.7586 (t80) REVERT: M 90 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: M 106 HIS cc_start: 0.8476 (OUTLIER) cc_final: 0.8141 (m170) REVERT: M 110 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7842 (mm-30) REVERT: O 97 GLU cc_start: 0.8246 (mt-10) cc_final: 0.8011 (mt-10) REVERT: Q 77 LYS cc_start: 0.8116 (mmmt) cc_final: 0.7746 (mmmt) outliers start: 33 outliers final: 27 residues processed: 146 average time/residue: 0.3260 time to fit residues: 63.4645 Evaluate side-chains 158 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 106 HIS Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain Q residue 25 ASN Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 38 optimal weight: 0.5980 chunk 27 optimal weight: 0.0980 chunk 83 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 44 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.163642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.117871 restraints weight = 19950.035| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.59 r_work: 0.3444 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13403 Z= 0.174 Angle : 0.630 6.235 19459 Z= 0.365 Chirality : 0.037 0.178 2218 Planarity : 0.004 0.044 1377 Dihedral : 33.334 178.748 4271 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.22 % Allowed : 20.89 % Favored : 73.89 % 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: 1.73 (0.29), residues: 760 helix: 1.91 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.82 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS O 39 PHE 0.017 0.002 PHE J 100 TYR 0.049 0.002 TYR S 80 ARG 0.003 0.000 ARG S 96 Details of bonding type rmsd hydrogen bonds : bond 0.06486 ( 792) hydrogen bonds : angle 3.05748 ( 1932) covalent geometry : bond 0.00396 (13403) covalent geometry : angle 0.62962 (19459) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: I 125 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8094 (mt0) REVERT: J 27 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7523 (tm-30) REVERT: J 59 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8128 (ttmt) REVERT: K 25 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.7611 (t80) REVERT: M 90 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: M 106 HIS cc_start: 0.8481 (OUTLIER) cc_final: 0.8157 (m170) REVERT: M 110 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7795 (mm-30) REVERT: O 42 ARG cc_start: 0.7885 (mpt180) cc_final: 0.7660 (mpt180) REVERT: O 97 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7957 (mt-10) REVERT: Q 77 LYS cc_start: 0.8066 (mmmt) cc_final: 0.7681 (mmmt) outliers start: 33 outliers final: 25 residues processed: 158 average time/residue: 0.3086 time to fit residues: 65.3042 Evaluate side-chains 166 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 106 HIS Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain Q residue 25 ASN Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 88 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 66 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 79 optimal weight: 0.0370 chunk 84 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.161713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.115717 restraints weight = 19696.932| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.58 r_work: 0.3409 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13403 Z= 0.200 Angle : 0.652 9.190 19459 Z= 0.375 Chirality : 0.038 0.186 2218 Planarity : 0.004 0.044 1377 Dihedral : 33.432 179.014 4271 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.75 % Allowed : 21.68 % Favored : 73.58 % 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: 1.66 (0.30), residues: 760 helix: 1.85 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.79 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS O 39 PHE 0.014 0.002 PHE O 67 TYR 0.052 0.002 TYR S 80 ARG 0.003 0.000 ARG Q 45 Details of bonding type rmsd hydrogen bonds : bond 0.06543 ( 792) hydrogen bonds : angle 3.13932 ( 1932) covalent geometry : bond 0.00457 (13403) covalent geometry : angle 0.65225 (19459) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: I 125 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8289 (mt0) REVERT: J 27 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7505 (tm-30) REVERT: K 25 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7605 (t80) REVERT: M 110 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7798 (mm-30) REVERT: O 97 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7990 (mt-10) REVERT: Q 77 LYS cc_start: 0.8127 (mmmt) cc_final: 0.7780 (mmmt) outliers start: 30 outliers final: 26 residues processed: 148 average time/residue: 0.3115 time to fit residues: 61.3482 Evaluate side-chains 158 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 85 GLN Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain Q residue 25 ASN Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 54 optimal weight: 0.0070 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.160847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.114844 restraints weight = 19664.527| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.63 r_work: 0.3378 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.6327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13403 Z= 0.181 Angle : 0.639 8.895 19459 Z= 0.369 Chirality : 0.038 0.192 2218 Planarity : 0.004 0.044 1377 Dihedral : 33.351 179.014 4271 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.75 % Allowed : 21.84 % Favored : 73.42 % 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: 1.79 (0.30), residues: 760 helix: 1.95 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.78 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS O 39 PHE 0.018 0.002 PHE J 100 TYR 0.049 0.002 TYR S 80 ARG 0.003 0.000 ARG S 96 Details of bonding type rmsd hydrogen bonds : bond 0.06461 ( 792) hydrogen bonds : angle 3.06432 ( 1932) covalent geometry : bond 0.00412 (13403) covalent geometry : angle 0.63894 (19459) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: I 125 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8100 (mt0) REVERT: J 27 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7402 (tm-30) REVERT: J 59 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8067 (ttmt) REVERT: K 25 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7526 (t80) REVERT: M 90 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: M 110 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7745 (mm-30) REVERT: O 97 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7973 (mt-10) REVERT: Q 77 LYS cc_start: 0.8068 (mmmt) cc_final: 0.7669 (mmmt) outliers start: 30 outliers final: 25 residues processed: 145 average time/residue: 0.3313 time to fit residues: 64.3127 Evaluate side-chains 161 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 25 ASN Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 77 LYS Chi-restraints excluded: chain K residue 25 PHE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain Q residue 25 ASN Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 102 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 80 TYR Chi-restraints excluded: chain S residue 82 LYS Chi-restraints excluded: chain S residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 38 ASN ** O 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.158003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.111749 restraints weight = 19674.675| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.64 r_work: 0.3331 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.6647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13403 Z= 0.218 Angle : 0.671 8.996 19459 Z= 0.383 Chirality : 0.039 0.191 2218 Planarity : 0.005 0.043 1377 Dihedral : 33.511 179.121 4271 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 5.06 % Allowed : 21.68 % Favored : 73.26 % 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: 1.60 (0.30), residues: 760 helix: 1.78 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.76 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS O 39 PHE 0.018 0.002 PHE J 100 TYR 0.055 0.002 TYR S 80 ARG 0.003 0.000 ARG R 32 Details of bonding type rmsd hydrogen bonds : bond 0.06594 ( 792) hydrogen bonds : angle 3.19577 ( 1932) covalent geometry : bond 0.00501 (13403) covalent geometry : angle 0.67099 (19459) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5971.35 seconds wall clock time: 104 minutes 6.68 seconds (6246.68 seconds total)