Starting phenix.real_space_refine on Wed Sep 25 10:49:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q85_18247/09_2024/8q85_18247.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q85_18247/09_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_18247/09_2024/8q85_18247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q85_18247/09_2024/8q85_18247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q85_18247/09_2024/8q85_18247.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q85_18247/09_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. Time to flip 50 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 6.82, per 1000 atoms: 0.66 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.3 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: 0.78 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: 3.25 Time building geometry restraints manager: 3.28 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: 0.00 - 3.49: 13949 3.49 - 6.99: 116 6.99 - 10.48: 23 10.48 - 13.98: 8 13.98 - 17.47: 2 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 3.040 nonbonded pdb=" O ALA a 15 " pdb=" OG SER a 18 " model vdw 2.159 3.040 nonbonded pdb=" O LYS V 73 " pdb=" NZ LYS V 73 " model vdw 2.170 3.120 nonbonded pdb=" O LEU G 336 " pdb=" N MET G 341 " model vdw 2.186 3.120 nonbonded pdb=" O LEU V 64 " pdb=" OG SER V 68 " model vdw 2.192 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 1.640 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.440 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.890 ------------------------------------------------------------------------------- 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 : 1.134 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: 0.2346 time to fit residues: 74.9286 Evaluate side-chains 223 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 221 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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: 1.9990 chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 50.0000 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 108 optimal weight: 30.0000 chunk 41 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 125 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 108 ASN ** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 ASN Z 41 GLN a 239 GLN c 63 GLN d 30 ASN d 92 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10394 Z= 0.201 Angle : 0.686 12.345 14098 Z= 0.350 Chirality : 0.042 0.475 1697 Planarity : 0.004 0.079 1868 Dihedral : 4.735 55.294 1503 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.41 % Allowed : 23.63 % Favored : 71.95 % 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: 3.05 (0.22), residues: 1408 helix: 2.48 (0.14), residues: 1184 sheet: -2.00 (1.03), residues: 12 loop : -0.45 (0.45), residues: 212 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 0.020 0.002 TYR a 230 ARG 0.004 0.001 ARG d 57 *********************** 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: 42 poor density : 246 time to evaluate : 1.227 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: 0.8178 (tm-30) cc_final: 0.7899 (tm-30) REVERT: U 93 ASP cc_start: 0.7985 (m-30) cc_final: 0.7772 (m-30) REVERT: U 120 ASP cc_start: 0.7871 (p0) cc_final: 0.7664 (p0) REVERT: W 11 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8186 (mtpt) REVERT: W 34 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7995 (mm-30) REVERT: W 72 GLN cc_start: 0.8153 (tp40) cc_final: 0.7894 (tp-100) REVERT: W 79 GLU cc_start: 0.8077 (mp0) cc_final: 0.7738 (pm20) REVERT: Z 16 TYR cc_start: 0.7876 (m-80) cc_final: 0.6671 (m-80) REVERT: Z 17 LYS cc_start: 0.9556 (mmtt) cc_final: 0.9180 (mmtt) REVERT: Z 38 HIS cc_start: 0.6293 (p-80) cc_final: 0.4858 (p-80) REVERT: a 93 MET cc_start: 0.7444 (mmt) cc_final: 0.6977 (mmm) REVERT: a 168 PHE cc_start: 0.8124 (m-80) cc_final: 0.6940 (m-80) REVERT: a 227 LYS cc_start: 0.9326 (mmmt) cc_final: 0.9002 (mmmt) REVERT: b 1 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7356 (ppp) REVERT: b 48 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8116 (tm-30) REVERT: d 63 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9042 (tp) REVERT: d 67 GLU cc_start: 0.8751 (tp30) cc_final: 0.8367 (tp30) outliers start: 42 outliers final: 15 residues processed: 271 average time/residue: 0.2382 time to fit residues: 88.5186 Evaluate side-chains 244 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 227 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain V residue 102 SER 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 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 29 THR Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain b residue 67 THR 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: 5.9990 chunk 38 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 50.0000 chunk 125 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 127 GLN ** 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** a 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10394 Z= 0.203 Angle : 0.667 12.792 14098 Z= 0.336 Chirality : 0.041 0.265 1697 Planarity : 0.004 0.061 1868 Dihedral : 4.541 56.044 1500 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.15 % Allowed : 23.95 % Favored : 72.90 % 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: 3.35 (0.22), residues: 1408 helix: 2.72 (0.14), residues: 1177 sheet: -2.07 (1.04), residues: 12 loop : -0.47 (0.44), residues: 219 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 0.018 0.002 PHE X 20 TYR 0.022 0.002 TYR a 230 ARG 0.004 0.001 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 271 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 241 time to evaluate : 1.204 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: 0.8181 (tm-30) cc_final: 0.7884 (tm-30) REVERT: U 93 ASP cc_start: 0.7991 (m-30) cc_final: 0.7684 (m-30) REVERT: U 98 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8542 (mm) REVERT: W 6 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8019 (pt0) REVERT: W 34 GLU cc_start: 0.8213 (mm-30) cc_final: 0.8010 (mm-30) REVERT: W 79 GLU cc_start: 0.8029 (mp0) cc_final: 0.7634 (pm20) REVERT: X 47 ILE cc_start: 0.7652 (mt) cc_final: 0.7413 (mm) REVERT: Z 16 TYR cc_start: 0.7680 (m-80) cc_final: 0.6452 (m-80) REVERT: Z 17 LYS cc_start: 0.9619 (mmtt) cc_final: 0.9280 (mmtt) REVERT: Z 22 ASP cc_start: 0.8175 (t0) cc_final: 0.7710 (p0) REVERT: Z 38 HIS cc_start: 0.6347 (p-80) cc_final: 0.4739 (p-80) REVERT: Z 51 ASP cc_start: 0.6814 (t0) cc_final: 0.6551 (p0) REVERT: a 188 MET cc_start: 0.4126 (ppp) cc_final: 0.3883 (ppp) REVERT: a 227 LYS cc_start: 0.9213 (mmmt) cc_final: 0.8942 (mmmt) REVERT: a 230 TYR cc_start: 0.8905 (t80) cc_final: 0.8142 (t80) REVERT: b 1 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7334 (ppp) REVERT: c 38 ASN cc_start: 0.8400 (m-40) cc_final: 0.8172 (m110) REVERT: d 63 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9085 (tp) REVERT: d 67 GLU cc_start: 0.8769 (tp30) cc_final: 0.8367 (tp30) outliers start: 30 outliers final: 19 residues processed: 260 average time/residue: 0.2347 time to fit residues: 83.2523 Evaluate side-chains 249 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 227 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 81 PHE Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain V residue 102 SER 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 X residue 28 LEU Chi-restraints excluded: chain X residue 58 GLU 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 74 SER Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 16 GLU Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 67 THR 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: 1.9990 chunk 65 optimal weight: 0.9990 chunk 13 optimal weight: 50.0000 chunk 59 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 35 optimal weight: 50.0000 chunk 111 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 109 HIS ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2012 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= 0.194 Angle : 0.665 13.266 14098 Z= 0.334 Chirality : 0.041 0.420 1697 Planarity : 0.004 0.051 1868 Dihedral : 4.495 56.374 1500 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.68 % Allowed : 24.89 % 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: 3.47 (0.21), residues: 1408 helix: 2.81 (0.14), residues: 1176 sheet: -1.94 (1.06), residues: 12 loop : -0.52 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 59 HIS 0.006 0.001 HIS a 31 PHE 0.025 0.002 PHE a 168 TYR 0.019 0.001 TYR a 230 ARG 0.005 0.001 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 287 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 252 time to evaluate : 1.138 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: U 78 ASP cc_start: 0.7491 (t0) cc_final: 0.7215 (t0) REVERT: U 83 ARG cc_start: 0.7469 (ptp-170) cc_final: 0.7189 (ptp-170) REVERT: U 89 GLU cc_start: 0.8278 (tm-30) cc_final: 0.8030 (tm-30) REVERT: U 93 ASP cc_start: 0.8065 (m-30) cc_final: 0.7758 (m-30) REVERT: U 94 LEU cc_start: 0.9001 (tp) cc_final: 0.8725 (tt) REVERT: U 98 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8481 (mm) REVERT: U 136 ASP cc_start: 0.9443 (m-30) cc_final: 0.9202 (p0) REVERT: V 77 MET cc_start: 0.9116 (ppp) cc_final: 0.8832 (ppp) REVERT: W 6 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8057 (pt0) REVERT: W 34 GLU cc_start: 0.8235 (mm-30) cc_final: 0.8011 (mm-30) REVERT: W 79 GLU cc_start: 0.8038 (mp0) cc_final: 0.7605 (pm20) REVERT: X 47 ILE cc_start: 0.7656 (mt) cc_final: 0.7455 (mm) REVERT: Z 16 TYR cc_start: 0.7726 (m-80) cc_final: 0.6318 (m-80) REVERT: Z 17 LYS cc_start: 0.9624 (mmtt) cc_final: 0.9290 (mmtt) REVERT: Z 35 TYR cc_start: 0.6495 (t80) cc_final: 0.6179 (t80) REVERT: Z 38 HIS cc_start: 0.6392 (p-80) cc_final: 0.5066 (p-80) REVERT: Z 51 ASP cc_start: 0.7062 (t0) cc_final: 0.6760 (p0) REVERT: a 168 PHE cc_start: 0.7865 (m-80) cc_final: 0.6862 (m-80) REVERT: a 188 MET cc_start: 0.4656 (ppp) cc_final: 0.3985 (ppp) REVERT: a 227 LYS cc_start: 0.9281 (mmmt) cc_final: 0.9016 (mmmt) REVERT: a 230 TYR cc_start: 0.8877 (t80) cc_final: 0.8253 (t80) REVERT: a 259 LYS cc_start: 0.9403 (mmmt) cc_final: 0.9042 (mtmm) REVERT: b 1 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7150 (ppp) REVERT: b 48 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8181 (tm-30) REVERT: c 6 GLN cc_start: 0.7852 (tm130) cc_final: 0.7441 (tm-30) REVERT: c 64 MET cc_start: 0.8744 (pmm) cc_final: 0.8340 (pmm) REVERT: d 67 GLU cc_start: 0.8783 (tp30) cc_final: 0.8383 (tp30) REVERT: d 86 ARG cc_start: 0.8611 (ptt180) cc_final: 0.8385 (ptt180) REVERT: d 89 ASP cc_start: 0.9393 (t0) cc_final: 0.8991 (m-30) outliers start: 35 outliers final: 22 residues processed: 272 average time/residue: 0.2530 time to fit residues: 93.6955 Evaluate side-chains 259 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 235 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 81 PHE Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain U residue 100 SER Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain V residue 102 SER 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 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 74 SER Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 202 VAL Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain b residue 16 GLU Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 11 GLN Chi-restraints excluded: chain c residue 44 GLN Chi-restraints excluded: chain d residue 2 THR 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: 0.9990 chunk 1 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 33 optimal weight: 50.0000 chunk 44 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 ASN ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 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: 0.7547 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10394 Z= 0.234 Angle : 0.692 13.109 14098 Z= 0.350 Chirality : 0.042 0.368 1697 Planarity : 0.004 0.049 1868 Dihedral : 4.505 58.861 1500 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.83 % Allowed : 25.53 % Favored : 69.64 % 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: 3.39 (0.21), residues: 1408 helix: 2.76 (0.14), residues: 1176 sheet: -2.14 (1.13), residues: 12 loop : -0.51 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 59 HIS 0.013 0.002 HIS a 109 PHE 0.018 0.002 PHE a 168 TYR 0.018 0.002 TYR a 230 ARG 0.014 0.001 ARG d 83 *********************** 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 293 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 247 time to evaluate : 1.216 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: 0.8247 (tm-30) cc_final: 0.7931 (tm-30) REVERT: U 93 ASP cc_start: 0.8084 (m-30) cc_final: 0.7715 (m-30) REVERT: U 94 LEU cc_start: 0.9020 (tp) cc_final: 0.8487 (tt) REVERT: U 98 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8523 (mm) REVERT: V 79 LYS cc_start: 0.9396 (mmmt) cc_final: 0.9166 (mmmt) REVERT: W 6 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8030 (pt0) REVERT: W 79 GLU cc_start: 0.7977 (mp0) cc_final: 0.7669 (pm20) REVERT: X 43 ASN cc_start: 0.7865 (m-40) cc_final: 0.7614 (m-40) REVERT: Z 16 TYR cc_start: 0.7825 (m-80) cc_final: 0.6481 (m-80) REVERT: Z 17 LYS cc_start: 0.9658 (mmtt) cc_final: 0.9359 (mmtt) REVERT: Z 22 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7156 (m-30) REVERT: Z 35 TYR cc_start: 0.6622 (t80) cc_final: 0.6305 (t80) REVERT: Z 38 HIS cc_start: 0.6414 (p-80) cc_final: 0.5043 (p-80) REVERT: Z 51 ASP cc_start: 0.7487 (t0) cc_final: 0.7042 (p0) REVERT: a 168 PHE cc_start: 0.7913 (m-80) cc_final: 0.7677 (m-80) REVERT: a 216 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7939 (pt0) REVERT: a 227 LYS cc_start: 0.9305 (mmmt) cc_final: 0.9030 (mmmt) REVERT: a 230 TYR cc_start: 0.8855 (t80) cc_final: 0.8298 (t80) REVERT: b 1 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7099 (ppp) REVERT: b 48 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8240 (tm-30) REVERT: c 6 GLN cc_start: 0.7924 (tm130) cc_final: 0.7504 (tm-30) REVERT: d 67 GLU cc_start: 0.8758 (tp30) cc_final: 0.8236 (tp30) REVERT: d 89 ASP cc_start: 0.9414 (t0) cc_final: 0.9065 (m-30) outliers start: 46 outliers final: 31 residues processed: 276 average time/residue: 0.2318 time to fit residues: 87.9087 Evaluate side-chains 260 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 225 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 81 PHE Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain U residue 100 SER Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 113 ILE 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 122 GLU Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 58 GLU 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 Y residue 51 CYS Chi-restraints excluded: chain Z residue 22 ASP Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 202 VAL Chi-restraints excluded: chain a residue 216 GLU Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain b residue 16 GLU Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 11 GLN Chi-restraints excluded: chain c residue 31 ASP 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: 0.8980 chunk 26 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 32 optimal weight: 40.0000 chunk 133 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 11 optimal weight: 40.0000 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 128 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 134 ASN ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 ASN ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10394 Z= 0.203 Angle : 0.718 13.812 14098 Z= 0.357 Chirality : 0.040 0.235 1697 Planarity : 0.004 0.048 1868 Dihedral : 4.512 59.127 1500 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.78 % Allowed : 27.63 % Favored : 68.59 % 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: 3.45 (0.22), residues: 1408 helix: 2.74 (0.14), residues: 1188 sheet: -0.98 (1.40), residues: 12 loop : -0.38 (0.44), residues: 208 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 0.015 0.002 PHE a 168 TYR 0.016 0.001 TYR Z 35 ARG 0.006 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 283 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 247 time to evaluate : 1.221 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: 0.8315 (tm-30) cc_final: 0.8054 (tm-30) REVERT: U 93 ASP cc_start: 0.8093 (m-30) cc_final: 0.7709 (m-30) REVERT: U 94 LEU cc_start: 0.8995 (tp) cc_final: 0.8733 (tt) REVERT: U 98 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8531 (mm) REVERT: V 79 LYS cc_start: 0.9399 (mmmt) cc_final: 0.9175 (mmmt) REVERT: W 6 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8101 (pt0) REVERT: W 79 GLU cc_start: 0.7955 (mp0) cc_final: 0.7538 (pm20) REVERT: Z 16 TYR cc_start: 0.7755 (m-80) cc_final: 0.6366 (m-80) REVERT: Z 17 LYS cc_start: 0.9650 (mmtt) cc_final: 0.9334 (mmtt) REVERT: Z 22 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7159 (m-30) REVERT: Z 24 LYS cc_start: 0.8758 (mttp) cc_final: 0.8311 (mttp) REVERT: Z 35 TYR cc_start: 0.6569 (t80) cc_final: 0.6060 (t80) REVERT: Z 38 HIS cc_start: 0.6276 (p-80) cc_final: 0.4950 (p-80) REVERT: Z 51 ASP cc_start: 0.7586 (t0) cc_final: 0.7104 (p0) REVERT: a 93 MET cc_start: 0.7775 (mmm) cc_final: 0.7552 (mtp) REVERT: a 168 PHE cc_start: 0.7873 (m-80) cc_final: 0.7661 (m-80) REVERT: a 216 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7919 (pt0) REVERT: a 227 LYS cc_start: 0.9337 (mmmt) cc_final: 0.9061 (mmmt) REVERT: a 230 TYR cc_start: 0.8777 (t80) cc_final: 0.8521 (t80) REVERT: b 1 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.6962 (ppp) REVERT: b 48 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8053 (tm-30) REVERT: c 1 MET cc_start: 0.7456 (tmm) cc_final: 0.7078 (tpt) REVERT: c 6 GLN cc_start: 0.7951 (tm130) cc_final: 0.7435 (tm-30) REVERT: c 9 TYR cc_start: 0.8780 (m-80) cc_final: 0.8501 (m-80) REVERT: d 71 ARG cc_start: 0.8952 (mmm160) cc_final: 0.8571 (mmm160) REVERT: d 89 ASP cc_start: 0.9415 (t0) cc_final: 0.9095 (m-30) outliers start: 36 outliers final: 25 residues processed: 270 average time/residue: 0.2488 time to fit residues: 91.1001 Evaluate side-chains 261 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 232 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 81 PHE Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain U residue 100 SER Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 118 VAL 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 Y residue 51 CYS Chi-restraints excluded: chain Z residue 22 ASP Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 216 GLU Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain b residue 16 GLU Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 11 GLN 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: 2.9990 chunk 97 optimal weight: 0.1980 chunk 75 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 82 optimal weight: 30.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 38 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10394 Z= 0.197 Angle : 0.733 13.707 14098 Z= 0.364 Chirality : 0.041 0.358 1697 Planarity : 0.004 0.049 1868 Dihedral : 4.494 58.990 1500 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.10 % Allowed : 28.05 % Favored : 67.86 % 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: 3.58 (0.22), residues: 1408 helix: 2.90 (0.14), residues: 1169 sheet: -0.45 (1.44), residues: 12 loop : -0.56 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 59 HIS 0.015 0.001 HIS a 109 PHE 0.013 0.002 PHE a 168 TYR 0.016 0.001 TYR Z 35 ARG 0.007 0.001 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 285 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 246 time to evaluate : 1.243 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: 0.8306 (tm-30) cc_final: 0.8067 (tm-30) REVERT: U 93 ASP cc_start: 0.8114 (m-30) cc_final: 0.7729 (m-30) REVERT: U 94 LEU cc_start: 0.8990 (tp) cc_final: 0.8616 (tt) REVERT: U 98 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8543 (mm) REVERT: U 135 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8630 (pp20) REVERT: W 6 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8119 (pt0) REVERT: W 79 GLU cc_start: 0.7942 (mp0) cc_final: 0.7540 (pm20) REVERT: Z 16 TYR cc_start: 0.7724 (m-80) cc_final: 0.6328 (m-80) REVERT: Z 17 LYS cc_start: 0.9678 (mmtt) cc_final: 0.9409 (mmtt) REVERT: Z 22 ASP cc_start: 0.8053 (t0) cc_final: 0.7583 (m-30) REVERT: Z 24 LYS cc_start: 0.8743 (mttp) cc_final: 0.8301 (mttp) REVERT: Z 33 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8039 (mm) REVERT: Z 34 ASN cc_start: 0.8524 (t0) cc_final: 0.8055 (p0) REVERT: Z 35 TYR cc_start: 0.6482 (t80) cc_final: 0.6162 (t80) REVERT: Z 38 HIS cc_start: 0.6269 (p-80) cc_final: 0.4965 (p-80) REVERT: Z 51 ASP cc_start: 0.7695 (t0) cc_final: 0.7077 (p0) REVERT: a 90 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8210 (m-30) REVERT: a 93 MET cc_start: 0.7772 (mmm) cc_final: 0.7543 (mtp) REVERT: a 216 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7958 (pt0) REVERT: a 227 LYS cc_start: 0.9354 (mmmt) cc_final: 0.9054 (mmmt) REVERT: c 1 MET cc_start: 0.7364 (tmm) cc_final: 0.7018 (tpt) REVERT: c 6 GLN cc_start: 0.7955 (tm130) cc_final: 0.7395 (tm-30) REVERT: c 9 TYR cc_start: 0.8792 (m-80) cc_final: 0.8503 (m-80) REVERT: c 15 GLU cc_start: 0.8363 (tp30) cc_final: 0.7967 (mm-30) REVERT: c 35 LYS cc_start: 0.9210 (ttmm) cc_final: 0.8990 (ttmm) REVERT: d 67 GLU cc_start: 0.8865 (tp30) cc_final: 0.8638 (tp30) REVERT: d 89 ASP cc_start: 0.9388 (t0) cc_final: 0.9095 (m-30) REVERT: d 95 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.8262 (m-80) outliers start: 39 outliers final: 27 residues processed: 274 average time/residue: 0.2420 time to fit residues: 90.7409 Evaluate side-chains 266 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 234 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 81 PHE Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain U residue 100 SER Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain V residue 102 SER 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 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 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 74 SER 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 202 VAL Chi-restraints excluded: chain a residue 216 GLU Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain b residue 16 GLU Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 11 GLN Chi-restraints excluded: chain d residue 2 THR Chi-restraints excluded: chain d residue 73 LEU Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 50.0000 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 134 ASN ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 ASN ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 8 GLN c 63 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10394 Z= 0.206 Angle : 0.748 14.755 14098 Z= 0.373 Chirality : 0.042 0.354 1697 Planarity : 0.004 0.048 1868 Dihedral : 4.486 59.454 1500 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.78 % Allowed : 29.31 % Favored : 66.91 % 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 (0.21), residues: 1408 helix: 2.90 (0.14), residues: 1175 sheet: -0.26 (1.34), residues: 12 loop : -0.44 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 59 HIS 0.017 0.001 HIS a 109 PHE 0.024 0.002 PHE a 168 TYR 0.022 0.002 TYR a 230 ARG 0.007 0.001 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 286 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 250 time to evaluate : 1.342 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: symmetry clash REVERT: U 89 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8070 (tm-30) REVERT: U 93 ASP cc_start: 0.8131 (m-30) cc_final: 0.7726 (m-30) REVERT: U 94 LEU cc_start: 0.8994 (tp) cc_final: 0.8618 (tt) REVERT: U 98 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8530 (mm) REVERT: U 135 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8674 (pp20) REVERT: W 6 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8151 (pt0) REVERT: W 79 GLU cc_start: 0.7971 (mp0) cc_final: 0.7563 (pm20) REVERT: Z 16 TYR cc_start: 0.7646 (m-80) cc_final: 0.6408 (m-80) REVERT: Z 17 LYS cc_start: 0.9705 (mmtt) cc_final: 0.9451 (mmtt) REVERT: Z 22 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7585 (m-30) REVERT: Z 24 LYS cc_start: 0.8730 (mttp) cc_final: 0.8305 (mttp) REVERT: Z 33 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8038 (mt) REVERT: Z 34 ASN cc_start: 0.8660 (t0) cc_final: 0.8149 (p0) REVERT: Z 35 TYR cc_start: 0.6480 (t80) cc_final: 0.6199 (t80) REVERT: Z 38 HIS cc_start: 0.6019 (p-80) cc_final: 0.4899 (p-80) REVERT: Z 51 ASP cc_start: 0.7742 (t0) cc_final: 0.7125 (p0) REVERT: Z 52 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8485 (tm-30) REVERT: a 93 MET cc_start: 0.7720 (mmm) cc_final: 0.7463 (mtp) REVERT: c 1 MET cc_start: 0.7157 (tmm) cc_final: 0.6558 (tpt) REVERT: c 15 GLU cc_start: 0.8358 (tp30) cc_final: 0.7909 (mm-30) REVERT: c 35 LYS cc_start: 0.9203 (ttmm) cc_final: 0.8971 (ttmm) REVERT: d 24 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7065 (tm-30) REVERT: d 89 ASP cc_start: 0.9382 (t0) cc_final: 0.9136 (m-30) REVERT: d 95 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.8261 (m-80) outliers start: 36 outliers final: 27 residues processed: 275 average time/residue: 0.2348 time to fit residues: 88.5745 Evaluate side-chains 273 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 242 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 81 PHE Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain U residue 100 SER 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 102 SER 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 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 13 LEU Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 51 CYS Chi-restraints excluded: chain Z residue 22 ASP Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain a residue 66 VAL 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 16 GLU Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 11 GLN Chi-restraints excluded: chain d residue 2 THR Chi-restraints excluded: chain d residue 73 LEU Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 ASN ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10394 Z= 0.210 Angle : 0.791 15.035 14098 Z= 0.394 Chirality : 0.043 0.334 1697 Planarity : 0.004 0.048 1868 Dihedral : 4.492 59.155 1500 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.78 % Allowed : 30.25 % Favored : 65.97 % 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: 1174 sheet: -0.26 (1.30), residues: 12 loop : -0.41 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 59 HIS 0.016 0.001 HIS a 109 PHE 0.016 0.002 PHE a 205 TYR 0.038 0.002 TYR a 230 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 289 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 253 time to evaluate : 1.168 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: 0.8297 (tm-30) cc_final: 0.8072 (tm-30) REVERT: U 93 ASP cc_start: 0.8135 (m-30) cc_final: 0.7730 (m-30) REVERT: U 94 LEU cc_start: 0.8991 (tp) cc_final: 0.8623 (tt) REVERT: U 98 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8526 (mm) REVERT: U 135 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8726 (pp20) REVERT: V 77 MET cc_start: 0.9168 (ppp) cc_final: 0.8702 (ppp) REVERT: W 6 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8199 (pt0) REVERT: W 79 GLU cc_start: 0.7920 (mp0) cc_final: 0.7634 (pm20) REVERT: Z 11 GLU cc_start: 0.9501 (tm-30) cc_final: 0.9126 (pp20) REVERT: Z 17 LYS cc_start: 0.9688 (mmtt) cc_final: 0.9478 (mmtt) REVERT: Z 24 LYS cc_start: 0.8722 (mttp) cc_final: 0.8288 (mttp) REVERT: Z 33 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8076 (mt) REVERT: Z 34 ASN cc_start: 0.8704 (t0) cc_final: 0.8183 (p0) REVERT: Z 35 TYR cc_start: 0.6511 (t80) cc_final: 0.6234 (t80) REVERT: Z 38 HIS cc_start: 0.6043 (p-80) cc_final: 0.4906 (p-80) REVERT: a 93 MET cc_start: 0.7668 (mmm) cc_final: 0.7390 (mtp) REVERT: a 227 LYS cc_start: 0.9418 (mmmt) cc_final: 0.9103 (mmmt) REVERT: c 1 MET cc_start: 0.6851 (tmm) cc_final: 0.6446 (tpt) REVERT: c 15 GLU cc_start: 0.8409 (tp30) cc_final: 0.7950 (mm-30) REVERT: d 24 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7062 (tm-30) REVERT: d 52 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8253 (tm-30) REVERT: d 67 GLU cc_start: 0.8746 (tp30) cc_final: 0.8397 (tp30) REVERT: d 83 ARG cc_start: 0.9272 (tmm-80) cc_final: 0.8886 (ptt90) REVERT: d 86 ARG cc_start: 0.8355 (ptt180) cc_final: 0.7986 (ptm160) REVERT: d 89 ASP cc_start: 0.9379 (t0) cc_final: 0.9119 (m-30) REVERT: d 95 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.8310 (m-80) outliers start: 36 outliers final: 25 residues processed: 276 average time/residue: 0.2350 time to fit residues: 89.1487 Evaluate side-chains 267 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 239 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 81 PHE 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 102 SER 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 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 Y residue 51 CYS 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 74 SER Chi-restraints excluded: chain a residue 66 VAL 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 16 GLU Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 11 GLN Chi-restraints excluded: chain d residue 2 THR Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 11 optimal weight: 50.0000 chunk 84 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 86 optimal weight: 0.0060 chunk 116 optimal weight: 0.9980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 ASN ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10394 Z= 0.213 Angle : 0.825 14.907 14098 Z= 0.416 Chirality : 0.044 0.359 1697 Planarity : 0.004 0.049 1868 Dihedral : 4.471 56.033 1500 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.15 % Allowed : 31.30 % Favored : 65.55 % 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: 3.51 (0.22), residues: 1408 helix: 2.80 (0.14), residues: 1177 sheet: -0.57 (1.26), residues: 12 loop : -0.35 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 59 HIS 0.017 0.002 HIS a 109 PHE 0.026 0.002 PHE a 168 TYR 0.023 0.001 TYR a 230 ARG 0.007 0.001 ARG a 14 ********************** 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 277 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 247 time to evaluate : 1.193 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: U 89 GLU cc_start: 0.8284 (tm-30) cc_final: 0.8055 (tm-30) REVERT: U 93 ASP cc_start: 0.8130 (m-30) cc_final: 0.7727 (m-30) REVERT: U 94 LEU cc_start: 0.8986 (tp) cc_final: 0.8630 (tt) REVERT: U 98 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8544 (mm) REVERT: U 135 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8765 (pp20) REVERT: W 6 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8223 (pt0) REVERT: W 79 GLU cc_start: 0.7896 (mp0) cc_final: 0.7633 (pm20) REVERT: Z 16 TYR cc_start: 0.7567 (m-80) cc_final: 0.6309 (m-80) REVERT: Z 17 LYS cc_start: 0.9686 (mmtt) cc_final: 0.9476 (mmtt) REVERT: Z 22 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7583 (m-30) REVERT: Z 24 LYS cc_start: 0.8718 (mttp) cc_final: 0.8270 (mttp) REVERT: Z 33 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8040 (mt) REVERT: Z 34 ASN cc_start: 0.8758 (t0) cc_final: 0.8217 (p0) REVERT: Z 35 TYR cc_start: 0.6533 (t80) cc_final: 0.6257 (t80) REVERT: Z 38 HIS cc_start: 0.6050 (p-80) cc_final: 0.4880 (p-80) REVERT: Z 85 GLU cc_start: 0.8772 (pm20) cc_final: 0.8365 (pm20) REVERT: a 93 MET cc_start: 0.7631 (mmm) cc_final: 0.7354 (mtp) REVERT: a 256 ASP cc_start: 0.9619 (m-30) cc_final: 0.9319 (p0) REVERT: c 1 MET cc_start: 0.6857 (tmm) cc_final: 0.6288 (tpt) REVERT: c 15 GLU cc_start: 0.8390 (tp30) cc_final: 0.7880 (mm-30) REVERT: d 52 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8283 (tm-30) REVERT: d 67 GLU cc_start: 0.8743 (tp30) cc_final: 0.8459 (tp30) REVERT: d 83 ARG cc_start: 0.9247 (tmm-80) cc_final: 0.9032 (ptt90) REVERT: d 89 ASP cc_start: 0.9384 (t0) cc_final: 0.9125 (m-30) REVERT: d 95 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.8357 (m-80) outliers start: 30 outliers final: 25 residues processed: 267 average time/residue: 0.2312 time to fit residues: 85.1493 Evaluate side-chains 265 residues out of total 1346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 236 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 81 PHE Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain U residue 100 SER Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain V residue 102 SER Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain W residue 61 ASN 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 Y residue 51 CYS Chi-restraints excluded: chain Z residue 22 ASP Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain a residue 66 VAL 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 16 GLU Chi-restraints excluded: chain b residue 38 ASP Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain c residue 11 GLN Chi-restraints excluded: chain d residue 2 THR Chi-restraints excluded: chain d residue 95 TYR 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: 0.6980 chunk 16 optimal weight: 30.0000 chunk 30 optimal weight: 40.0000 chunk 109 optimal weight: 0.0010 chunk 45 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 13 optimal weight: 50.0000 chunk 20 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 ASN ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 232 GLN ** a 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 236 ASN ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.145998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.103974 restraints weight = 32377.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.106434 restraints weight = 19354.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.108050 restraints weight = 13837.063| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.178 10394 Z= 0.352 Angle : 1.043 59.199 14098 Z= 0.579 Chirality : 0.048 0.781 1697 Planarity : 0.004 0.048 1868 Dihedral : 4.573 56.025 1500 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.27 % Favored : 97.66 % Rotamer: Outliers : 3.68 % Allowed : 31.20 % Favored : 65.13 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 3.46 (0.22), residues: 1408 helix: 2.76 (0.14), residues: 1177 sheet: -0.57 (1.25), residues: 12 loop : -0.36 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 59 HIS 0.026 0.002 HIS a 57 PHE 0.029 0.002 PHE a 168 TYR 0.016 0.002 TYR Z 35 ARG 0.006 0.000 ARG a 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2476.37 seconds wall clock time: 45 minutes 7.14 seconds (2707.14 seconds total)