Starting phenix.real_space_refine on Sat Jul 20 06:39:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q85_18247/07_2024/8q85_18247.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q85_18247/07_2024/8q85_18247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q85_18247/07_2024/8q85_18247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q85_18247/07_2024/8q85_18247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q85_18247/07_2024/8q85_18247.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q85_18247/07_2024/8q85_18247.cif" } resolution = 3.97 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 6366 2.51 5 N 1836 2.21 5 O 2056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "U ASP 72": "OD1" <-> "OD2" Residue "U GLU 89": "OE1" <-> "OE2" Residue "U GLU 96": "OE1" <-> "OE2" Residue "U ASP 123": "OD1" <-> "OD2" Residue "U GLU 144": "OE1" <-> "OE2" Residue "V ASP 72": "OD1" <-> "OD2" Residue "V GLU 98": "OE1" <-> "OE2" Residue "V ASP 108": "OD1" <-> "OD2" Residue "W ASP 26": "OD1" <-> "OD2" Residue "W GLU 34": "OE1" <-> "OE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W ASP 57": "OD1" <-> "OD2" Residue "W GLU 75": "OE1" <-> "OE2" Residue "W GLU 79": "OE1" <-> "OE2" Residue "W ASP 116": "OD1" <-> "OD2" Residue "W GLU 122": "OE1" <-> "OE2" Residue "W ASP 130": "OD1" <-> "OD2" Residue "Y GLU 63": "OE1" <-> "OE2" Residue "Z GLU 11": "OE1" <-> "OE2" Residue "Z TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 32": "OE1" <-> "OE2" Residue "Z GLU 56": "OE1" <-> "OE2" Residue "Z GLU 85": "OE1" <-> "OE2" Residue "a ASP 10": "OD1" <-> "OD2" Residue "a ASP 17": "OD1" <-> "OD2" Residue "a TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 69": "OE1" <-> "OE2" Residue "a GLU 80": "OE1" <-> "OE2" Residue "a PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 104": "OE1" <-> "OE2" Residue "a TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 182": "OE1" <-> "OE2" Residue "a PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 231": "OD1" <-> "OD2" Residue "a GLU 238": "OE1" <-> "OE2" Residue "b ASP 38": "OD1" <-> "OD2" Residue "b GLU 48": "OE1" <-> "OE2" Residue "b ASP 55": "OD1" <-> "OD2" Residue "b PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 25": "OE1" <-> "OE2" Residue "c GLU 39": "OE1" <-> "OE2" Residue "c TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 3": "OD1" <-> "OD2" Residue "d GLU 6": "OE1" <-> "OE2" Residue "d GLU 24": "OE1" <-> "OE2" Residue "d GLU 67": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10299 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1145 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 1, 'TRANS': 228} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 744 Unresolved non-hydrogen angles: 925 Unresolved non-hydrogen dihedrals: 593 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 18, 'ASP:plan': 14, 'PHE:plan': 5, 'GLU:plan': 26, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 374 Chain: "G" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 886 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 173} Link IDs: {'PTRANS': 1, 'TRANS': 176} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 588 Unresolved non-hydrogen angles: 740 Unresolved non-hydrogen dihedrals: 460 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 13, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 23, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 292 Chain: "U" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "V" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 935 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain: "W" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 837 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "X" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 535 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "Y" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "Z" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 761 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "a" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1925 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Chain breaks: 1 Chain: "b" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 561 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "c" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 527 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "d" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 859 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Time building chain proxies: 6.49, per 1000 atoms: 0.63 Number of scatterers: 10299 At special positions: 0 Unit cell: (203.52, 142.04, 216.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 2056 8.00 N 1836 7.00 C 6366 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 - 3.50 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: 4.38 Conformation dependent library (CDL) restraints added in 2.1 seconds 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2776 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 86.6% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'F' and resid 434 through 478 Processing helix chain 'F' and resid 484 through 489 removed outlier: 3.688A pdb=" N LEU F 488 " --> pdb=" O ASN F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 511 removed outlier: 3.776A pdb=" N LEU F 510 " --> pdb=" O SER F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 663 Processing helix chain 'G' and resid 271 through 307 Processing helix chain 'G' and resid 307 through 337 Processing helix chain 'G' and resid 339 through 386 Processing helix chain 'G' and resid 386 through 400 Processing helix chain 'G' and resid 405 through 446 Processing helix chain 'U' and resid 58 through 110 Proline residue: U 65 - end of helix Processing helix chain 'U' and resid 120 through 151 Processing helix chain 'V' and resid 61 through 125 removed outlier: 4.618A pdb=" N LEU V 89 " --> pdb=" O LEU V 85 " (cutoff:3.500A) Proline residue: V 90 - end of helix Processing helix chain 'V' and resid 126 through 143 removed outlier: 3.670A pdb=" N LEU V 130 " --> pdb=" O ASP V 126 " (cutoff:3.500A) Processing helix chain 'V' and resid 146 through 150 Processing helix chain 'V' and resid 151 through 176 Processing helix chain 'W' and resid 3 through 67 removed outlier: 4.104A pdb=" N GLN W 7 " --> pdb=" O SER W 3 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASN W 55 " --> pdb=" O GLN W 51 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TRP W 56 " --> pdb=" O LEU W 52 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP W 57 " --> pdb=" O MET W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 73 Processing helix chain 'W' and resid 74 through 78 Processing helix chain 'W' and resid 80 through 84 Processing helix chain 'X' and resid 14 through 57 Processing helix chain 'X' and resid 58 through 67 removed outlier: 3.897A pdb=" N VAL X 62 " --> pdb=" O GLU X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 80 removed outlier: 4.066A pdb=" N ASP X 78 " --> pdb=" O GLU X 74 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA X 80 " --> pdb=" O LEU X 76 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 41 removed outlier: 4.189A pdb=" N VAL Y 8 " --> pdb=" O PRO Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 41 through 65 removed outlier: 4.030A pdb=" N GLU Y 45 " --> pdb=" O ASN Y 41 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE Y 46 " --> pdb=" O LYS Y 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 6 through 35 Processing helix chain 'Z' and resid 53 through 65 removed outlier: 3.523A pdb=" N ASP Z 59 " --> pdb=" O GLN Z 55 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS Z 63 " --> pdb=" O ASP Z 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 94 removed outlier: 3.509A pdb=" N LYS Z 72 " --> pdb=" O GLY Z 68 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL Z 75 " --> pdb=" O LEU Z 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 22 Processing helix chain 'a' and resid 28 through 37 removed outlier: 3.941A pdb=" N ASN a 32 " --> pdb=" O GLY a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 40 through 51 Processing helix chain 'a' and resid 56 through 63 Processing helix chain 'a' and resid 81 through 99 Processing helix chain 'a' and resid 111 through 125 removed outlier: 3.570A pdb=" N TYR a 115 " --> pdb=" O PRO a 111 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS a 118 " --> pdb=" O VAL a 114 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU a 121 " --> pdb=" O ASN a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 158 through 168 Processing helix chain 'a' and resid 171 through 183 Processing helix chain 'a' and resid 203 through 205 No H-bonds generated for 'chain 'a' and resid 203 through 205' Processing helix chain 'a' and resid 206 through 221 removed outlier: 3.516A pdb=" N ILE a 210 " --> pdb=" O PRO a 206 " (cutoff:3.500A) Processing helix chain 'a' and resid 223 through 265 removed outlier: 4.068A pdb=" N SER a 242 " --> pdb=" O GLU a 238 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 38 Processing helix chain 'b' and resid 38 through 57 removed outlier: 3.512A pdb=" N THR b 57 " --> pdb=" O ILE b 53 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 69 removed outlier: 3.532A pdb=" N GLY b 61 " --> pdb=" O THR b 57 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR b 67 " --> pdb=" O MET b 63 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 40 Processing helix chain 'c' and resid 44 through 63 Processing helix chain 'd' and resid 2 through 40 Proline residue: d 32 - end of helix removed outlier: 3.676A pdb=" N THR d 39 " --> pdb=" O ASN d 35 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET d 40 " --> pdb=" O LEU d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 65 Processing helix chain 'd' and resid 65 through 108 Processing sheet with id=AA1, first strand: chain 'U' and resid 112 through 113 Processing sheet with id=AA2, first strand: chain 'a' and resid 52 through 54 Processing sheet with id=AA3, first strand: chain 'a' and resid 64 through 67 Processing sheet with id=AA4, first strand: chain 'a' and resid 185 through 189 1042 hydrogen bonds defined for protein. 3102 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3628 1.34 - 1.46: 1787 1.46 - 1.58: 4905 1.58 - 1.70: 1 1.70 - 1.82: 73 Bond restraints: 10394 Sorted by residual: bond pdb=" CB PRO Z 7 " pdb=" CG PRO Z 7 " ideal model delta sigma weight residual 1.492 1.620 -0.128 5.00e-02 4.00e+02 6.56e+00 bond pdb=" CG GLU b 16 " pdb=" CD GLU b 16 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.30e+00 bond pdb=" CB ILE a 247 " pdb=" CG2 ILE a 247 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.30e+00 bond pdb=" CB ASP b 25 " pdb=" CG ASP b 25 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.70e+00 bond pdb=" CG ASP Z 22 " pdb=" OD1 ASP Z 22 " ideal model delta sigma weight residual 1.249 1.225 0.024 1.90e-02 2.77e+03 1.63e+00 ... (remaining 10389 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.21: 143 106.21 - 113.17: 5814 113.17 - 120.12: 3603 120.12 - 127.07: 4476 127.07 - 134.02: 62 Bond angle restraints: 14098 Sorted by residual: angle pdb=" CA PRO Z 7 " pdb=" N PRO Z 7 " pdb=" CD PRO Z 7 " ideal model delta sigma weight residual 112.00 100.33 11.67 1.40e+00 5.10e-01 6.95e+01 angle pdb=" CA GLU Z 85 " pdb=" CB GLU Z 85 " pdb=" CG GLU Z 85 " ideal model delta sigma weight residual 114.10 125.15 -11.05 2.00e+00 2.50e-01 3.05e+01 angle pdb=" CA LYS Z 17 " pdb=" CB LYS Z 17 " pdb=" CG LYS Z 17 " ideal model delta sigma weight residual 114.10 124.41 -10.31 2.00e+00 2.50e-01 2.66e+01 angle pdb=" CA LEU Z 23 " pdb=" CB LEU Z 23 " pdb=" CG LEU Z 23 " ideal model delta sigma weight residual 116.30 133.77 -17.47 3.50e+00 8.16e-02 2.49e+01 angle pdb=" CA MET V 77 " pdb=" CB MET V 77 " pdb=" CG MET V 77 " ideal model delta sigma weight residual 114.10 123.75 -9.65 2.00e+00 2.50e-01 2.33e+01 ... (remaining 14093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 5609 17.88 - 35.76: 618 35.76 - 53.63: 142 53.63 - 71.51: 38 71.51 - 89.39: 20 Dihedral angle restraints: 6427 sinusoidal: 2201 harmonic: 4226 Sorted by residual: dihedral pdb=" CA PHE a 64 " pdb=" C PHE a 64 " pdb=" N LYS a 65 " pdb=" CA LYS a 65 " ideal model delta harmonic sigma weight residual 180.00 154.02 25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA ILE Z 53 " pdb=" C ILE Z 53 " pdb=" N LEU Z 54 " pdb=" CA LEU Z 54 " ideal model delta harmonic sigma weight residual -180.00 -158.89 -21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA PRO Z 7 " pdb=" C PRO Z 7 " pdb=" N LEU Z 8 " pdb=" CA LEU Z 8 " ideal model delta harmonic sigma weight residual 180.00 161.06 18.94 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 6424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1640 0.106 - 0.213: 54 0.213 - 0.319: 1 0.319 - 0.426: 1 0.426 - 0.532: 1 Chirality restraints: 1697 Sorted by residual: chirality pdb=" CG LEU Z 23 " pdb=" CB LEU Z 23 " pdb=" CD1 LEU Z 23 " pdb=" CD2 LEU Z 23 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 7.07e+00 chirality pdb=" CA PRO Z 7 " pdb=" N PRO Z 7 " pdb=" C PRO Z 7 " pdb=" CB PRO Z 7 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB THR V 82 " pdb=" CA THR V 82 " pdb=" OG1 THR V 82 " pdb=" CG2 THR V 82 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1694 not shown) Planarity restraints: 1868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER Z 6 " 0.087 5.00e-02 4.00e+02 1.23e-01 2.43e+01 pdb=" N PRO Z 7 " -0.213 5.00e-02 4.00e+02 pdb=" CA PRO Z 7 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO Z 7 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP a 221 " 0.079 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO a 222 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO a 222 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO a 222 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS Y 69 " -0.047 5.00e-02 4.00e+02 6.97e-02 7.76e+00 pdb=" N PRO Y 70 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO Y 70 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO Y 70 " -0.038 5.00e-02 4.00e+02 ... (remaining 1865 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 346 2.70 - 3.25: 11884 3.25 - 3.80: 18387 3.80 - 4.35: 20876 4.35 - 4.90: 33178 Nonbonded interactions: 84671 Sorted by model distance: nonbonded pdb=" OG SER W 3 " pdb=" OD1 ASP W 5 " model vdw 2.146 2.440 nonbonded pdb=" O ALA a 15 " pdb=" OG SER a 18 " model vdw 2.159 2.440 nonbonded pdb=" O LYS V 73 " pdb=" NZ LYS V 73 " model vdw 2.170 2.520 nonbonded pdb=" O LEU G 336 " pdb=" N MET G 341 " model vdw 2.186 2.520 nonbonded pdb=" O LEU V 64 " pdb=" OG SER V 68 " model vdw 2.192 2.440 ... (remaining 84666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 31.370 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 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 : 0.004 0.128 10394 Z= 0.259 Angle : 0.923 17.470 14098 Z= 0.491 Chirality : 0.047 0.532 1697 Planarity : 0.007 0.123 1868 Dihedral : 17.196 89.389 3651 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.53 % Allowed : 31.30 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.93 (0.22), residues: 1408 helix: 1.67 (0.14), residues: 1181 sheet: -2.04 (1.08), residues: 12 loop : -0.54 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP b 59 HIS 0.006 0.001 HIS a 31 PHE 0.026 0.002 PHE a 83 TYR 0.028 0.002 TYR a 230 ARG 0.007 0.001 ARG d 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 234 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 34 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8038 (mm-30) REVERT: W 79 GLU cc_start: 0.8083 (mp0) cc_final: 0.7725 (pm20) REVERT: Y 1 MET cc_start: 0.3898 (OUTLIER) cc_final: 0.3238 (mmt) REVERT: Z 11 GLU cc_start: 0.9588 (tm-30) cc_final: 0.9220 (pp20) REVERT: Z 38 HIS cc_start: 0.6533 (p-80) cc_final: 0.5048 (p-80) REVERT: a 230 TYR cc_start: 0.8856 (t80) cc_final: 0.8228 (t80) REVERT: d 67 GLU cc_start: 0.8602 (tp30) cc_final: 0.8346 (tp30) outliers start: 5 outliers final: 1 residues processed: 235 average time/residue: 0.2389 time to fit residues: 76.2676 Evaluate side-chains 223 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 221 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain Y residue 1 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 50.0000 chunk 70 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 ASN Y 31 ASN ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 41 GLN ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 30 ASN ** d 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10394 Z= 0.206 Angle : 0.664 12.239 14098 Z= 0.337 Chirality : 0.041 0.475 1697 Planarity : 0.004 0.076 1868 Dihedral : 4.700 55.543 1503 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.62 % Allowed : 23.95 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.22), residues: 1408 helix: 2.60 (0.14), residues: 1179 sheet: -1.98 (1.03), residues: 12 loop : -0.48 (0.45), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 59 HIS 0.006 0.001 HIS a 31 PHE 0.021 0.002 PHE X 20 TYR 0.019 0.002 TYR Z 16 ARG 0.005 0.000 ARG V 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 244 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 89 GLU cc_start: 0.8280 (tm-30) cc_final: 0.8039 (tm-30) REVERT: U 93 ASP cc_start: 0.7976 (m-30) cc_final: 0.7766 (m-30) REVERT: U 120 ASP cc_start: 0.7885 (p0) cc_final: 0.7667 (p0) REVERT: W 34 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8037 (mm-30) REVERT: W 72 GLN cc_start: 0.8165 (tp40) cc_final: 0.7889 (tp-100) REVERT: W 75 GLU cc_start: 0.8305 (tp30) cc_final: 0.8075 (tm-30) REVERT: W 79 GLU cc_start: 0.8090 (mp0) cc_final: 0.7732 (pm20) REVERT: Z 17 LYS cc_start: 0.9555 (mmtt) cc_final: 0.9202 (mmtt) REVERT: Z 38 HIS cc_start: 0.6350 (OUTLIER) cc_final: 0.4769 (p-80) REVERT: a 93 MET cc_start: 0.7397 (mmt) cc_final: 0.6960 (mmm) REVERT: a 168 PHE cc_start: 0.8144 (m-80) cc_final: 0.6906 (m-80) REVERT: a 227 LYS cc_start: 0.9285 (mmmt) cc_final: 0.9002 (mmmt) REVERT: b 1 MET cc_start: 0.7918 (tmm) cc_final: 0.7556 (tmm) REVERT: d 57 ARG cc_start: 0.8841 (tpp80) cc_final: 0.8574 (tpp80) REVERT: d 63 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9056 (tp) outliers start: 44 outliers final: 18 residues processed: 268 average time/residue: 0.2298 time to fit residues: 84.4530 Evaluate side-chains 245 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 225 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 82 THR Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain W residue 118 VAL Chi-restraints excluded: chain W residue 122 GLU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 132 ASN Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 9 GLN Chi-restraints excluded: chain Y residue 51 CYS Chi-restraints excluded: chain Z residue 38 HIS Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 56 SER Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 63 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 104 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 40.0000 chunk 125 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 239 GLN ** c 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10394 Z= 0.194 Angle : 0.647 12.160 14098 Z= 0.324 Chirality : 0.039 0.276 1697 Planarity : 0.004 0.060 1868 Dihedral : 4.502 56.177 1500 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.10 % Allowed : 24.79 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.22), residues: 1408 helix: 2.85 (0.14), residues: 1183 sheet: -2.04 (1.04), residues: 12 loop : -0.41 (0.45), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 59 HIS 0.006 0.001 HIS a 31 PHE 0.019 0.002 PHE X 20 TYR 0.024 0.001 TYR a 230 ARG 0.005 0.000 ARG d 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 241 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 89 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7898 (tm-30) REVERT: U 93 ASP cc_start: 0.7959 (m-30) cc_final: 0.7628 (m-30) REVERT: U 98 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8499 (mm) REVERT: U 120 ASP cc_start: 0.7866 (p0) cc_final: 0.7650 (p0) REVERT: W 72 GLN cc_start: 0.8146 (tp40) cc_final: 0.7930 (tp-100) REVERT: W 79 GLU cc_start: 0.8025 (mp0) cc_final: 0.7676 (pm20) REVERT: X 47 ILE cc_start: 0.7627 (mt) cc_final: 0.7399 (mm) REVERT: Z 16 TYR cc_start: 0.7792 (m-80) cc_final: 0.6406 (m-80) REVERT: Z 17 LYS cc_start: 0.9625 (mmtt) cc_final: 0.9261 (mmtt) REVERT: Z 22 ASP cc_start: 0.8387 (t0) cc_final: 0.7790 (p0) REVERT: Z 38 HIS cc_start: 0.6332 (OUTLIER) cc_final: 0.4694 (p-80) REVERT: Z 51 ASP cc_start: 0.6721 (t0) cc_final: 0.6520 (p0) REVERT: a 227 LYS cc_start: 0.9302 (mmmt) cc_final: 0.9013 (mmmt) REVERT: a 230 TYR cc_start: 0.8886 (t80) cc_final: 0.8117 (t80) REVERT: a 259 LYS cc_start: 0.9426 (mmmt) cc_final: 0.9115 (mttp) REVERT: b 1 MET cc_start: 0.7886 (tmm) cc_final: 0.7464 (tmm) REVERT: d 63 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9077 (tp) REVERT: d 67 GLU cc_start: 0.8677 (tp30) cc_final: 0.8293 (tp30) outliers start: 39 outliers final: 21 residues processed: 261 average time/residue: 0.2417 time to fit residues: 87.2528 Evaluate side-chains 252 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 228 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 81 PHE Chi-restraints excluded: chain U residue 82 THR Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain W residue 118 VAL Chi-restraints excluded: chain W residue 132 ASN Chi-restraints excluded: chain X residue 58 GLU Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 9 GLN Chi-restraints excluded: chain Y residue 51 CYS Chi-restraints excluded: chain Z residue 38 HIS Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain d residue 2 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.7980 chunk 94 optimal weight: 0.1980 chunk 65 optimal weight: 0.7980 chunk 13 optimal weight: 40.0000 chunk 59 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 35 optimal weight: 50.0000 chunk 111 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 109 HIS a 239 GLN ** c 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10394 Z= 0.192 Angle : 0.644 13.155 14098 Z= 0.323 Chirality : 0.039 0.409 1697 Planarity : 0.004 0.049 1868 Dihedral : 4.473 56.664 1500 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.20 % Allowed : 26.05 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.22), residues: 1408 helix: 2.94 (0.14), residues: 1189 sheet: -1.01 (1.26), residues: 12 loop : -0.25 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 59 HIS 0.005 0.001 HIS a 31 PHE 0.021 0.002 PHE a 168 TYR 0.019 0.001 TYR a 230 ARG 0.006 0.000 ARG d 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 243 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 89 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7876 (tm-30) REVERT: U 93 ASP cc_start: 0.7979 (m-30) cc_final: 0.7598 (m-30) REVERT: U 94 LEU cc_start: 0.9037 (tp) cc_final: 0.8811 (tt) REVERT: U 98 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8463 (mm) REVERT: U 120 ASP cc_start: 0.7798 (p0) cc_final: 0.7580 (p0) REVERT: U 136 ASP cc_start: 0.9408 (m-30) cc_final: 0.9163 (p0) REVERT: V 77 MET cc_start: 0.9143 (ppp) cc_final: 0.8871 (ppp) REVERT: W 79 GLU cc_start: 0.8015 (mp0) cc_final: 0.7745 (pm20) REVERT: Z 16 TYR cc_start: 0.7801 (m-80) cc_final: 0.6435 (m-80) REVERT: Z 17 LYS cc_start: 0.9624 (mmtt) cc_final: 0.9280 (mmtt) REVERT: Z 38 HIS cc_start: 0.6419 (OUTLIER) cc_final: 0.4866 (p-80) REVERT: Z 51 ASP cc_start: 0.7069 (t0) cc_final: 0.6711 (p0) REVERT: a 188 MET cc_start: 0.5194 (ppp) cc_final: 0.4817 (ppp) REVERT: a 227 LYS cc_start: 0.9273 (mmmt) cc_final: 0.9024 (mmmt) REVERT: a 230 TYR cc_start: 0.8869 (t80) cc_final: 0.8300 (t80) REVERT: b 1 MET cc_start: 0.7892 (tmm) cc_final: 0.7406 (tmm) REVERT: d 67 GLU cc_start: 0.8733 (tp30) cc_final: 0.8313 (tp30) outliers start: 40 outliers final: 23 residues processed: 265 average time/residue: 0.2292 time to fit residues: 83.4992 Evaluate side-chains 256 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 231 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 81 PHE Chi-restraints excluded: chain U residue 82 THR Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain W residue 118 VAL Chi-restraints excluded: chain W residue 132 ASN Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 9 GLN Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 38 HIS Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain a residue 202 VAL Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 11 GLN Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 68 optimal weight: 0.1980 chunk 119 optimal weight: 0.7980 chunk 33 optimal weight: 50.0000 chunk 44 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 ASN ** Y 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10394 Z= 0.194 Angle : 0.666 13.094 14098 Z= 0.331 Chirality : 0.040 0.350 1697 Planarity : 0.004 0.043 1868 Dihedral : 4.432 57.179 1500 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.89 % Allowed : 27.31 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.22), residues: 1408 helix: 2.92 (0.14), residues: 1190 sheet: -0.47 (1.35), residues: 12 loop : -0.28 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 59 HIS 0.005 0.001 HIS a 31 PHE 0.015 0.001 PHE X 20 TYR 0.016 0.001 TYR a 230 ARG 0.007 0.000 ARG d 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 246 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 89 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7885 (tm-30) REVERT: U 93 ASP cc_start: 0.8002 (m-30) cc_final: 0.7495 (m-30) REVERT: U 94 LEU cc_start: 0.9034 (tp) cc_final: 0.8708 (tt) REVERT: U 98 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8442 (mm) REVERT: U 119 HIS cc_start: 0.7754 (OUTLIER) cc_final: 0.7127 (m-70) REVERT: U 120 ASP cc_start: 0.7836 (p0) cc_final: 0.7592 (p0) REVERT: W 79 GLU cc_start: 0.7923 (mp0) cc_final: 0.7635 (pm20) REVERT: Z 16 TYR cc_start: 0.7806 (m-80) cc_final: 0.6440 (m-80) REVERT: Z 17 LYS cc_start: 0.9651 (mmtt) cc_final: 0.9307 (mmtt) REVERT: Z 24 LYS cc_start: 0.8720 (mttp) cc_final: 0.8289 (mttp) REVERT: Z 38 HIS cc_start: 0.6465 (OUTLIER) cc_final: 0.5033 (p-80) REVERT: Z 51 ASP cc_start: 0.7326 (t0) cc_final: 0.6967 (p0) REVERT: a 168 PHE cc_start: 0.7945 (m-80) cc_final: 0.7548 (m-80) REVERT: a 188 MET cc_start: 0.5019 (ppp) cc_final: 0.4764 (ppp) REVERT: a 227 LYS cc_start: 0.9300 (mmmt) cc_final: 0.9048 (mmmt) REVERT: a 230 TYR cc_start: 0.8825 (t80) cc_final: 0.8334 (t80) REVERT: b 1 MET cc_start: 0.7795 (tmm) cc_final: 0.7299 (tmm) REVERT: c 1 MET cc_start: 0.7913 (tmm) cc_final: 0.7510 (tmm) REVERT: d 67 GLU cc_start: 0.8753 (tp30) cc_final: 0.8255 (tp30) outliers start: 37 outliers final: 26 residues processed: 267 average time/residue: 0.2498 time to fit residues: 91.3329 Evaluate side-chains 258 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 229 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 82 THR Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain U residue 119 HIS Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 118 VAL Chi-restraints excluded: chain W residue 132 ASN Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 58 GLU Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 9 GLN Chi-restraints excluded: chain Z residue 22 ASP Chi-restraints excluded: chain Z residue 38 HIS Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 90 ASP Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 11 GLN Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 78 optimal weight: 0.5980 chunk 32 optimal weight: 40.0000 chunk 133 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 50.0000 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 128 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 109 HIS a 239 GLN c 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10394 Z= 0.191 Angle : 0.678 14.346 14098 Z= 0.336 Chirality : 0.039 0.258 1697 Planarity : 0.003 0.041 1868 Dihedral : 4.419 57.637 1500 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.62 % Allowed : 28.26 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.75 (0.22), residues: 1408 helix: 2.96 (0.14), residues: 1183 sheet: -0.26 (1.39), residues: 12 loop : -0.37 (0.45), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 59 HIS 0.005 0.001 HIS a 31 PHE 0.014 0.001 PHE X 20 TYR 0.014 0.001 TYR a 230 ARG 0.005 0.000 ARG d 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 244 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 89 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7886 (tm-30) REVERT: U 93 ASP cc_start: 0.8005 (m-30) cc_final: 0.7467 (m-30) REVERT: U 94 LEU cc_start: 0.9038 (tp) cc_final: 0.8701 (tt) REVERT: U 98 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8381 (mm) REVERT: U 119 HIS cc_start: 0.7710 (OUTLIER) cc_final: 0.6957 (m-70) REVERT: U 120 ASP cc_start: 0.7668 (p0) cc_final: 0.7435 (p0) REVERT: V 79 LYS cc_start: 0.9416 (mmmt) cc_final: 0.9180 (mmmt) REVERT: W 79 GLU cc_start: 0.7907 (mp0) cc_final: 0.7615 (pm20) REVERT: Z 16 TYR cc_start: 0.7734 (m-80) cc_final: 0.6365 (m-80) REVERT: Z 17 LYS cc_start: 0.9643 (mmtt) cc_final: 0.9325 (mmtt) REVERT: Z 22 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7044 (m-30) REVERT: Z 24 LYS cc_start: 0.8734 (mttp) cc_final: 0.8284 (mttp) REVERT: Z 38 HIS cc_start: 0.6503 (p-80) cc_final: 0.5075 (p-80) REVERT: Z 51 ASP cc_start: 0.7407 (t0) cc_final: 0.6955 (p0) REVERT: b 1 MET cc_start: 0.7690 (tmm) cc_final: 0.7137 (tmm) REVERT: c 1 MET cc_start: 0.7312 (tmm) cc_final: 0.6693 (tmm) REVERT: d 86 ARG cc_start: 0.8415 (ptt180) cc_final: 0.8122 (ptt180) outliers start: 44 outliers final: 28 residues processed: 270 average time/residue: 0.2396 time to fit residues: 89.1669 Evaluate side-chains 262 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 231 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 82 THR Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain U residue 119 HIS Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 118 VAL Chi-restraints excluded: chain W residue 132 ASN Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 9 GLN Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Z residue 22 ASP Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 90 ASP Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain a residue 202 VAL Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 11 GLN Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 69 LEU Chi-restraints excluded: chain d residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 30.0000 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 82 optimal weight: 30.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 ASN ** Y 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 34 ASN ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10394 Z= 0.206 Angle : 0.709 14.766 14098 Z= 0.352 Chirality : 0.040 0.351 1697 Planarity : 0.003 0.042 1868 Dihedral : 4.461 59.258 1500 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.31 % Allowed : 30.67 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.22), residues: 1408 helix: 2.93 (0.14), residues: 1181 sheet: -0.29 (1.38), residues: 12 loop : -0.32 (0.45), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 59 HIS 0.005 0.001 HIS a 31 PHE 0.027 0.002 PHE a 168 TYR 0.028 0.001 TYR a 230 ARG 0.007 0.000 ARG d 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 239 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 89 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7843 (tm-30) REVERT: U 93 ASP cc_start: 0.8007 (m-30) cc_final: 0.7456 (m-30) REVERT: U 94 LEU cc_start: 0.9045 (tp) cc_final: 0.8702 (tt) REVERT: U 98 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8430 (mm) REVERT: U 119 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.6818 (m-70) REVERT: U 120 ASP cc_start: 0.7589 (p0) cc_final: 0.7328 (p0) REVERT: U 135 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8695 (pp20) REVERT: W 79 GLU cc_start: 0.7943 (mp0) cc_final: 0.7629 (pm20) REVERT: Z 11 GLU cc_start: 0.9626 (tm-30) cc_final: 0.9386 (pp20) REVERT: Z 16 TYR cc_start: 0.7764 (m-80) cc_final: 0.6396 (m-80) REVERT: Z 17 LYS cc_start: 0.9681 (mmtt) cc_final: 0.9418 (mmtt) REVERT: Z 22 ASP cc_start: 0.8107 (t0) cc_final: 0.7613 (m-30) REVERT: Z 24 LYS cc_start: 0.8753 (mttp) cc_final: 0.8315 (mttp) REVERT: Z 34 ASN cc_start: 0.8526 (t0) cc_final: 0.8092 (p0) REVERT: Z 35 TYR cc_start: 0.6665 (t80) cc_final: 0.6436 (t80) REVERT: Z 38 HIS cc_start: 0.6270 (p-80) cc_final: 0.5246 (p-80) REVERT: Z 51 ASP cc_start: 0.7669 (t0) cc_final: 0.7072 (p0) REVERT: b 1 MET cc_start: 0.7719 (tmm) cc_final: 0.7094 (tmm) REVERT: c 1 MET cc_start: 0.7234 (tmm) cc_final: 0.6499 (tmm) REVERT: d 63 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.9073 (tp) REVERT: d 67 GLU cc_start: 0.8868 (tp30) cc_final: 0.8574 (tp30) outliers start: 41 outliers final: 31 residues processed: 264 average time/residue: 0.2229 time to fit residues: 81.7433 Evaluate side-chains 259 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 225 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 82 THR Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain U residue 119 HIS Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 118 VAL Chi-restraints excluded: chain W residue 132 ASN Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 9 GLN Chi-restraints excluded: chain Y residue 11 ASN Chi-restraints excluded: chain Y residue 13 LEU Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 90 ASP Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 11 GLN Chi-restraints excluded: chain c residue 56 SER Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 50.0000 chunk 84 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 12 optimal weight: 50.0000 chunk 104 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 239 GLN c 8 GLN ** c 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10394 Z= 0.202 Angle : 0.733 15.385 14098 Z= 0.361 Chirality : 0.041 0.363 1697 Planarity : 0.003 0.045 1868 Dihedral : 4.437 59.618 1500 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.68 % Allowed : 31.41 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.22), residues: 1408 helix: 2.91 (0.14), residues: 1182 sheet: -0.20 (1.36), residues: 12 loop : -0.33 (0.45), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 59 HIS 0.006 0.001 HIS a 31 PHE 0.012 0.002 PHE X 20 TYR 0.024 0.001 TYR a 230 ARG 0.007 0.000 ARG d 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 238 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 89 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7885 (tm-30) REVERT: U 93 ASP cc_start: 0.8006 (m-30) cc_final: 0.7449 (m-30) REVERT: U 94 LEU cc_start: 0.9037 (tp) cc_final: 0.8702 (tt) REVERT: U 98 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8453 (mm) REVERT: U 119 HIS cc_start: 0.7619 (OUTLIER) cc_final: 0.6698 (m-70) REVERT: U 120 ASP cc_start: 0.7520 (p0) cc_final: 0.7281 (p0) REVERT: U 135 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8713 (pp20) REVERT: W 19 GLN cc_start: 0.8664 (mt0) cc_final: 0.7852 (mm-40) REVERT: W 79 GLU cc_start: 0.7928 (mp0) cc_final: 0.7596 (pm20) REVERT: Z 16 TYR cc_start: 0.7603 (m-80) cc_final: 0.6309 (m-80) REVERT: Z 17 LYS cc_start: 0.9686 (mmtt) cc_final: 0.9454 (mmtt) REVERT: Z 22 ASP cc_start: 0.8132 (t0) cc_final: 0.7586 (m-30) REVERT: Z 24 LYS cc_start: 0.8726 (mttp) cc_final: 0.8295 (mttp) REVERT: Z 33 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8064 (mt) REVERT: Z 34 ASN cc_start: 0.8492 (t0) cc_final: 0.8056 (p0) REVERT: Z 35 TYR cc_start: 0.6534 (t80) cc_final: 0.6300 (t80) REVERT: Z 38 HIS cc_start: 0.6073 (p-80) cc_final: 0.4748 (p-80) REVERT: Z 51 ASP cc_start: 0.7743 (t0) cc_final: 0.7120 (p0) REVERT: b 1 MET cc_start: 0.7741 (tmm) cc_final: 0.7073 (tmm) REVERT: c 1 MET cc_start: 0.6983 (tmm) cc_final: 0.6182 (tmm) REVERT: c 15 GLU cc_start: 0.8312 (tp30) cc_final: 0.7875 (mm-30) REVERT: d 67 GLU cc_start: 0.8881 (tp30) cc_final: 0.8586 (tp30) outliers start: 35 outliers final: 27 residues processed: 259 average time/residue: 0.2302 time to fit residues: 82.6183 Evaluate side-chains 257 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 227 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 82 THR Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain U residue 119 HIS Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 118 VAL Chi-restraints excluded: chain W residue 132 ASN Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 9 GLN Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 90 ASP Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 11 GLN Chi-restraints excluded: chain c residue 56 SER Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 239 GLN ** c 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10394 Z= 0.204 Angle : 0.746 15.976 14098 Z= 0.368 Chirality : 0.042 0.352 1697 Planarity : 0.004 0.047 1868 Dihedral : 4.436 59.135 1500 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.68 % Allowed : 31.62 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.22), residues: 1408 helix: 2.90 (0.14), residues: 1182 sheet: -0.27 (1.29), residues: 12 loop : -0.33 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 59 HIS 0.006 0.001 HIS a 31 PHE 0.016 0.002 PHE a 205 TYR 0.014 0.001 TYR Z 35 ARG 0.008 0.000 ARG d 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 241 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 89 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7875 (tm-30) REVERT: U 93 ASP cc_start: 0.8046 (m-30) cc_final: 0.7466 (m-30) REVERT: U 94 LEU cc_start: 0.9041 (tp) cc_final: 0.8700 (tt) REVERT: U 98 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8409 (mm) REVERT: U 119 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.6699 (m-70) REVERT: U 120 ASP cc_start: 0.7601 (p0) cc_final: 0.7355 (p0) REVERT: U 135 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8756 (pp20) REVERT: W 13 LYS cc_start: 0.8795 (ptpp) cc_final: 0.8570 (ptpp) REVERT: W 79 GLU cc_start: 0.7862 (mp0) cc_final: 0.7376 (pm20) REVERT: Z 24 LYS cc_start: 0.8715 (mttp) cc_final: 0.8251 (mttp) REVERT: Z 33 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8106 (mm) REVERT: Z 34 ASN cc_start: 0.8527 (t0) cc_final: 0.8106 (p0) REVERT: Z 35 TYR cc_start: 0.6555 (t80) cc_final: 0.6310 (t80) REVERT: Z 38 HIS cc_start: 0.6041 (p-80) cc_final: 0.4642 (p-80) REVERT: Z 51 ASP cc_start: 0.7833 (t0) cc_final: 0.7141 (p0) REVERT: b 1 MET cc_start: 0.7660 (tmm) cc_final: 0.6971 (tmm) REVERT: c 15 GLU cc_start: 0.8395 (tp30) cc_final: 0.7960 (mm-30) REVERT: d 67 GLU cc_start: 0.8845 (tp30) cc_final: 0.8550 (tp30) REVERT: d 84 MET cc_start: 0.8641 (mtm) cc_final: 0.8250 (mtm) outliers start: 35 outliers final: 27 residues processed: 260 average time/residue: 0.2378 time to fit residues: 85.1135 Evaluate side-chains 257 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 227 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 82 THR Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain U residue 119 HIS Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 118 VAL Chi-restraints excluded: chain W residue 132 ASN Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 9 GLN Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Z residue 22 ASP Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 64 ILE Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain a residue 17 ASP Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 11 GLN Chi-restraints excluded: chain c residue 56 SER Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 73 LEU Chi-restraints excluded: chain d residue 108 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 109 optimal weight: 0.2980 chunk 11 optimal weight: 50.0000 chunk 84 optimal weight: 0.8980 chunk 67 optimal weight: 0.3980 chunk 86 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 127 GLN ** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 ASN Y 5 HIS ** Y 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10394 Z= 0.202 Angle : 0.780 16.352 14098 Z= 0.387 Chirality : 0.042 0.345 1697 Planarity : 0.004 0.051 1868 Dihedral : 4.444 56.559 1500 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.15 % Allowed : 32.56 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.22), residues: 1408 helix: 2.86 (0.14), residues: 1182 sheet: -0.17 (1.28), residues: 12 loop : -0.28 (0.45), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 59 HIS 0.005 0.001 HIS a 31 PHE 0.026 0.002 PHE b 30 TYR 0.014 0.001 TYR Z 35 ARG 0.007 0.000 ARG d 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 239 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 89 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7864 (tm-30) REVERT: U 93 ASP cc_start: 0.8039 (m-30) cc_final: 0.7464 (m-30) REVERT: U 94 LEU cc_start: 0.9035 (tp) cc_final: 0.8715 (tt) REVERT: U 98 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8396 (mm) REVERT: U 119 HIS cc_start: 0.7556 (OUTLIER) cc_final: 0.6713 (m-70) REVERT: U 120 ASP cc_start: 0.7530 (p0) cc_final: 0.7298 (p0) REVERT: W 79 GLU cc_start: 0.7839 (mp0) cc_final: 0.7557 (pm20) REVERT: Z 17 LYS cc_start: 0.9698 (mmtt) cc_final: 0.9497 (mmtt) REVERT: Z 22 ASP cc_start: 0.8063 (t0) cc_final: 0.7531 (m-30) REVERT: Z 24 LYS cc_start: 0.8704 (mttp) cc_final: 0.8239 (mttp) REVERT: Z 33 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8105 (mm) REVERT: Z 34 ASN cc_start: 0.8533 (t0) cc_final: 0.8096 (p0) REVERT: Z 35 TYR cc_start: 0.6507 (t80) cc_final: 0.6283 (t80) REVERT: Z 38 HIS cc_start: 0.6014 (p-80) cc_final: 0.4569 (p-80) REVERT: Z 51 ASP cc_start: 0.7820 (t0) cc_final: 0.7071 (p0) REVERT: a 168 PHE cc_start: 0.7947 (m-80) cc_final: 0.7468 (m-80) REVERT: b 1 MET cc_start: 0.7624 (tmm) cc_final: 0.6928 (tmm) REVERT: c 1 MET cc_start: 0.7294 (ttp) cc_final: 0.6252 (tmm) REVERT: c 15 GLU cc_start: 0.8360 (tp30) cc_final: 0.7886 (mm-30) REVERT: d 67 GLU cc_start: 0.8843 (tp30) cc_final: 0.8552 (tp30) REVERT: d 84 MET cc_start: 0.8617 (mtm) cc_final: 0.8234 (mtm) outliers start: 30 outliers final: 23 residues processed: 257 average time/residue: 0.2263 time to fit residues: 80.0352 Evaluate side-chains 253 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 227 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 82 THR Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain U residue 119 HIS Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain V residue 127 GLN Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 118 VAL Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 9 GLN Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 64 ILE Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain a residue 17 ASP Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 73 LEU Chi-restraints excluded: chain d residue 108 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 50.0000 chunk 100 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 30.0000 chunk 109 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 13 optimal weight: 40.0000 chunk 20 optimal weight: 30.0000 chunk 96 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.144497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.103424 restraints weight = 32585.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.105875 restraints weight = 19643.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.107388 restraints weight = 14022.172| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.287 10394 Z= 0.436 Angle : 1.027 59.195 14098 Z= 0.565 Chirality : 0.052 1.107 1697 Planarity : 0.004 0.074 1868 Dihedral : 4.421 56.432 1500 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.94 % Allowed : 33.09 % Favored : 63.97 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.22), residues: 1408 helix: 2.83 (0.14), residues: 1182 sheet: -0.17 (1.28), residues: 12 loop : -0.30 (0.45), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 59 HIS 0.016 0.002 HIS a 109 PHE 0.020 0.002 PHE a 168 TYR 0.014 0.001 TYR Z 35 ARG 0.015 0.001 ARG a 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2448.41 seconds wall clock time: 44 minutes 54.70 seconds (2694.70 seconds total)