Starting phenix.real_space_refine on Sat Apr 6 18:16:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8z_36082/04_2024/8j8z_36082_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8z_36082/04_2024/8j8z_36082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8z_36082/04_2024/8j8z_36082.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8z_36082/04_2024/8j8z_36082.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8z_36082/04_2024/8j8z_36082_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8z_36082/04_2024/8j8z_36082_updated.pdb" } resolution = 3.4 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= 0.025 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 6 5.49 5 S 34 5.16 5 C 5564 2.51 5 N 1458 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 32": "OD1" <-> "OD2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 65": "OD1" <-> "OD2" Residue "H ASP 76": "OD1" <-> "OD2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 93": "OD1" <-> "OD2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "L ASP 2": "OD1" <-> "OD2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "L PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 32": "OD1" <-> "OD2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 240": "OD1" <-> "OD2" Residue "B TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 76": "OD1" <-> "OD2" Residue "I ASP 93": "OD1" <-> "OD2" Residue "I TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 106": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8722 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2601 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 25, 'TRANS': 314} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 81 Chain: "H" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 898 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2607 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 314} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 80 Chain: "I" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 895 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "M" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 795 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 3} Unresolved non-hydrogen planarities: 12 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Time building chain proxies: 5.11, per 1000 atoms: 0.59 Number of scatterers: 8722 At special positions: 0 Unit cell: (81.9448, 144.867, 90.7246, 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 34 16.00 P 6 15.00 O 1660 8.00 N 1458 7.00 C 5564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 99 " distance=2.03 Simple disulfide: pdb=" SG CYS M 24 " - pdb=" SG CYS M 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.42 Conformation dependent library (CDL) restraints added in 1.7 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 23 sheets defined 4.5% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'B' and resid 66 through 69 No H-bonds generated for 'chain 'B' and resid 66 through 69' Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 91 through 93 No H-bonds generated for 'chain 'I' and resid 91 through 93' Processing helix chain 'M' and resid 81 through 83 No H-bonds generated for 'chain 'M' and resid 81 through 83' Processing sheet with id= A, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.516A pdb=" N LEU A 22 " --> pdb=" O PHE A 9 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 19 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 39 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 115 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 26 through 29 removed outlier: 6.810A pdb=" N ARG A 169 " --> pdb=" O PHE A 27 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASP A 29 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A 171 " --> pdb=" O ASP A 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 163 through 166 removed outlier: 3.750A pdb=" N PHE A 80 " --> pdb=" O CYS A 59 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE A 61 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASP A 78 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR A 63 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ARG A 76 " --> pdb=" O TYR A 63 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 127 through 129 Processing sheet with id= E, first strand: chain 'A' and resid 183 through 188 removed outlier: 3.524A pdb=" N LYS A 270 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 246 through 248 removed outlier: 3.795A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 231 through 237 removed outlier: 5.617A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 7 through 10 removed outlier: 3.639A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 60 through 63 removed outlier: 3.600A pdb=" N TYR H 60 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ARG H 103 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N LEU H 110 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= K, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.040A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'L' and resid 86 through 91 removed outlier: 6.294A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 9 through 12 removed outlier: 3.561A pdb=" N GLY B 39 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE B 115 " --> pdb=" O GLY B 39 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 26 through 29 removed outlier: 6.621A pdb=" N ARG B 169 " --> pdb=" O PHE B 27 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ASP B 29 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 171 " --> pdb=" O ASP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'B' and resid 164 through 168 removed outlier: 4.008A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE B 61 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 78 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 127 through 129 Processing sheet with id= Q, first strand: chain 'B' and resid 183 through 188 Processing sheet with id= R, first strand: chain 'B' and resid 343 through 349 removed outlier: 4.248A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 254 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLN B 237 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ALA B 239 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS B 250 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 7 through 10 Processing sheet with id= T, first strand: chain 'I' and resid 60 through 63 removed outlier: 3.623A pdb=" N TYR I 60 " --> pdb=" O SER I 55 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TRP I 39 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER I 53 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE I 37 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N SER I 55 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER I 35 " --> pdb=" O SER I 55 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR I 112 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ARG I 103 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N LEU I 110 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'M' and resid 5 through 8 Processing sheet with id= V, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.061A pdb=" N LYS M 104 " --> pdb=" O LEU M 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'M' and resid 86 through 91 removed outlier: 3.885A pdb=" N THR M 86 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN M 38 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU M 47 " --> pdb=" O GLN M 38 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 741 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: 2.53 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2099 1.33 - 1.45: 1728 1.45 - 1.57: 5030 1.57 - 1.69: 16 1.69 - 1.81: 44 Bond restraints: 8917 Sorted by residual: bond pdb=" O1P SEP V 348 " pdb=" P SEP V 348 " ideal model delta sigma weight residual 1.610 1.504 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" O3P SEP U 351 " pdb=" P SEP U 351 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" O3P SEP V 351 " pdb=" P SEP V 351 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" O1P SEP V 351 " pdb=" P SEP V 351 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" O2P SEP U 351 " pdb=" P SEP U 351 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.51e+01 ... (remaining 8912 not shown) Histogram of bond angle deviations from ideal: 98.20 - 105.35: 234 105.35 - 112.50: 4716 112.50 - 119.64: 2764 119.64 - 126.79: 4323 126.79 - 133.94: 109 Bond angle restraints: 12146 Sorted by residual: angle pdb=" CA PRO A 180 " pdb=" N PRO A 180 " pdb=" CD PRO A 180 " ideal model delta sigma weight residual 112.00 104.52 7.48 1.40e+00 5.10e-01 2.85e+01 angle pdb=" C GLN M 39 " pdb=" CA GLN M 39 " pdb=" CB GLN M 39 " ideal model delta sigma weight residual 111.77 103.75 8.02 1.52e+00 4.33e-01 2.78e+01 angle pdb=" C SER L 31 " pdb=" CA SER L 31 " pdb=" CB SER L 31 " ideal model delta sigma weight residual 116.34 110.85 5.49 1.40e+00 5.10e-01 1.54e+01 angle pdb=" CA GLN M 90 " pdb=" C GLN M 90 " pdb=" O GLN M 90 " ideal model delta sigma weight residual 120.32 116.33 3.99 1.11e+00 8.12e-01 1.30e+01 angle pdb=" CA TYR M 37 " pdb=" C TYR M 37 " pdb=" O TYR M 37 " ideal model delta sigma weight residual 120.66 116.72 3.94 1.15e+00 7.56e-01 1.18e+01 ... (remaining 12141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4905 17.85 - 35.70: 336 35.70 - 53.56: 87 53.56 - 71.41: 19 71.41 - 89.26: 11 Dihedral angle restraints: 5358 sinusoidal: 2023 harmonic: 3335 Sorted by residual: dihedral pdb=" CB CYS I 25 " pdb=" SG CYS I 25 " pdb=" SG CYS I 99 " pdb=" CB CYS I 99 " ideal model delta sinusoidal sigma weight residual 93.00 58.38 34.62 1 1.00e+01 1.00e-02 1.70e+01 dihedral pdb=" C TYR M 37 " pdb=" N TYR M 37 " pdb=" CA TYR M 37 " pdb=" CB TYR M 37 " ideal model delta harmonic sigma weight residual -122.60 -114.13 -8.47 0 2.50e+00 1.60e-01 1.15e+01 dihedral pdb=" CA LYS I 79 " pdb=" C LYS I 79 " pdb=" N ASN I 80 " pdb=" CA ASN I 80 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 5355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1227 0.066 - 0.132: 163 0.132 - 0.198: 4 0.198 - 0.264: 3 0.264 - 0.331: 2 Chirality restraints: 1399 Sorted by residual: chirality pdb=" CA ILE U 352 " pdb=" N ILE U 352 " pdb=" C ILE U 352 " pdb=" CB ILE U 352 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA TYR B 249 " pdb=" N TYR B 249 " pdb=" C TYR B 249 " pdb=" CB TYR B 249 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA TYR M 37 " pdb=" N TYR M 37 " pdb=" C TYR M 37 " pdb=" CB TYR M 37 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1396 not shown) Planarity restraints: 1538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS V 347 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C CYS V 347 " 0.036 2.00e-02 2.50e+03 pdb=" O CYS V 347 " -0.014 2.00e-02 2.50e+03 pdb=" N SEP V 348 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 251 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO B 252 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 252 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 252 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 179 " -0.031 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 180 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 180 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 180 " -0.025 5.00e-02 4.00e+02 ... (remaining 1535 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 240 2.67 - 3.23: 8442 3.23 - 3.79: 12420 3.79 - 4.34: 17236 4.34 - 4.90: 29740 Nonbonded interactions: 68078 Sorted by model distance: nonbonded pdb=" N GLU B 50 " pdb=" OE1 GLU B 50 " model vdw 2.118 2.520 nonbonded pdb=" N GLU L 82 " pdb=" OE1 GLU L 82 " model vdw 2.239 2.520 nonbonded pdb=" N GLU M 82 " pdb=" OE1 GLU M 82 " model vdw 2.274 2.520 nonbonded pdb=" O LEU A 68 " pdb=" ND2 ASN B 245 " model vdw 2.299 2.520 nonbonded pdb=" O ASN H 87 " pdb=" OG SER H 88 " model vdw 2.302 2.440 ... (remaining 68073 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 66 or (resid 67 and (name N or name \ CA or name C or name O or name CB )) or resid 68 or (resid 69 and (name N or na \ me CA or name C or name O or name CB )) or resid 70 through 133 or (resid 134 th \ rough 135 and (name N or name CA or name C or name O or name CB )) or resid 136 \ through 159 or (resid 160 through 161 and (name N or name CA or name C or name O \ or name CB )) or resid 162 through 175 or (resid 176 through 177 and (name N or \ name CA or name C or name O or name CB )) or resid 178 through 357)) selection = (chain 'B' and (resid 6 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB )) or resid 72 through 76 or (resid 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 134 or (resid 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 through 156 or \ (resid 157 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 8 through 176 or (resid 177 and (name N or name CA or name C or name O or name C \ B )) or resid 178 through 214 or (resid 215 and (name N or name CA or name C or \ name O or name CB )) or resid 216 through 248 or (resid 249 and (name N or name \ CA or name C or name O or name CB )) or resid 250 through 284 or (resid 285 and \ (name N or name CA or name C or name O or name CB )) or resid 286 through 357)) } ncs_group { reference = (chain 'H' and (resid 5 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 through 121)) selection = chain 'I' } ncs_group { reference = (chain 'L' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 50 or (resid 51 through 52 and (name N \ or name CA or name C or name O or name CB )) or resid 53 through 89 or (resid 9 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 91 through 1 \ 07)) selection = chain 'M' } ncs_group { reference = chain 'U' selection = chain 'V' } 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.390 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.660 Find NCS groups from input model: 0.500 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 0.118 8917 Z= 0.359 Angle : 0.730 8.694 12146 Z= 0.399 Chirality : 0.047 0.331 1399 Planarity : 0.004 0.046 1538 Dihedral : 14.135 89.261 3202 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.86 % Allowed : 13.89 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: -0.49 (0.26), residues: 1112 helix: -1.05 (0.79), residues: 36 sheet: -0.30 (0.23), residues: 526 loop : -0.13 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 50 HIS 0.006 0.001 HIS A 159 PHE 0.012 0.001 PHE M 99 TYR 0.016 0.001 TYR L 94 ARG 0.005 0.001 ARG M 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 1.129 Fit side-chains REVERT: H 33 TYR cc_start: 0.8669 (m-80) cc_final: 0.8368 (m-80) REVERT: H 49 GLU cc_start: 0.8121 (tt0) cc_final: 0.7808 (pt0) REVERT: L 106 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7067 (mt-10) REVERT: B 272 TYR cc_start: 0.7460 (m-80) cc_final: 0.7086 (m-10) REVERT: B 321 TYR cc_start: 0.8221 (m-80) cc_final: 0.7774 (m-80) REVERT: I 33 TYR cc_start: 0.8730 (m-80) cc_final: 0.8390 (m-80) REVERT: I 79 LYS cc_start: 0.8276 (ptpp) cc_final: 0.8071 (ptpp) REVERT: I 102 SER cc_start: 0.9151 (t) cc_final: 0.8880 (p) REVERT: M 28 GLN cc_start: 0.7027 (mp10) cc_final: 0.6653 (mp10) outliers start: 8 outliers final: 5 residues processed: 148 average time/residue: 0.2214 time to fit residues: 45.2007 Evaluate side-chains 129 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain U residue 347 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN L 28 GLN L 39 GLN I 42 GLN M 38 GLN M 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8917 Z= 0.316 Angle : 0.654 6.473 12146 Z= 0.335 Chirality : 0.046 0.139 1399 Planarity : 0.004 0.043 1538 Dihedral : 6.453 59.641 1261 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.83 % Allowed : 14.75 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: -0.29 (0.26), residues: 1112 helix: -0.40 (0.87), residues: 36 sheet: -0.21 (0.22), residues: 562 loop : 0.04 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 50 HIS 0.005 0.001 HIS B 353 PHE 0.016 0.002 PHE A 268 TYR 0.015 0.002 TYR A 238 ARG 0.007 0.001 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.128 Fit side-chains REVERT: A 144 TYR cc_start: 0.7978 (m-80) cc_final: 0.7287 (m-10) REVERT: H 33 TYR cc_start: 0.8859 (m-80) cc_final: 0.8545 (m-80) REVERT: H 49 GLU cc_start: 0.7935 (tt0) cc_final: 0.7632 (pt0) REVERT: H 87 ASN cc_start: 0.8036 (m-40) cc_final: 0.7765 (m-40) REVERT: L 5 MET cc_start: 0.9058 (mmt) cc_final: 0.8245 (mmt) REVERT: L 106 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6973 (mt-10) REVERT: B 321 TYR cc_start: 0.8351 (m-80) cc_final: 0.8089 (m-80) REVERT: I 87 ASN cc_start: 0.8080 (m-40) cc_final: 0.7799 (m-40) REVERT: I 89 LEU cc_start: 0.7877 (mm) cc_final: 0.7453 (mm) outliers start: 17 outliers final: 10 residues processed: 143 average time/residue: 0.2027 time to fit residues: 40.8949 Evaluate side-chains 128 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 0.0060 chunk 68 optimal weight: 0.2980 chunk 27 optimal weight: 0.0170 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 0.0770 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 overall best weight: 0.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN H 80 ASN L 28 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8917 Z= 0.152 Angle : 0.544 5.121 12146 Z= 0.279 Chirality : 0.043 0.137 1399 Planarity : 0.004 0.037 1538 Dihedral : 5.737 61.253 1252 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.58 % Allowed : 14.64 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: -0.02 (0.26), residues: 1112 helix: 2.02 (1.07), residues: 24 sheet: -0.02 (0.22), residues: 536 loop : 0.06 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 50 HIS 0.004 0.001 HIS A 159 PHE 0.010 0.001 PHE A 268 TYR 0.012 0.001 TYR B 272 ARG 0.006 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: H 22 ARG cc_start: 0.7712 (ttt90) cc_final: 0.7346 (ttm170) REVERT: H 49 GLU cc_start: 0.7922 (tt0) cc_final: 0.7613 (pt0) REVERT: H 87 ASN cc_start: 0.7918 (m-40) cc_final: 0.7684 (m-40) REVERT: L 5 MET cc_start: 0.9009 (mmt) cc_final: 0.8598 (mmt) REVERT: B 75 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7167 (p90) REVERT: B 314 ILE cc_start: 0.7395 (mm) cc_final: 0.6966 (mp) REVERT: B 321 TYR cc_start: 0.8267 (m-80) cc_final: 0.8010 (m-80) REVERT: I 89 LEU cc_start: 0.7830 (mm) cc_final: 0.7461 (mm) outliers start: 24 outliers final: 13 residues processed: 154 average time/residue: 0.1937 time to fit residues: 42.4308 Evaluate side-chains 135 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain M residue 2 ASP Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 0.2980 chunk 106 optimal weight: 0.0470 chunk 52 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN L 7 GLN L 28 GLN L 90 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8917 Z= 0.201 Angle : 0.546 4.970 12146 Z= 0.280 Chirality : 0.043 0.131 1399 Planarity : 0.004 0.038 1538 Dihedral : 5.668 59.520 1252 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.34 % Allowed : 15.72 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: 0.07 (0.26), residues: 1112 helix: 2.13 (1.08), residues: 24 sheet: 0.01 (0.22), residues: 574 loop : 0.18 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 50 HIS 0.004 0.001 HIS B 353 PHE 0.014 0.002 PHE B 87 TYR 0.014 0.001 TYR B 54 ARG 0.005 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 129 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 144 TYR cc_start: 0.7976 (m-80) cc_final: 0.7106 (m-10) REVERT: A 321 TYR cc_start: 0.8302 (m-80) cc_final: 0.7875 (m-80) REVERT: H 49 GLU cc_start: 0.7943 (tt0) cc_final: 0.7618 (pt0) REVERT: B 75 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7531 (p90) REVERT: B 255 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7892 (tmm) REVERT: B 314 ILE cc_start: 0.7659 (mm) cc_final: 0.7301 (mp) REVERT: I 41 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7654 (ptt180) REVERT: I 89 LEU cc_start: 0.7739 (mm) cc_final: 0.7461 (mm) outliers start: 31 outliers final: 18 residues processed: 149 average time/residue: 0.2097 time to fit residues: 43.6188 Evaluate side-chains 141 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.0000 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.0570 chunk 95 optimal weight: 0.0870 chunk 26 optimal weight: 1.9990 overall best weight: 0.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN B 101 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8917 Z= 0.207 Angle : 0.540 6.177 12146 Z= 0.275 Chirality : 0.043 0.130 1399 Planarity : 0.004 0.039 1538 Dihedral : 5.624 59.830 1252 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.34 % Allowed : 16.25 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: 0.07 (0.26), residues: 1112 helix: 2.24 (1.08), residues: 24 sheet: 0.02 (0.22), residues: 576 loop : 0.17 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 50 HIS 0.003 0.001 HIS B 353 PHE 0.013 0.001 PHE A 277 TYR 0.013 0.001 TYR B 272 ARG 0.004 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 1.095 Fit side-chains REVERT: A 321 TYR cc_start: 0.8293 (m-80) cc_final: 0.7841 (m-80) REVERT: H 87 ASN cc_start: 0.8129 (m-40) cc_final: 0.7764 (m-40) REVERT: B 75 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7478 (p90) REVERT: B 314 ILE cc_start: 0.7830 (mm) cc_final: 0.7407 (mp) REVERT: B 321 TYR cc_start: 0.8214 (m-80) cc_final: 0.7738 (m-80) REVERT: I 41 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7681 (ptt180) REVERT: I 89 LEU cc_start: 0.7683 (mm) cc_final: 0.7376 (mm) outliers start: 31 outliers final: 23 residues processed: 148 average time/residue: 0.2007 time to fit residues: 41.6798 Evaluate side-chains 140 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 115 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.0770 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN L 28 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8917 Z= 0.208 Angle : 0.546 8.200 12146 Z= 0.277 Chirality : 0.043 0.137 1399 Planarity : 0.004 0.039 1538 Dihedral : 5.567 59.923 1252 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.55 % Allowed : 16.68 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: 0.14 (0.26), residues: 1112 helix: 2.33 (1.07), residues: 24 sheet: 0.08 (0.22), residues: 574 loop : 0.18 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 50 HIS 0.003 0.001 HIS B 353 PHE 0.016 0.001 PHE B 87 TYR 0.012 0.001 TYR L 37 ARG 0.006 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 120 time to evaluate : 0.980 Fit side-chains REVERT: A 321 TYR cc_start: 0.8315 (m-80) cc_final: 0.7884 (m-80) REVERT: H 87 ASN cc_start: 0.8024 (m-40) cc_final: 0.7715 (m-40) REVERT: B 75 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.7525 (p90) REVERT: B 314 ILE cc_start: 0.7827 (mm) cc_final: 0.7442 (mp) REVERT: B 321 TYR cc_start: 0.8400 (m-80) cc_final: 0.7950 (m-80) REVERT: I 41 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7683 (ptt180) REVERT: I 89 LEU cc_start: 0.7666 (mm) cc_final: 0.7337 (mm) outliers start: 33 outliers final: 25 residues processed: 144 average time/residue: 0.1911 time to fit residues: 39.3244 Evaluate side-chains 143 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain V residue 353 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.0030 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8917 Z= 0.224 Angle : 0.550 6.664 12146 Z= 0.279 Chirality : 0.043 0.133 1399 Planarity : 0.004 0.041 1538 Dihedral : 5.556 59.270 1252 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.44 % Allowed : 17.55 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.26), residues: 1112 helix: 2.31 (1.06), residues: 24 sheet: 0.06 (0.22), residues: 576 loop : 0.19 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.004 0.001 HIS B 353 PHE 0.012 0.001 PHE A 277 TYR 0.016 0.001 TYR L 37 ARG 0.005 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 125 time to evaluate : 1.002 Fit side-chains REVERT: A 321 TYR cc_start: 0.8234 (m-80) cc_final: 0.7861 (m-80) REVERT: H 87 ASN cc_start: 0.8043 (m-40) cc_final: 0.7736 (m-40) REVERT: B 75 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7545 (p90) REVERT: B 242 CYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7770 (p) REVERT: B 314 ILE cc_start: 0.7851 (mm) cc_final: 0.7353 (mp) REVERT: B 321 TYR cc_start: 0.8403 (m-80) cc_final: 0.7893 (m-80) REVERT: I 33 TYR cc_start: 0.8700 (m-80) cc_final: 0.8423 (m-80) REVERT: I 41 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7698 (ptt180) REVERT: I 89 LEU cc_start: 0.7624 (mm) cc_final: 0.7270 (mm) outliers start: 32 outliers final: 22 residues processed: 146 average time/residue: 0.1971 time to fit residues: 40.7080 Evaluate side-chains 145 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.0040 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8917 Z= 0.222 Angle : 0.558 7.621 12146 Z= 0.282 Chirality : 0.043 0.135 1399 Planarity : 0.004 0.041 1538 Dihedral : 5.516 59.422 1252 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.66 % Allowed : 17.44 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: 0.06 (0.26), residues: 1112 helix: 0.38 (0.95), residues: 36 sheet: 0.07 (0.22), residues: 574 loop : 0.18 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 50 HIS 0.004 0.001 HIS A 353 PHE 0.021 0.002 PHE B 87 TYR 0.013 0.001 TYR L 37 ARG 0.005 0.000 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 124 time to evaluate : 1.063 Fit side-chains REVERT: A 321 TYR cc_start: 0.8213 (m-80) cc_final: 0.7844 (m-80) REVERT: H 87 ASN cc_start: 0.8039 (m-40) cc_final: 0.7749 (m-40) REVERT: H 101 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8444 (tmm160) REVERT: B 75 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.7681 (p90) REVERT: B 177 ARG cc_start: 0.7303 (tmm160) cc_final: 0.7076 (tmm160) REVERT: B 242 CYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7638 (p) REVERT: B 314 ILE cc_start: 0.7841 (mm) cc_final: 0.7376 (mp) REVERT: B 321 TYR cc_start: 0.8366 (m-80) cc_final: 0.7870 (m-80) REVERT: I 33 TYR cc_start: 0.8700 (m-80) cc_final: 0.8418 (m-80) REVERT: I 41 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7686 (ptt180) REVERT: I 89 LEU cc_start: 0.7582 (mm) cc_final: 0.7271 (mm) outliers start: 34 outliers final: 24 residues processed: 146 average time/residue: 0.1953 time to fit residues: 40.5383 Evaluate side-chains 149 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 30 optimal weight: 0.0010 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 104 optimal weight: 0.0170 chunk 63 optimal weight: 0.5980 overall best weight: 0.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8917 Z= 0.177 Angle : 0.552 8.183 12146 Z= 0.276 Chirality : 0.043 0.130 1399 Planarity : 0.004 0.040 1538 Dihedral : 5.375 60.714 1252 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.12 % Allowed : 18.19 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: 0.09 (0.26), residues: 1112 helix: -0.06 (0.82), residues: 48 sheet: 0.12 (0.22), residues: 574 loop : 0.20 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 50 HIS 0.003 0.001 HIS A 353 PHE 0.018 0.001 PHE A 87 TYR 0.013 0.001 TYR L 37 ARG 0.004 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 0.982 Fit side-chains REVERT: A 321 TYR cc_start: 0.8373 (m-80) cc_final: 0.7942 (m-80) REVERT: H 87 ASN cc_start: 0.7990 (m-40) cc_final: 0.7693 (m-40) REVERT: H 101 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8425 (tmm160) REVERT: L 82 GLU cc_start: 0.7541 (pm20) cc_final: 0.7145 (pm20) REVERT: B 75 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7239 (p90) REVERT: B 195 LYS cc_start: 0.7393 (mmmt) cc_final: 0.7097 (mmmt) REVERT: B 242 CYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7758 (p) REVERT: B 314 ILE cc_start: 0.7800 (mm) cc_final: 0.7422 (mp) REVERT: B 321 TYR cc_start: 0.8356 (m-80) cc_final: 0.7832 (m-80) REVERT: I 41 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7649 (ptt180) REVERT: I 89 LEU cc_start: 0.7537 (mm) cc_final: 0.7205 (mm) REVERT: M 94 TYR cc_start: 0.7317 (m-80) cc_final: 0.7078 (m-10) outliers start: 29 outliers final: 20 residues processed: 143 average time/residue: 0.2057 time to fit residues: 41.3213 Evaluate side-chains 146 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.0070 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 67 optimal weight: 0.5980 chunk 53 optimal weight: 0.0870 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8917 Z= 0.182 Angle : 0.553 8.275 12146 Z= 0.276 Chirality : 0.043 0.130 1399 Planarity : 0.004 0.053 1538 Dihedral : 5.349 60.268 1252 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.69 % Allowed : 19.05 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: 0.10 (0.26), residues: 1112 helix: -0.12 (0.82), residues: 48 sheet: 0.18 (0.22), residues: 558 loop : 0.13 (0.30), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 50 HIS 0.003 0.001 HIS B 353 PHE 0.025 0.001 PHE B 87 TYR 0.013 0.001 TYR L 37 ARG 0.011 0.000 ARG B 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 1.050 Fit side-chains REVERT: A 321 TYR cc_start: 0.8281 (m-80) cc_final: 0.7882 (m-80) REVERT: H 87 ASN cc_start: 0.7993 (m-40) cc_final: 0.7671 (m-40) REVERT: H 101 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8317 (tmm160) REVERT: L 82 GLU cc_start: 0.7536 (pm20) cc_final: 0.7151 (pm20) REVERT: B 75 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7256 (p90) REVERT: B 177 ARG cc_start: 0.7063 (tmm160) cc_final: 0.6789 (tmm160) REVERT: B 242 CYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7630 (p) REVERT: B 314 ILE cc_start: 0.7886 (mm) cc_final: 0.7499 (mp) REVERT: B 321 TYR cc_start: 0.8352 (m-80) cc_final: 0.7831 (m-80) REVERT: B 352 MET cc_start: 0.8812 (ptp) cc_final: 0.8557 (ptp) REVERT: I 41 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7640 (ptt180) REVERT: I 89 LEU cc_start: 0.7501 (mm) cc_final: 0.7179 (mm) REVERT: M 94 TYR cc_start: 0.7148 (m-80) cc_final: 0.6919 (m-10) outliers start: 25 outliers final: 20 residues processed: 140 average time/residue: 0.2039 time to fit residues: 40.1315 Evaluate side-chains 146 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain I residue 41 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 5.9990 chunk 12 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 0.0170 chunk 63 optimal weight: 0.0040 overall best weight: 0.3430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.144240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.116958 restraints weight = 14356.782| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.98 r_work: 0.3415 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8917 Z= 0.176 Angle : 0.553 8.374 12146 Z= 0.273 Chirality : 0.043 0.130 1399 Planarity : 0.004 0.040 1538 Dihedral : 5.304 60.071 1252 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.58 % Allowed : 19.05 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.19 % 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: 0.21 (0.26), residues: 1112 helix: 0.88 (0.91), residues: 36 sheet: 0.24 (0.23), residues: 558 loop : 0.15 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 50 HIS 0.003 0.001 HIS B 353 PHE 0.023 0.001 PHE B 87 TYR 0.012 0.001 TYR L 37 ARG 0.008 0.000 ARG B 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2150.66 seconds wall clock time: 40 minutes 8.01 seconds (2408.01 seconds total)