Starting phenix.real_space_refine on Sat Aug 23 06:06:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q85_18247/08_2025/8q85_18247.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q85_18247/08_2025/8q85_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 { model { file = "/net/cci-nas-00/data/ceres_data/8q85_18247/08_2025/8q85_18247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q85_18247/08_2025/8q85_18247.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q85_18247/08_2025/8q85_18247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q85_18247/08_2025/8q85_18247.map" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASN:plan1': 18, 'GLN:plan1': 12, 'ASP:plan': 14, 'ARG:plan': 10, 'GLU:plan': 26, 'PHE:plan': 5, 'TYR:plan': 3, 'HIS:plan': 5} 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: {'ASP:plan': 12, 'GLN:plan1': 13, 'ASN:plan1': 13, 'PHE:plan': 3, 'GLU:plan': 23, 'TYR:plan': 5, 'ARG:plan': 3, 'HIS:plan': 1} 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: 2.76, per 1000 atoms: 0.27 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: 1.16 Conformation dependent library (CDL) restraints added in 433.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.42 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: 1.79 Time building geometry restraints manager: 1.47 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: 2.400 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: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.750 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.050 ------------------------------------------------------------------------------- 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= 0.188 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG d 86 TYR 0.028 0.002 TYR a 230 PHE 0.026 0.002 PHE a 83 TRP 0.021 0.002 TRP b 59 HIS 0.006 0.001 HIS a 31 Details of bonding type rmsd covalent geometry : bond 0.00399 (10394) covalent geometry : angle 0.92310 (14098) hydrogen bonds : bond 0.09394 ( 1042) hydrogen bonds : angle 5.53288 ( 3102) *********************** 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 to be fit. rotamer outliers: 5 poor density : 234 time to evaluate : 0.472 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: 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: 0.8227 (t80) REVERT: a 256 ASP cc_start: 0.9662 (m-30) cc_final: 0.9351 (p0) 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: 0.1174 time to fit residues: 37.7090 Evaluate side-chains 222 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 220 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 108 ASN ** 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 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 ASN Y 31 ASN Y 55 HIS Z 41 GLN a 239 GLN c 63 GLN d 30 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.146794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.104501 restraints weight = 33490.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.107042 restraints weight = 20117.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.108708 restraints weight = 14364.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.109798 restraints weight = 11569.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.110411 restraints weight = 10118.696| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1202 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= 0.153 Angle : 0.698 12.652 14098 Z= 0.356 Chirality : 0.042 0.474 1697 Planarity : 0.004 0.079 1868 Dihedral : 4.715 55.367 1503 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.10 % Allowed : 23.84 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.06 (0.21), residues: 1408 helix: 2.50 (0.14), residues: 1178 sheet: -2.00 (1.03), residues: 12 loop : -0.48 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG d 57 TYR 0.018 0.002 TYR Z 16 PHE 0.021 0.002 PHE X 20 TRP 0.019 0.001 TRP b 59 HIS 0.006 0.001 HIS a 31 Details of bonding type rmsd covalent geometry : bond 0.00319 (10394) covalent geometry : angle 0.69834 (14098) hydrogen bonds : bond 0.04301 ( 1042) hydrogen bonds : angle 4.03160 ( 3102) *********************** 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 285 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 246 time to evaluate : 0.417 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: 0.8249 (tm-30) cc_final: 0.7953 (tm-30) REVERT: U 93 ASP cc_start: 0.7976 (m-30) cc_final: 0.7712 (m-30) REVERT: U 120 ASP cc_start: 0.7863 (p0) cc_final: 0.7661 (p0) REVERT: U 125 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7817 (mm) REVERT: W 11 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8178 (mtpt) REVERT: W 34 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8077 (mm-30) REVERT: W 72 GLN cc_start: 0.8200 (tp40) cc_final: 0.7919 (tp-100) REVERT: W 79 GLU cc_start: 0.8052 (mp0) cc_final: 0.7704 (pm20) REVERT: Z 16 TYR cc_start: 0.7867 (m-80) cc_final: 0.6676 (m-80) REVERT: Z 17 LYS cc_start: 0.9541 (mmtt) cc_final: 0.9171 (mmtt) REVERT: Z 38 HIS cc_start: 0.5513 (p-80) cc_final: 0.4252 (p-80) REVERT: a 93 MET cc_start: 0.7366 (mmt) cc_final: 0.6876 (mmm) REVERT: a 168 PHE cc_start: 0.7574 (m-80) cc_final: 0.6342 (m-80) REVERT: a 227 LYS cc_start: 0.9263 (mmmt) cc_final: 0.8975 (mmmt) REVERT: b 1 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6670 (ppp) REVERT: b 48 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8134 (tm-30) REVERT: c 38 ASN cc_start: 0.8292 (m-40) cc_final: 0.7989 (m110) REVERT: d 63 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8918 (tp) REVERT: d 67 GLU cc_start: 0.8465 (tp30) cc_final: 0.8082 (tp30) outliers start: 39 outliers final: 14 residues processed: 270 average time/residue: 0.1011 time to fit residues: 37.5701 Evaluate side-chains 245 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 228 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 106 MET Chi-restraints excluded: chain U residue 125 LEU 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 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 48 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 21 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 115 optimal weight: 0.3980 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 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** a 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.146590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.104302 restraints weight = 33371.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.106769 restraints weight = 20041.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.108432 restraints weight = 14412.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.109506 restraints weight = 11615.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.110189 restraints weight = 10153.408| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1683 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= 0.144 Angle : 0.666 12.982 14098 Z= 0.336 Chirality : 0.041 0.273 1697 Planarity : 0.004 0.062 1868 Dihedral : 4.535 55.767 1500 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.15 % Allowed : 24.16 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.34 (0.22), residues: 1408 helix: 2.74 (0.14), residues: 1171 sheet: -2.05 (1.03), residues: 12 loop : -0.56 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG d 83 TYR 0.026 0.002 TYR a 230 PHE 0.019 0.002 PHE X 20 TRP 0.017 0.001 TRP b 59 HIS 0.006 0.001 HIS a 31 Details of bonding type rmsd covalent geometry : bond 0.00302 (10394) covalent geometry : angle 0.66555 (14098) hydrogen bonds : bond 0.04150 ( 1042) hydrogen bonds : angle 3.85263 ( 3102) *********************** 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 272 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 242 time to evaluate : 0.557 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: U 89 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8042 (tm-30) REVERT: U 93 ASP cc_start: 0.8067 (m-30) cc_final: 0.7715 (m-30) REVERT: U 98 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8416 (mm) REVERT: U 120 ASP cc_start: 0.7973 (p0) cc_final: 0.7732 (p0) REVERT: U 125 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7791 (mm) REVERT: W 6 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7899 (pt0) REVERT: W 34 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8150 (mm-30) REVERT: W 72 GLN cc_start: 0.8219 (tp40) cc_final: 0.7991 (tp-100) REVERT: W 79 GLU cc_start: 0.8005 (mp0) cc_final: 0.7621 (pm20) REVERT: X 47 ILE cc_start: 0.7608 (mt) cc_final: 0.7368 (mm) REVERT: Z 16 TYR cc_start: 0.7667 (m-80) cc_final: 0.6356 (m-80) REVERT: Z 17 LYS cc_start: 0.9603 (mmtt) cc_final: 0.9238 (mmtt) REVERT: Z 22 ASP cc_start: 0.8376 (t0) cc_final: 0.7782 (p0) REVERT: Z 38 HIS cc_start: 0.5746 (p-80) cc_final: 0.4276 (p-80) REVERT: Z 87 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8129 (tm-30) REVERT: a 227 LYS cc_start: 0.9202 (mmmt) cc_final: 0.8946 (mmmt) REVERT: a 230 TYR cc_start: 0.8639 (t80) cc_final: 0.7944 (t80) REVERT: a 259 LYS cc_start: 0.9342 (mmmt) cc_final: 0.8993 (mtmm) REVERT: b 1 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6582 (ppp) REVERT: b 48 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8249 (tm-30) REVERT: c 38 ASN cc_start: 0.8442 (m-40) cc_final: 0.8211 (m110) REVERT: d 63 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8982 (tp) REVERT: d 67 GLU cc_start: 0.8502 (tp30) cc_final: 0.7992 (tp30) REVERT: d 85 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8863 (tm-30) outliers start: 30 outliers final: 16 residues processed: 260 average time/residue: 0.1137 time to fit residues: 40.3179 Evaluate side-chains 244 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 224 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 U residue 125 LEU 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 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 38 ASP Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 67 THR 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 64 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 50.0000 chunk 34 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 17 optimal weight: 70.0000 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 109 HIS ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.146468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.104775 restraints weight = 32669.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.107356 restraints weight = 19165.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.109015 restraints weight = 13486.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.110121 restraints weight = 10826.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.110724 restraints weight = 9416.708| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10394 Z= 0.139 Angle : 0.684 13.692 14098 Z= 0.340 Chirality : 0.041 0.429 1697 Planarity : 0.004 0.051 1868 Dihedral : 4.473 55.745 1500 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.89 % Allowed : 24.58 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.52 (0.21), residues: 1408 helix: 2.82 (0.14), residues: 1182 sheet: -2.01 (1.08), residues: 12 loop : -0.37 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG d 83 TYR 0.020 0.001 TYR a 230 PHE 0.025 0.002 PHE a 168 TRP 0.014 0.001 TRP b 59 HIS 0.006 0.001 HIS a 31 Details of bonding type rmsd covalent geometry : bond 0.00291 (10394) covalent geometry : angle 0.68371 (14098) hydrogen bonds : bond 0.04107 ( 1042) hydrogen bonds : angle 3.76426 ( 3102) *********************** 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 282 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 245 time to evaluate : 0.439 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: U 78 ASP cc_start: 0.7653 (t0) cc_final: 0.7385 (t0) REVERT: U 83 ARG cc_start: 0.7628 (ptp-170) cc_final: 0.7365 (ptp-170) REVERT: U 89 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8089 (tm-30) REVERT: U 93 ASP cc_start: 0.8101 (m-30) cc_final: 0.7708 (m-30) REVERT: U 94 LEU cc_start: 0.8968 (tp) cc_final: 0.8709 (tt) REVERT: U 98 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8372 (mm) REVERT: U 120 ASP cc_start: 0.7807 (p0) cc_final: 0.7588 (p0) REVERT: U 125 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7817 (mm) REVERT: U 136 ASP cc_start: 0.9531 (m-30) cc_final: 0.9175 (p0) REVERT: V 77 MET cc_start: 0.9082 (ppp) cc_final: 0.8861 (ppp) REVERT: W 34 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8124 (mm-30) REVERT: W 79 GLU cc_start: 0.8046 (mp0) cc_final: 0.7612 (pm20) REVERT: X 47 ILE cc_start: 0.7610 (mt) cc_final: 0.7410 (mm) REVERT: Z 16 TYR cc_start: 0.7669 (m-80) cc_final: 0.6289 (m-80) REVERT: Z 17 LYS cc_start: 0.9592 (mmtt) cc_final: 0.9259 (mmtt) REVERT: Z 35 TYR cc_start: 0.5846 (t80) cc_final: 0.5635 (t80) REVERT: Z 38 HIS cc_start: 0.5604 (p-80) cc_final: 0.4586 (p-80) REVERT: Z 87 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8218 (tm-30) REVERT: a 227 LYS cc_start: 0.9189 (mmmt) cc_final: 0.8967 (mmmt) REVERT: a 230 TYR cc_start: 0.8634 (t80) cc_final: 0.8037 (t80) REVERT: b 1 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6470 (ppp) REVERT: b 48 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8254 (tm-30) REVERT: b 51 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7203 (tm-30) REVERT: c 1 MET cc_start: 0.7751 (tmm) cc_final: 0.7539 (tmm) REVERT: c 61 MET cc_start: 0.7987 (mmt) cc_final: 0.7785 (mmt) REVERT: c 64 MET cc_start: 0.8840 (pmm) cc_final: 0.8426 (pmm) REVERT: d 63 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8981 (tp) REVERT: d 71 ARG cc_start: 0.8735 (mmm160) cc_final: 0.8520 (mmm160) REVERT: d 85 GLN cc_start: 0.9032 (tm-30) cc_final: 0.8802 (tm-30) REVERT: d 86 ARG cc_start: 0.8234 (ptt180) cc_final: 0.8011 (ptt180) outliers start: 37 outliers final: 22 residues processed: 270 average time/residue: 0.1154 time to fit residues: 42.7279 Evaluate side-chains 255 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 U residue 125 LEU 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 a residue 249 LYS Chi-restraints excluded: chain b residue 1 MET 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 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 63 ILE 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 8 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 38 ASN ** 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 = 0.4328 r_free = 0.4328 target = 0.147027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.105907 restraints weight = 31883.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.108307 restraints weight = 18933.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.109790 restraints weight = 13518.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.110792 restraints weight = 10953.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.111419 restraints weight = 9603.029| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10394 Z= 0.141 Angle : 0.676 13.840 14098 Z= 0.341 Chirality : 0.041 0.370 1697 Planarity : 0.004 0.049 1868 Dihedral : 4.447 56.813 1500 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.52 % Allowed : 26.05 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.58 (0.21), residues: 1408 helix: 2.84 (0.14), residues: 1182 sheet: -1.01 (1.33), residues: 12 loop : -0.35 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG d 83 TYR 0.019 0.001 TYR a 230 PHE 0.015 0.002 PHE X 20 TRP 0.014 0.001 TRP b 59 HIS 0.013 0.001 HIS a 109 Details of bonding type rmsd covalent geometry : bond 0.00299 (10394) covalent geometry : angle 0.67599 (14098) hydrogen bonds : bond 0.04046 ( 1042) hydrogen bonds : angle 3.70282 ( 3102) *********************** 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 to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 0.428 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: 0.8396 (tm-30) cc_final: 0.8124 (tm-30) REVERT: U 93 ASP cc_start: 0.8117 (m-30) cc_final: 0.7720 (m-30) REVERT: U 94 LEU cc_start: 0.8966 (tp) cc_final: 0.8724 (tt) REVERT: U 98 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8372 (mm) REVERT: U 120 ASP cc_start: 0.7779 (p0) cc_final: 0.7552 (p0) REVERT: U 125 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7743 (mm) REVERT: V 79 LYS cc_start: 0.9389 (mmmt) cc_final: 0.9157 (mmmt) REVERT: W 34 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8135 (mm-30) REVERT: W 79 GLU cc_start: 0.7963 (mp0) cc_final: 0.7642 (pm20) REVERT: X 43 ASN cc_start: 0.7840 (m-40) cc_final: 0.7559 (m-40) REVERT: Z 16 TYR cc_start: 0.7717 (m-80) cc_final: 0.6378 (m-80) REVERT: Z 17 LYS cc_start: 0.9621 (mmtt) cc_final: 0.9299 (mmtt) REVERT: Z 21 LEU cc_start: 0.9100 (pp) cc_final: 0.8754 (pp) REVERT: Z 22 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7060 (m-30) REVERT: Z 24 LYS cc_start: 0.8749 (mttp) cc_final: 0.8328 (mttp) REVERT: Z 38 HIS cc_start: 0.5499 (p-80) cc_final: 0.4450 (p-80) REVERT: a 227 LYS cc_start: 0.9226 (mmmt) cc_final: 0.8986 (mmmt) REVERT: a 230 TYR cc_start: 0.8564 (t80) cc_final: 0.8065 (t80) REVERT: b 1 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6383 (ppp) REVERT: b 48 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8145 (tm-30) REVERT: c 1 MET cc_start: 0.7547 (tmm) cc_final: 0.7047 (tmm) REVERT: c 61 MET cc_start: 0.8073 (mmt) cc_final: 0.7873 (mmt) REVERT: c 64 MET cc_start: 0.8861 (pmm) cc_final: 0.8448 (pmm) REVERT: d 63 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8955 (tp) REVERT: d 86 ARG cc_start: 0.8256 (ptt180) cc_final: 0.8004 (ptt180) outliers start: 43 outliers final: 24 residues processed: 281 average time/residue: 0.1166 time to fit residues: 44.7843 Evaluate side-chains 259 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 125 LEU 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 74 SER Chi-restraints excluded: chain a residue 66 VAL 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 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 38 SER Chi-restraints excluded: chain d residue 63 ILE 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 103 optimal weight: 0.6980 chunk 15 optimal weight: 30.0000 chunk 81 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 50.0000 chunk 122 optimal weight: 0.3980 chunk 14 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.146808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.105767 restraints weight = 32369.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.108235 restraints weight = 19197.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.109850 restraints weight = 13638.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.110910 restraints weight = 10941.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.111364 restraints weight = 9516.732| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10394 Z= 0.143 Angle : 0.718 14.209 14098 Z= 0.364 Chirality : 0.041 0.259 1697 Planarity : 0.004 0.049 1868 Dihedral : 4.501 57.133 1500 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.68 % Allowed : 28.05 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.49 (0.22), residues: 1408 helix: 2.78 (0.14), residues: 1183 sheet: -0.48 (1.48), residues: 12 loop : -0.40 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG d 83 TYR 0.015 0.001 TYR a 230 PHE 0.026 0.002 PHE a 168 TRP 0.013 0.001 TRP b 59 HIS 0.014 0.001 HIS a 109 Details of bonding type rmsd covalent geometry : bond 0.00301 (10394) covalent geometry : angle 0.71760 (14098) hydrogen bonds : bond 0.04016 ( 1042) hydrogen bonds : angle 3.71892 ( 3102) *********************** 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 284 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 249 time to evaluate : 0.412 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: 0.8361 (tm-30) cc_final: 0.8108 (tm-30) REVERT: U 93 ASP cc_start: 0.8129 (m-30) cc_final: 0.7750 (m-30) REVERT: U 94 LEU cc_start: 0.8964 (tp) cc_final: 0.8716 (tt) REVERT: U 98 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8401 (mm) REVERT: U 120 ASP cc_start: 0.7699 (p0) cc_final: 0.7449 (p0) REVERT: U 129 LYS cc_start: 0.9306 (mmtt) cc_final: 0.9079 (mmtt) REVERT: W 34 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8114 (mm-30) REVERT: W 79 GLU cc_start: 0.7932 (mp0) cc_final: 0.7519 (pm20) REVERT: Z 16 TYR cc_start: 0.7639 (m-80) cc_final: 0.6310 (m-80) REVERT: Z 17 LYS cc_start: 0.9595 (mmtt) cc_final: 0.9294 (mmtt) REVERT: Z 21 LEU cc_start: 0.9076 (pp) cc_final: 0.8652 (pp) REVERT: Z 24 LYS cc_start: 0.8731 (mttp) cc_final: 0.8274 (mttp) REVERT: Z 33 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8003 (mm) REVERT: Z 38 HIS cc_start: 0.5294 (p-80) cc_final: 0.4038 (p-80) REVERT: Z 52 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8446 (tm-30) REVERT: a 168 PHE cc_start: 0.7364 (m-80) cc_final: 0.6833 (m-80) REVERT: a 216 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7858 (pt0) REVERT: a 230 TYR cc_start: 0.8450 (t80) cc_final: 0.8230 (t80) REVERT: b 1 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6258 (ppp) REVERT: b 48 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8130 (tm-30) REVERT: c 1 MET cc_start: 0.7533 (tmm) cc_final: 0.6857 (tmm) REVERT: c 15 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8112 (mm-30) REVERT: c 36 GLN cc_start: 0.8487 (mp10) cc_final: 0.8278 (pm20) REVERT: c 64 MET cc_start: 0.8998 (pmm) cc_final: 0.8760 (pmm) REVERT: d 63 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8956 (tp) outliers start: 35 outliers final: 25 residues processed: 274 average time/residue: 0.1202 time to fit residues: 44.9679 Evaluate side-chains 259 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 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 33 LEU Chi-restraints excluded: chain Z residue 35 TYR 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 249 LYS 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 38 ASP 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 63 ILE 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 120 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 2 optimal weight: 30.0000 chunk 27 optimal weight: 50.0000 chunk 12 optimal weight: 50.0000 chunk 96 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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** Y 5 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.146354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.104135 restraints weight = 32446.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.106680 restraints weight = 19310.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.108298 restraints weight = 13720.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.109287 restraints weight = 11055.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.109942 restraints weight = 9705.728| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2789 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= 0.149 Angle : 0.720 14.222 14098 Z= 0.367 Chirality : 0.041 0.245 1697 Planarity : 0.004 0.048 1868 Dihedral : 4.505 58.644 1500 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.52 % Allowed : 27.42 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.56 (0.22), residues: 1408 helix: 2.86 (0.14), residues: 1175 sheet: -0.76 (1.37), residues: 12 loop : -0.42 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG d 78 TYR 0.013 0.001 TYR Z 35 PHE 0.017 0.002 PHE a 168 TRP 0.013 0.001 TRP b 59 HIS 0.016 0.001 HIS a 109 Details of bonding type rmsd covalent geometry : bond 0.00322 (10394) covalent geometry : angle 0.72020 (14098) hydrogen bonds : bond 0.03995 ( 1042) hydrogen bonds : angle 3.73431 ( 3102) *********************** 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 286 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 243 time to evaluate : 0.439 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: 0.8384 (tm-30) cc_final: 0.8100 (tm-30) REVERT: U 93 ASP cc_start: 0.8085 (m-30) cc_final: 0.7658 (m-30) REVERT: U 94 LEU cc_start: 0.8978 (tp) cc_final: 0.8728 (tt) REVERT: U 98 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8433 (mm) REVERT: U 120 ASP cc_start: 0.7810 (p0) cc_final: 0.7597 (p0) REVERT: W 34 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8096 (mm-30) REVERT: W 79 GLU cc_start: 0.7953 (mp0) cc_final: 0.7645 (pm20) REVERT: Z 16 TYR cc_start: 0.7675 (m-80) cc_final: 0.6281 (m-80) REVERT: Z 17 LYS cc_start: 0.9648 (mmtt) cc_final: 0.9387 (mmtt) REVERT: Z 21 LEU cc_start: 0.9086 (pp) cc_final: 0.8661 (pp) REVERT: Z 24 LYS cc_start: 0.8744 (mttp) cc_final: 0.8299 (mttp) REVERT: Z 33 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7998 (mm) REVERT: Z 34 ASN cc_start: 0.8368 (t0) cc_final: 0.8024 (p0) REVERT: Z 38 HIS cc_start: 0.5369 (p-80) cc_final: 0.3979 (p-80) REVERT: b 48 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8019 (tm-30) REVERT: c 15 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8187 (mm-30) REVERT: d 24 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7123 (tm-30) REVERT: d 57 ARG cc_start: 0.8754 (tpp80) cc_final: 0.8547 (tpp80) REVERT: d 67 GLU cc_start: 0.8507 (tp30) cc_final: 0.8081 (tp30) REVERT: d 86 ARG cc_start: 0.8250 (ptt180) cc_final: 0.7962 (ptm160) outliers start: 43 outliers final: 29 residues processed: 271 average time/residue: 0.1173 time to fit residues: 43.2137 Evaluate side-chains 258 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 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 35 TYR Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 197 ARG Chi-restraints excluded: chain a residue 249 LYS 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 67 THR Chi-restraints excluded: chain c residue 4 ASN Chi-restraints excluded: chain c residue 11 GLN Chi-restraints excluded: chain d residue 38 SER 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 116 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 20 optimal weight: 40.0000 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 60.0000 chunk 106 optimal weight: 9.9990 chunk 21 optimal weight: 40.0000 chunk 129 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** ** 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 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.145446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.105226 restraints weight = 31970.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.107685 restraints weight = 18801.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.109249 restraints weight = 13224.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.110276 restraints weight = 10576.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.110711 restraints weight = 9210.226| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10394 Z= 0.152 Angle : 0.752 15.572 14098 Z= 0.387 Chirality : 0.042 0.233 1697 Planarity : 0.004 0.063 1868 Dihedral : 4.556 59.615 1500 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.89 % Allowed : 29.31 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.52 (0.22), residues: 1408 helix: 2.81 (0.14), residues: 1176 sheet: -0.68 (1.35), residues: 12 loop : -0.38 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG d 83 TYR 0.022 0.002 TYR a 230 PHE 0.016 0.002 PHE a 168 TRP 0.013 0.001 TRP b 59 HIS 0.019 0.002 HIS a 109 Details of bonding type rmsd covalent geometry : bond 0.00329 (10394) covalent geometry : angle 0.75201 (14098) hydrogen bonds : bond 0.04031 ( 1042) hydrogen bonds : angle 3.75852 ( 3102) *********************** 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 274 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 0.354 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: 0.8412 (tm-30) cc_final: 0.8128 (tm-30) REVERT: U 93 ASP cc_start: 0.8113 (m-30) cc_final: 0.7734 (m-30) REVERT: U 94 LEU cc_start: 0.8974 (tp) cc_final: 0.8726 (tt) REVERT: U 98 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8425 (mm) REVERT: U 120 ASP cc_start: 0.7883 (p0) cc_final: 0.7670 (p0) REVERT: W 34 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8127 (mm-30) REVERT: W 72 GLN cc_start: 0.8318 (tp-100) cc_final: 0.8103 (tp-100) REVERT: W 79 GLU cc_start: 0.7977 (mp0) cc_final: 0.7647 (pm20) REVERT: X 24 ARG cc_start: 0.8543 (mtp180) cc_final: 0.7843 (mtm-85) REVERT: Z 16 TYR cc_start: 0.7553 (m-80) cc_final: 0.6320 (m-80) REVERT: Z 17 LYS cc_start: 0.9665 (mmtt) cc_final: 0.9416 (mmtt) REVERT: Z 21 LEU cc_start: 0.9071 (pp) cc_final: 0.8689 (pp) REVERT: Z 22 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: Z 24 LYS cc_start: 0.8731 (mttp) cc_final: 0.8288 (mttp) REVERT: Z 33 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8000 (mm) REVERT: Z 34 ASN cc_start: 0.8468 (t0) cc_final: 0.8107 (p0) REVERT: Z 38 HIS cc_start: 0.5210 (p-80) cc_final: 0.3955 (p-80) REVERT: a 168 PHE cc_start: 0.7468 (m-80) cc_final: 0.7156 (m-80) REVERT: a 197 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.6150 (ptm-80) REVERT: a 256 ASP cc_start: 0.9477 (m-30) cc_final: 0.9172 (p0) REVERT: b 48 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8035 (tm-30) REVERT: c 1 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7052 (tmm) REVERT: c 6 GLN cc_start: 0.7955 (tm130) cc_final: 0.7474 (tm-30) REVERT: c 15 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8190 (mm-30) REVERT: d 3 ASP cc_start: 0.7304 (p0) cc_final: 0.6347 (p0) REVERT: d 24 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7153 (tm-30) REVERT: d 67 GLU cc_start: 0.8517 (tp30) cc_final: 0.8080 (tp30) REVERT: d 86 ARG cc_start: 0.8212 (ptt180) cc_final: 0.7916 (ptm160) outliers start: 37 outliers final: 28 residues processed: 261 average time/residue: 0.1056 time to fit residues: 37.5217 Evaluate side-chains 262 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 197 ARG Chi-restraints excluded: chain a residue 249 LYS 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 67 THR Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 4 ASN Chi-restraints excluded: chain c residue 11 GLN 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 44 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** ** W 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.145531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.105085 restraints weight = 32107.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.107567 restraints weight = 18998.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.109152 restraints weight = 13376.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.110152 restraints weight = 10702.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.110791 restraints weight = 9325.005| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3153 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= 0.151 Angle : 0.785 15.030 14098 Z= 0.401 Chirality : 0.042 0.219 1697 Planarity : 0.004 0.061 1868 Dihedral : 4.566 55.926 1500 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.47 % Allowed : 29.73 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.50 (0.22), residues: 1408 helix: 2.80 (0.14), residues: 1173 sheet: -0.49 (1.32), residues: 12 loop : -0.35 (0.43), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG d 78 TYR 0.027 0.001 TYR a 230 PHE 0.018 0.002 PHE a 168 TRP 0.013 0.001 TRP b 59 HIS 0.016 0.001 HIS a 109 Details of bonding type rmsd covalent geometry : bond 0.00323 (10394) covalent geometry : angle 0.78454 (14098) hydrogen bonds : bond 0.04055 ( 1042) hydrogen bonds : angle 3.78923 ( 3102) *********************** 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 279 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 246 time to evaluate : 0.324 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 83 ARG cc_start: 0.7692 (ptp-170) cc_final: 0.7491 (ptp-170) REVERT: U 89 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8147 (tm-30) REVERT: U 93 ASP cc_start: 0.8123 (m-30) cc_final: 0.7735 (m-30) REVERT: U 94 LEU cc_start: 0.8967 (tp) cc_final: 0.8608 (tt) REVERT: U 98 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8434 (mm) REVERT: U 120 ASP cc_start: 0.7734 (p0) cc_final: 0.7493 (p0) REVERT: W 34 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8144 (mm-30) REVERT: W 79 GLU cc_start: 0.7911 (mp0) cc_final: 0.7607 (pm20) REVERT: X 24 ARG cc_start: 0.8565 (mtp180) cc_final: 0.7855 (mtm-85) REVERT: Z 11 GLU cc_start: 0.9551 (tm-30) cc_final: 0.9344 (pp20) REVERT: Z 16 TYR cc_start: 0.7638 (m-80) cc_final: 0.6419 (m-80) REVERT: Z 17 LYS cc_start: 0.9660 (mmtt) cc_final: 0.9426 (mmtt) REVERT: Z 21 LEU cc_start: 0.9070 (pp) cc_final: 0.8667 (pp) REVERT: Z 22 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7515 (m-30) REVERT: Z 24 LYS cc_start: 0.8743 (mttp) cc_final: 0.8287 (mttp) REVERT: Z 33 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8020 (mm) REVERT: Z 34 ASN cc_start: 0.8482 (t0) cc_final: 0.8148 (p0) REVERT: Z 38 HIS cc_start: 0.5218 (p-80) cc_final: 0.4040 (p-80) REVERT: a 168 PHE cc_start: 0.7406 (m-80) cc_final: 0.7054 (m-80) REVERT: a 197 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6202 (ptm-80) REVERT: b 48 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8060 (tm-30) REVERT: c 6 GLN cc_start: 0.7915 (tm130) cc_final: 0.7394 (tm-30) REVERT: c 15 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8196 (mm-30) REVERT: d 24 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7176 (tm-30) REVERT: d 67 GLU cc_start: 0.8552 (tp30) cc_final: 0.8312 (tp30) outliers start: 33 outliers final: 26 residues processed: 270 average time/residue: 0.1129 time to fit residues: 41.4896 Evaluate side-chains 258 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 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 197 ARG Chi-restraints excluded: chain a residue 249 LYS 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 67 THR Chi-restraints excluded: chain c residue 11 GLN Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 0 optimal weight: 40.0000 chunk 78 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 2 optimal weight: 30.0000 chunk 27 optimal weight: 90.0000 chunk 105 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** ** c 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.145410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.104844 restraints weight = 31793.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.107321 restraints weight = 18792.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.108880 restraints weight = 13266.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.109855 restraints weight = 10666.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.110518 restraints weight = 9321.238| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3332 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= 0.159 Angle : 0.820 15.390 14098 Z= 0.424 Chirality : 0.043 0.236 1697 Planarity : 0.004 0.060 1868 Dihedral : 4.540 56.270 1500 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.57 % Allowed : 30.67 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.40 (0.22), residues: 1408 helix: 2.72 (0.14), residues: 1178 sheet: -0.34 (1.31), residues: 12 loop : -0.37 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 78 TYR 0.016 0.001 TYR Z 16 PHE 0.026 0.002 PHE b 30 TRP 0.013 0.001 TRP b 59 HIS 0.016 0.002 HIS a 109 Details of bonding type rmsd covalent geometry : bond 0.00342 (10394) covalent geometry : angle 0.81959 (14098) hydrogen bonds : bond 0.04157 ( 1042) hydrogen bonds : angle 3.82228 ( 3102) ********************** 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 279 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 0.465 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: 0.8343 (tm-30) cc_final: 0.8044 (tm-30) REVERT: U 93 ASP cc_start: 0.8111 (m-30) cc_final: 0.7716 (m-30) REVERT: U 94 LEU cc_start: 0.8968 (tp) cc_final: 0.8603 (tt) REVERT: U 98 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8448 (mm) REVERT: U 120 ASP cc_start: 0.7712 (p0) cc_final: 0.7433 (p0) REVERT: U 135 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8617 (pp20) REVERT: W 34 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8138 (mm-30) REVERT: W 79 GLU cc_start: 0.7901 (mp0) cc_final: 0.7619 (pm20) REVERT: X 24 ARG cc_start: 0.8577 (mtp180) cc_final: 0.7866 (mtm-85) REVERT: Z 16 TYR cc_start: 0.7619 (m-80) cc_final: 0.6373 (m-80) REVERT: Z 21 LEU cc_start: 0.9025 (pp) cc_final: 0.8630 (pp) REVERT: Z 22 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: Z 24 LYS cc_start: 0.8746 (mttp) cc_final: 0.8300 (mttp) REVERT: Z 33 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8016 (mm) REVERT: Z 34 ASN cc_start: 0.8522 (t0) cc_final: 0.8188 (p0) REVERT: Z 38 HIS cc_start: 0.5344 (p-80) cc_final: 0.4034 (p-80) REVERT: a 168 PHE cc_start: 0.7457 (m-80) cc_final: 0.7177 (m-80) REVERT: a 256 ASP cc_start: 0.9457 (m-30) cc_final: 0.9153 (p0) REVERT: b 1 MET cc_start: 0.6854 (ppp) cc_final: 0.5568 (ppp) REVERT: b 48 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8044 (tm-30) REVERT: c 6 GLN cc_start: 0.7937 (tm130) cc_final: 0.7419 (tm-30) REVERT: c 15 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8168 (mm-30) REVERT: d 24 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7196 (tm-30) REVERT: d 67 GLU cc_start: 0.8567 (tp30) cc_final: 0.8326 (tp30) REVERT: d 86 ARG cc_start: 0.8098 (ptt180) cc_final: 0.7801 (ptm160) outliers start: 34 outliers final: 28 residues processed: 270 average time/residue: 0.1132 time to fit residues: 42.1757 Evaluate side-chains 267 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 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 249 LYS 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 67 THR Chi-restraints excluded: chain c residue 11 GLN Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 50.0000 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 120 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 52 optimal weight: 0.0010 chunk 84 optimal weight: 5.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 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** ** c 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.145630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.103691 restraints weight = 32970.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.106226 restraints weight = 19643.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.107815 restraints weight = 13901.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.108834 restraints weight = 11204.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.109510 restraints weight = 9792.487| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3412 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= 0.155 Angle : 0.842 15.930 14098 Z= 0.433 Chirality : 0.044 0.241 1697 Planarity : 0.004 0.063 1868 Dihedral : 4.514 57.104 1500 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.36 % Allowed : 30.99 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.37 (0.22), residues: 1408 helix: 2.72 (0.14), residues: 1172 sheet: -0.32 (1.33), residues: 12 loop : -0.46 (0.43), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG d 78 TYR 0.013 0.001 TYR Z 35 PHE 0.015 0.002 PHE a 168 TRP 0.014 0.001 TRP b 59 HIS 0.016 0.002 HIS a 109 Details of bonding type rmsd covalent geometry : bond 0.00335 (10394) covalent geometry : angle 0.84232 (14098) hydrogen bonds : bond 0.04143 ( 1042) hydrogen bonds : angle 3.83103 ( 3102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2917.35 seconds wall clock time: 50 minutes 48.72 seconds (3048.72 seconds total)