Starting phenix.real_space_refine on Fri Dec 27 22:26:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whz_32516/12_2024/7whz_32516.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whz_32516/12_2024/7whz_32516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7whz_32516/12_2024/7whz_32516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whz_32516/12_2024/7whz_32516.map" model { file = "/net/cci-nas-00/data/ceres_data/7whz_32516/12_2024/7whz_32516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whz_32516/12_2024/7whz_32516.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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 30 5.16 5 C 4288 2.51 5 N 1142 2.21 5 O 1350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6810 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "B" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "C" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "E" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 830 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 935 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.59, per 1000 atoms: 0.82 Number of scatterers: 6810 At special positions: 0 Unit cell: (81.69, 94.916, 119.812, 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 30 16.00 O 1350 8.00 N 1142 7.00 C 4288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 1.0 seconds 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1602 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 23 sheets defined 2.6% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.578A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.735A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.610A pdb=" N ASP C 90 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C 91 " --> pdb=" O VAL C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.576A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.555A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.538A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.988A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 18 " --> pdb=" O MET C 83 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 81 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.668A pdb=" N TYR C 59 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS C 35 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N CYS C 96 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N TRP C 112 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS C 98 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.051A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 72 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.737A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.737A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 90 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AB6, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB7, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.699A pdb=" N GLU H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA H 92 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.568A pdb=" N ASN H 59 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 68 through 69 removed outlier: 3.609A pdb=" N THR H 69 " --> pdb=" O ASP H 82 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 72 through 73 removed outlier: 3.524A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 17 through 23 removed outlier: 3.503A pdb=" N SER L 67 " --> pdb=" O SER L 74 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 36 through 40 Processing sheet with id=AC5, first strand: chain 'L' and resid 36 through 40 163 hydrogen bonds defined for protein. 381 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2184 1.35 - 1.47: 1977 1.47 - 1.60: 2773 1.60 - 1.73: 0 1.73 - 1.86: 40 Bond restraints: 6974 Sorted by residual: bond pdb=" C LYS L 106 " pdb=" O LYS L 106 " ideal model delta sigma weight residual 1.235 1.273 -0.038 1.13e-02 7.83e+03 1.13e+01 bond pdb=" CA THR H 117 " pdb=" CB THR H 117 " ideal model delta sigma weight residual 1.527 1.450 0.078 2.48e-02 1.63e+03 9.81e+00 bond pdb=" CA TYR D 87 " pdb=" C TYR D 87 " ideal model delta sigma weight residual 1.526 1.496 0.029 1.36e-02 5.41e+03 4.67e+00 bond pdb=" CB VAL B 50 " pdb=" CG2 VAL B 50 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.75e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.49e+00 ... (remaining 6969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 9394 3.45 - 6.89: 69 6.89 - 10.34: 10 10.34 - 13.78: 3 13.78 - 17.23: 1 Bond angle restraints: 9477 Sorted by residual: angle pdb=" N CYS A 432 " pdb=" CA CYS A 432 " pdb=" C CYS A 432 " ideal model delta sigma weight residual 110.17 121.04 -10.87 1.61e+00 3.86e-01 4.56e+01 angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 109.95 120.55 -10.60 1.59e+00 3.96e-01 4.45e+01 angle pdb=" N ASN A 394 " pdb=" CA ASN A 394 " pdb=" C ASN A 394 " ideal model delta sigma weight residual 108.99 117.30 -8.31 1.57e+00 4.06e-01 2.80e+01 angle pdb=" C GLU E 50 " pdb=" N THR E 51 " pdb=" CA THR E 51 " ideal model delta sigma weight residual 121.54 131.51 -9.97 1.91e+00 2.74e-01 2.73e+01 angle pdb=" N LYS L 106 " pdb=" CA LYS L 106 " pdb=" C LYS L 106 " ideal model delta sigma weight residual 108.02 98.90 9.12 1.78e+00 3.16e-01 2.62e+01 ... (remaining 9472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3662 17.53 - 35.07: 361 35.07 - 52.60: 67 52.60 - 70.14: 10 70.14 - 87.67: 4 Dihedral angle restraints: 4104 sinusoidal: 1569 harmonic: 2535 Sorted by residual: dihedral pdb=" CA GLY A 447 " pdb=" C GLY A 447 " pdb=" N ASN A 448 " pdb=" CA ASN A 448 " ideal model delta harmonic sigma weight residual -180.00 -149.32 -30.68 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA GLY B 105 " pdb=" C GLY B 105 " pdb=" N SER B 106 " pdb=" CA SER B 106 " ideal model delta harmonic sigma weight residual 180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA CYS A 361 " pdb=" C CYS A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 4101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 764 0.058 - 0.116: 204 0.116 - 0.174: 44 0.174 - 0.232: 12 0.232 - 0.290: 2 Chirality restraints: 1026 Sorted by residual: chirality pdb=" CB ILE B 70 " pdb=" CA ILE B 70 " pdb=" CG1 ILE B 70 " pdb=" CG2 ILE B 70 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA TYR E 94 " pdb=" N TYR E 94 " pdb=" C TYR E 94 " pdb=" CB TYR E 94 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL D 58 " pdb=" CA VAL D 58 " pdb=" CG1 VAL D 58 " pdb=" CG2 VAL D 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1023 not shown) Planarity restraints: 1226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 58 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO D 59 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 94 " 0.044 5.00e-02 4.00e+02 6.57e-02 6.90e+00 pdb=" N PRO E 95 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO E 95 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 95 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 45 " 0.039 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO L 46 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO L 46 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 46 " 0.033 5.00e-02 4.00e+02 ... (remaining 1223 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1976 2.80 - 3.33: 5469 3.33 - 3.85: 11092 3.85 - 4.38: 12404 4.38 - 4.90: 22385 Nonbonded interactions: 53326 Sorted by model distance: nonbonded pdb=" OG SER H 102 " pdb=" O TYR H 105 " model vdw 2.276 3.040 nonbonded pdb=" O SER L 26 " pdb=" OG SER L 31 " model vdw 2.305 3.040 nonbonded pdb=" OE1 GLN H 6 " pdb=" OG1 THR H 117 " model vdw 2.306 3.040 nonbonded pdb=" O ASP A 442 " pdb=" ND2 ASN A 448 " model vdw 2.321 3.120 nonbonded pdb=" OD1 ASP C 73 " pdb=" OG SER C 75 " model vdw 2.324 3.040 ... (remaining 53321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 1 through 8 or resid 10 through 30 or resid 33 or resid 35 \ through 49 or resid 52 through 54 or resid 56 through 69 or resid 71 through 80 \ or resid 82 through 90 or resid 93 or resid 98 through 103 or resid 105 through \ 107)) selection = (chain 'E' and (resid 1 through 8 or resid 10 through 30 or resid 33 or resid 35 \ through 49 or resid 52 through 54 or resid 56 through 69 or resid 71 through 80 \ or resid 82 through 90 or resid 93 or resid 98 through 103 or resid 105 through \ 107)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.170 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.007 0.078 6974 Z= 0.470 Angle : 0.937 17.228 9477 Z= 0.536 Chirality : 0.059 0.290 1026 Planarity : 0.007 0.069 1225 Dihedral : 14.214 87.672 2478 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.40 % Allowed : 9.69 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.24), residues: 873 helix: -5.10 (0.18), residues: 24 sheet: -2.74 (0.24), residues: 349 loop : -2.73 (0.23), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 52 HIS 0.006 0.001 HIS B 35 PHE 0.024 0.002 PHE E 83 TYR 0.026 0.002 TYR A 453 ARG 0.007 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 495 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7602 (m-10) REVERT: B 25 SER cc_start: 0.8764 (t) cc_final: 0.8403 (m) REVERT: C 105 LEU cc_start: 0.8011 (pp) cc_final: 0.7789 (pt) REVERT: D 33 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8201 (tp) REVERT: E 70 GLU cc_start: 0.8315 (pt0) cc_final: 0.8096 (pt0) REVERT: H 62 GLN cc_start: 0.8295 (tm-30) cc_final: 0.8005 (tp40) REVERT: H 74 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7174 (tm-30) REVERT: L 67 SER cc_start: 0.7561 (t) cc_final: 0.7275 (p) outliers start: 3 outliers final: 0 residues processed: 193 average time/residue: 0.2149 time to fit residues: 53.3553 Evaluate side-chains 138 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain D residue 33 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 360 ASN A 394 ASN A 506 GLN C 99 HIS D 100 GLN E 38 GLN L 53 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6974 Z= 0.222 Angle : 0.595 11.769 9477 Z= 0.313 Chirality : 0.044 0.191 1026 Planarity : 0.005 0.050 1225 Dihedral : 5.655 46.728 999 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.23 % Allowed : 15.48 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.25), residues: 873 helix: -4.96 (0.25), residues: 20 sheet: -2.24 (0.25), residues: 346 loop : -2.18 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 353 HIS 0.003 0.001 HIS C 99 PHE 0.011 0.001 PHE H 64 TYR 0.021 0.001 TYR E 94 ARG 0.005 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9223 (t) cc_final: 0.8775 (p) REVERT: A 495 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7096 (m-10) REVERT: C 99 HIS cc_start: 0.8242 (OUTLIER) cc_final: 0.7391 (m90) REVERT: D 33 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7947 (tp) REVERT: H 74 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6665 (tm-30) REVERT: H 88 SER cc_start: 0.8442 (t) cc_final: 0.8108 (m) REVERT: H 90 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8417 (t0) REVERT: L 67 SER cc_start: 0.7680 (t) cc_final: 0.7464 (p) outliers start: 24 outliers final: 10 residues processed: 145 average time/residue: 0.2365 time to fit residues: 43.3841 Evaluate side-chains 137 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN C 99 HIS L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6974 Z= 0.224 Angle : 0.581 14.343 9477 Z= 0.301 Chirality : 0.045 0.186 1026 Planarity : 0.004 0.045 1225 Dihedral : 5.215 34.539 999 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.77 % Allowed : 17.50 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.26), residues: 873 helix: -4.66 (0.41), residues: 20 sheet: -2.00 (0.25), residues: 349 loop : -1.82 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.017 0.003 HIS C 99 PHE 0.011 0.001 PHE A 377 TYR 0.020 0.001 TYR E 94 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9160 (t) cc_final: 0.8759 (p) REVERT: A 449 TYR cc_start: 0.8712 (p90) cc_final: 0.8430 (p90) REVERT: A 495 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.7657 (m-10) REVERT: C 99 HIS cc_start: 0.8494 (OUTLIER) cc_final: 0.7363 (m170) REVERT: D 33 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8056 (tp) REVERT: H 74 GLU cc_start: 0.7480 (tm-30) cc_final: 0.6659 (tm-30) REVERT: H 88 SER cc_start: 0.8539 (t) cc_final: 0.8193 (m) REVERT: H 90 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8419 (t0) REVERT: L 74 SER cc_start: 0.8052 (p) cc_final: 0.7818 (t) outliers start: 28 outliers final: 17 residues processed: 143 average time/residue: 0.2295 time to fit residues: 42.8006 Evaluate side-chains 136 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.0010 chunk 58 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN C 99 HIS L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6974 Z= 0.189 Angle : 0.562 14.645 9477 Z= 0.290 Chirality : 0.044 0.176 1026 Planarity : 0.004 0.043 1225 Dihedral : 4.892 33.731 999 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.77 % Allowed : 19.78 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.27), residues: 873 helix: -4.61 (0.46), residues: 20 sheet: -1.90 (0.25), residues: 359 loop : -1.54 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.008 0.002 HIS C 99 PHE 0.013 0.001 PHE A 377 TYR 0.020 0.001 TYR E 94 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9184 (t) cc_final: 0.8714 (p) REVERT: A 449 TYR cc_start: 0.8682 (p90) cc_final: 0.8438 (p90) REVERT: B 13 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8244 (mt0) REVERT: B 108 SER cc_start: 0.7866 (t) cc_final: 0.7604 (m) REVERT: C 99 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.7223 (m170) REVERT: H 74 GLU cc_start: 0.7466 (tm-30) cc_final: 0.6622 (tm-30) REVERT: H 88 SER cc_start: 0.8603 (t) cc_final: 0.8243 (m) REVERT: H 90 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8396 (t0) REVERT: L 74 SER cc_start: 0.8144 (p) cc_final: 0.7865 (t) outliers start: 28 outliers final: 17 residues processed: 145 average time/residue: 0.2172 time to fit residues: 40.7255 Evaluate side-chains 136 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 0.0670 chunk 20 optimal weight: 0.0050 overall best weight: 0.5934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 99 HIS L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6974 Z= 0.201 Angle : 0.563 14.305 9477 Z= 0.287 Chirality : 0.044 0.177 1026 Planarity : 0.004 0.042 1225 Dihedral : 4.499 22.041 995 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.63 % Allowed : 20.59 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.27), residues: 873 helix: -4.58 (0.49), residues: 20 sheet: -1.83 (0.26), residues: 354 loop : -1.32 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.006 0.001 HIS C 99 PHE 0.016 0.001 PHE A 377 TYR 0.024 0.001 TYR B 60 ARG 0.003 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 399 SER cc_start: 0.9163 (t) cc_final: 0.8733 (p) REVERT: A 449 TYR cc_start: 0.8734 (p90) cc_final: 0.8525 (p90) REVERT: B 13 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8249 (mt0) REVERT: B 108 SER cc_start: 0.7828 (t) cc_final: 0.7578 (m) REVERT: H 62 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7707 (tp-100) REVERT: H 74 GLU cc_start: 0.7456 (tm-30) cc_final: 0.6621 (tm-30) REVERT: H 88 SER cc_start: 0.8645 (t) cc_final: 0.8269 (m) REVERT: H 90 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8410 (t0) REVERT: L 74 SER cc_start: 0.8210 (p) cc_final: 0.7945 (t) outliers start: 27 outliers final: 20 residues processed: 139 average time/residue: 0.2157 time to fit residues: 39.1521 Evaluate side-chains 139 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 0.0770 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 0.0870 chunk 20 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 80 optimal weight: 0.0270 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6974 Z= 0.147 Angle : 0.543 14.776 9477 Z= 0.277 Chirality : 0.043 0.164 1026 Planarity : 0.003 0.041 1225 Dihedral : 4.313 19.876 995 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.36 % Allowed : 21.27 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.28), residues: 873 helix: -4.54 (0.52), residues: 20 sheet: -1.64 (0.26), residues: 352 loop : -1.17 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.008 0.001 HIS C 99 PHE 0.014 0.001 PHE A 377 TYR 0.018 0.001 TYR B 60 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 SER cc_start: 0.9119 (t) cc_final: 0.8660 (p) REVERT: B 13 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8238 (mt0) REVERT: H 62 GLN cc_start: 0.8258 (tm-30) cc_final: 0.7700 (tp-100) REVERT: H 74 GLU cc_start: 0.7421 (tm-30) cc_final: 0.6577 (tm-30) REVERT: H 87 ARG cc_start: 0.7331 (ttp-110) cc_final: 0.7081 (ttm-80) REVERT: H 88 SER cc_start: 0.8642 (t) cc_final: 0.8257 (m) REVERT: H 90 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8462 (t0) REVERT: L 74 SER cc_start: 0.8106 (p) cc_final: 0.7875 (t) outliers start: 25 outliers final: 19 residues processed: 143 average time/residue: 0.2037 time to fit residues: 38.1564 Evaluate side-chains 141 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 49 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: B 84 ASN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6974 Z= 0.253 Angle : 0.576 14.633 9477 Z= 0.296 Chirality : 0.045 0.191 1026 Planarity : 0.004 0.042 1225 Dihedral : 4.486 23.591 995 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.63 % Allowed : 21.67 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.28), residues: 873 helix: -4.50 (0.58), residues: 20 sheet: -1.59 (0.27), residues: 346 loop : -1.17 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.008 0.002 HIS C 99 PHE 0.020 0.001 PHE A 377 TYR 0.018 0.001 TYR E 94 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 SER cc_start: 0.9169 (t) cc_final: 0.8680 (p) REVERT: A 495 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.7926 (m-10) REVERT: B 13 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8254 (mt0) REVERT: B 108 SER cc_start: 0.7834 (t) cc_final: 0.7576 (m) REVERT: H 62 GLN cc_start: 0.8310 (tm-30) cc_final: 0.7730 (tp-100) REVERT: H 74 GLU cc_start: 0.7429 (tm-30) cc_final: 0.6608 (tm-30) REVERT: H 87 ARG cc_start: 0.7432 (ttp-110) cc_final: 0.7222 (ttp80) REVERT: H 88 SER cc_start: 0.8731 (t) cc_final: 0.8313 (m) REVERT: H 90 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8350 (t0) REVERT: L 74 SER cc_start: 0.8256 (p) cc_final: 0.8000 (t) outliers start: 27 outliers final: 22 residues processed: 143 average time/residue: 0.2063 time to fit residues: 38.2955 Evaluate side-chains 147 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 75 optimal weight: 0.0070 chunk 79 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6974 Z= 0.184 Angle : 0.556 14.910 9477 Z= 0.284 Chirality : 0.044 0.175 1026 Planarity : 0.003 0.041 1225 Dihedral : 4.382 22.853 995 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.63 % Allowed : 21.53 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.28), residues: 873 helix: -4.49 (0.59), residues: 20 sheet: -1.37 (0.27), residues: 344 loop : -1.18 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.007 0.001 HIS C 99 PHE 0.020 0.001 PHE A 377 TYR 0.019 0.001 TYR E 94 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 SER cc_start: 0.9157 (t) cc_final: 0.8646 (p) REVERT: B 13 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8247 (mt0) REVERT: H 62 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7706 (tp-100) REVERT: H 74 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6527 (tm-30) REVERT: H 88 SER cc_start: 0.8732 (t) cc_final: 0.8331 (m) REVERT: H 90 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8346 (t0) REVERT: L 74 SER cc_start: 0.8209 (p) cc_final: 0.7965 (t) outliers start: 27 outliers final: 23 residues processed: 145 average time/residue: 0.2151 time to fit residues: 40.4848 Evaluate side-chains 146 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.0980 chunk 76 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6974 Z= 0.180 Angle : 0.552 14.933 9477 Z= 0.281 Chirality : 0.044 0.170 1026 Planarity : 0.003 0.041 1225 Dihedral : 4.319 22.682 995 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.50 % Allowed : 22.21 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.28), residues: 873 helix: -4.53 (0.54), residues: 20 sheet: -1.34 (0.27), residues: 347 loop : -1.10 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.002 0.001 HIS C 99 PHE 0.018 0.001 PHE A 377 TYR 0.018 0.001 TYR E 94 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 SER cc_start: 0.9133 (t) cc_final: 0.8668 (p) REVERT: B 13 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8269 (mt0) REVERT: H 62 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7716 (tp-100) REVERT: H 74 GLU cc_start: 0.7389 (tm-30) cc_final: 0.6508 (tm-30) REVERT: H 88 SER cc_start: 0.8735 (t) cc_final: 0.8305 (m) REVERT: H 90 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8342 (t0) REVERT: L 74 SER cc_start: 0.8201 (p) cc_final: 0.7963 (t) outliers start: 26 outliers final: 24 residues processed: 145 average time/residue: 0.2119 time to fit residues: 39.7960 Evaluate side-chains 148 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 99 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6974 Z= 0.288 Angle : 0.594 14.646 9477 Z= 0.305 Chirality : 0.045 0.201 1026 Planarity : 0.004 0.042 1225 Dihedral : 4.549 24.702 995 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.90 % Allowed : 21.53 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.28), residues: 873 helix: -4.55 (0.53), residues: 20 sheet: -1.37 (0.27), residues: 352 loop : -1.13 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 47 HIS 0.007 0.002 HIS C 99 PHE 0.025 0.002 PHE A 377 TYR 0.024 0.002 TYR B 60 ARG 0.002 0.000 ARG L 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1746 Ramachandran restraints generated. 873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 SER cc_start: 0.9151 (t) cc_final: 0.8694 (p) REVERT: A 403 ARG cc_start: 0.6542 (ptp-170) cc_final: 0.5848 (ptm160) REVERT: B 13 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8281 (mt0) REVERT: H 62 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7794 (tp-100) REVERT: H 74 GLU cc_start: 0.7389 (tm-30) cc_final: 0.6522 (tm-30) REVERT: H 88 SER cc_start: 0.8828 (t) cc_final: 0.8320 (m) REVERT: H 90 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8277 (t0) REVERT: L 74 SER cc_start: 0.8367 (p) cc_final: 0.8106 (t) outliers start: 29 outliers final: 26 residues processed: 146 average time/residue: 0.2047 time to fit residues: 38.7795 Evaluate side-chains 151 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 91 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 8 optimal weight: 0.0870 chunk 12 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 99 HIS ** D 100 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 = 0.3641 r_free = 0.3641 target = 0.139298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.110920 restraints weight = 8905.666| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.48 r_work: 0.3155 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6974 Z= 0.218 Angle : 0.582 14.759 9477 Z= 0.297 Chirality : 0.045 0.182 1026 Planarity : 0.003 0.041 1225 Dihedral : 4.483 24.486 995 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.36 % Allowed : 21.94 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.28), residues: 873 helix: -4.53 (0.54), residues: 20 sheet: -1.34 (0.27), residues: 346 loop : -1.02 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.004 0.001 HIS C 99 PHE 0.040 0.002 PHE A 377 TYR 0.021 0.001 TYR B 60 ARG 0.002 0.000 ARG L 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2049.48 seconds wall clock time: 38 minutes 11.02 seconds (2291.02 seconds total)