Starting phenix.real_space_refine on Thu Jul 24 03:34:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iv8_35746/07_2025/8iv8_35746.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iv8_35746/07_2025/8iv8_35746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iv8_35746/07_2025/8iv8_35746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iv8_35746/07_2025/8iv8_35746.map" model { file = "/net/cci-nas-00/data/ceres_data/8iv8_35746/07_2025/8iv8_35746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iv8_35746/07_2025/8iv8_35746.cif" } resolution = 3.92 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= 0.010 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 24 5.16 5 C 3137 2.51 5 N 808 2.21 5 O 975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4944 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 100} Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "G" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1435 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 1 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': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "C" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 947 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 15.89, per 1000 atoms: 3.21 Number of scatterers: 4944 At special positions: 0 Unit cell: (107.364, 87.914, 69.242, 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 24 16.00 O 975 8.00 N 808 7.00 C 3137 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " 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 BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN G 343 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 973.1 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 18 sheets defined 4.6% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.039A pdb=" N THR H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'G' and resid 338 through 343 Processing helix chain 'G' and resid 349 through 353 removed outlier: 3.771A pdb=" N TRP G 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 370 Processing helix chain 'G' and resid 405 through 411 removed outlier: 4.579A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE G 410 " --> pdb=" O VAL G 407 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.608A pdb=" N MET L 11 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP L 34 " --> pdb=" O PHE L 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 19 through 21 removed outlier: 3.592A pdb=" N ILE L 19 " --> pdb=" O ILE L 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA5, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.873A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER H 35 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N CYS H 96 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TRP H 111 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG H 98 " --> pdb=" O ASP H 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.873A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER H 35 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 357 through 358 removed outlier: 3.558A pdb=" N VAL G 395 " --> pdb=" O ILE G 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 376 through 379 removed outlier: 3.608A pdb=" N ILE G 402 " --> pdb=" O TYR G 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'D' and resid 5 through 6 removed outlier: 7.493A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE D 75 " --> pdb=" O VAL D 19 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 5 through 6 removed outlier: 7.493A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR D 72 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER D 65 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 45 through 48 removed outlier: 7.163A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D 89 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 45 through 48 removed outlier: 7.163A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D 89 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR D 102 " --> pdb=" O TYR D 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.530A pdb=" N VAL C 18 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.530A pdb=" N VAL C 18 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR C 78 " --> pdb=" O GLU C 73 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C 73 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AB8, first strand: chain 'C' and resid 37 through 39 removed outlier: 3.596A pdb=" N THR C 93 " --> pdb=" O GLN C 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 49 through 51 133 hydrogen bonds defined for protein. 315 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: 2.50 Time building geometry restraints manager: 2.70 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: 1539 1.34 - 1.46: 1342 1.46 - 1.58: 2155 1.58 - 1.70: 0 1.70 - 1.82: 33 Bond restraints: 5069 Sorted by residual: bond pdb=" C THR D 93 " pdb=" N TRP D 94 " ideal model delta sigma weight residual 1.331 1.280 0.051 1.59e-02 3.96e+03 1.05e+01 bond pdb=" C1 BMA A 3 " pdb=" C2 BMA A 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.44e+00 ... (remaining 5064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 6738 2.29 - 4.59: 127 4.59 - 6.88: 15 6.88 - 9.17: 6 9.17 - 11.47: 1 Bond angle restraints: 6887 Sorted by residual: angle pdb=" N VAL H 48 " pdb=" CA VAL H 48 " pdb=" C VAL H 48 " ideal model delta sigma weight residual 113.53 109.40 4.13 9.80e-01 1.04e+00 1.78e+01 angle pdb=" C SER L 49 " pdb=" N THR L 50 " pdb=" CA THR L 50 " ideal model delta sigma weight residual 121.54 129.19 -7.65 1.91e+00 2.74e-01 1.60e+01 angle pdb=" C SER L 92 " pdb=" N TRP L 93 " pdb=" CA TRP L 93 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C LEU G 461 " pdb=" N LYS G 462 " pdb=" CA LYS G 462 " ideal model delta sigma weight residual 120.69 132.16 -11.47 2.95e+00 1.15e-01 1.51e+01 angle pdb=" C SER D 40 " pdb=" N HIS D 41 " pdb=" CA HIS D 41 " ideal model delta sigma weight residual 122.07 127.29 -5.22 1.43e+00 4.89e-01 1.33e+01 ... (remaining 6882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.47: 2782 22.47 - 44.93: 189 44.93 - 67.40: 9 67.40 - 89.86: 10 89.86 - 112.33: 4 Dihedral angle restraints: 2994 sinusoidal: 1181 harmonic: 1813 Sorted by residual: dihedral pdb=" CA TRP C 104 " pdb=" C TRP C 104 " pdb=" N TYR C 105 " pdb=" CA TYR C 105 " ideal model delta harmonic sigma weight residual 180.00 156.85 23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CB CYS G 336 " pdb=" SG CYS G 336 " pdb=" SG CYS G 361 " pdb=" CB CYS G 361 " ideal model delta sinusoidal sigma weight residual 93.00 57.47 35.53 1 1.00e+01 1.00e-02 1.79e+01 dihedral pdb=" CA SER L 92 " pdb=" C SER L 92 " pdb=" N TRP L 93 " pdb=" CA TRP L 93 " ideal model delta harmonic sigma weight residual -180.00 -160.51 -19.49 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 2991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 564 0.055 - 0.109: 145 0.109 - 0.164: 39 0.164 - 0.219: 5 0.219 - 0.273: 1 Chirality restraints: 754 Sorted by residual: chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.27e+00 chirality pdb=" CB THR C 91 " pdb=" CA THR C 91 " pdb=" OG1 THR C 91 " pdb=" CG2 THR C 91 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 751 not shown) Planarity restraints: 872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS G 462 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO G 463 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO G 463 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 463 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS G 336 " 0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO G 337 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO G 337 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 337 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO H 14 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.027 5.00e-02 4.00e+02 ... (remaining 869 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1348 2.80 - 3.32: 3976 3.32 - 3.85: 8028 3.85 - 4.37: 8639 4.37 - 4.90: 15466 Nonbonded interactions: 37457 Sorted by model distance: nonbonded pdb=" OH TYR H 59 " pdb=" OH TYR H 103 " model vdw 2.272 3.040 nonbonded pdb=" OG SER G 349 " pdb=" O LEU G 452 " model vdw 2.274 3.040 nonbonded pdb=" O SER L 62 " pdb=" OG1 THR L 73 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR D 14 " pdb=" OD2 ASP D 17 " model vdw 2.290 3.040 nonbonded pdb=" O SER H 30 " pdb=" OG SER H 30 " model vdw 2.307 3.040 ... (remaining 37452 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=0.83 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: 1793.320 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: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 35.340 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 1832.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 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 : 0.005 0.051 5079 Z= 0.222 Angle : 0.821 11.467 6910 Z= 0.453 Chirality : 0.054 0.273 754 Planarity : 0.006 0.055 871 Dihedral : 15.131 112.328 1823 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.74 % Allowed : 7.39 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -3.56 (0.29), residues: 618 helix: -4.87 (0.33), residues: 12 sheet: -1.93 (0.35), residues: 212 loop : -2.65 (0.25), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.002 0.001 HIS H 99 PHE 0.022 0.002 PHE L 46 TYR 0.020 0.002 TYR C 105 ARG 0.002 0.000 ARG G 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 1) link_NAG-ASN : angle 4.20579 ( 3) link_BETA1-4 : bond 0.01030 ( 2) link_BETA1-4 : angle 2.10522 ( 6) hydrogen bonds : bond 0.29075 ( 104) hydrogen bonds : angle 11.50099 ( 315) SS BOND : bond 0.00350 ( 7) SS BOND : angle 1.34297 ( 14) covalent geometry : bond 0.00466 ( 5069) covalent geometry : angle 0.81260 ( 6887) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 204 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8303 (tm-30) REVERT: L 73 THR cc_start: 0.7646 (p) cc_final: 0.7432 (p) REVERT: L 81 ASP cc_start: 0.7831 (m-30) cc_final: 0.7278 (m-30) REVERT: H 19 LYS cc_start: 0.8604 (tttt) cc_final: 0.8383 (tttp) REVERT: H 27 PHE cc_start: 0.8554 (p90) cc_final: 0.8298 (p90) REVERT: H 29 PHE cc_start: 0.7968 (t80) cc_final: 0.7722 (t80) REVERT: H 34 MET cc_start: 0.8570 (mtp) cc_final: 0.6943 (mmt) REVERT: H 60 TYR cc_start: 0.8774 (m-80) cc_final: 0.8492 (m-10) REVERT: H 73 ASP cc_start: 0.6767 (t70) cc_final: 0.6461 (t70) REVERT: H 76 MET cc_start: 0.8241 (ttt) cc_final: 0.7909 (tpt) REVERT: H 87 ARG cc_start: 0.7942 (mtt90) cc_final: 0.7002 (mpt180) REVERT: H 97 VAL cc_start: 0.9091 (m) cc_final: 0.8389 (m) REVERT: G 389 ASP cc_start: 0.7983 (t0) cc_final: 0.7563 (p0) REVERT: G 458 LYS cc_start: 0.8798 (ttmt) cc_final: 0.8356 (tptt) REVERT: G 467 ASP cc_start: 0.7512 (p0) cc_final: 0.7192 (p0) REVERT: D 17 ASP cc_start: 0.5154 (m-30) cc_final: 0.4618 (t70) REVERT: D 47 LEU cc_start: 0.7765 (mt) cc_final: 0.7539 (mp) REVERT: D 105 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7586 (tm-30) REVERT: C 5 VAL cc_start: 0.6889 (p) cc_final: 0.6598 (m) REVERT: C 12 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7705 (mmtt) REVERT: C 16 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6726 (mt-10) REVERT: C 60 TYR cc_start: 0.9017 (m-80) cc_final: 0.8569 (m-10) REVERT: C 65 ARG cc_start: 0.7769 (ttp-110) cc_final: 0.7500 (mmm160) REVERT: C 82 LYS cc_start: 0.7994 (tttt) cc_final: 0.7467 (ttmm) REVERT: C 86 LEU cc_start: 0.7536 (mt) cc_final: 0.7294 (mp) REVERT: C 87 LYS cc_start: 0.8311 (mttt) cc_final: 0.7922 (ttmm) REVERT: C 104 TRP cc_start: 0.7882 (m-90) cc_final: 0.7135 (m-90) outliers start: 4 outliers final: 2 residues processed: 207 average time/residue: 0.2054 time to fit residues: 52.7790 Evaluate side-chains 131 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain C residue 51 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 ASN H 99 HIS G 409 GLN G 439 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.117114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.099095 restraints weight = 9441.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.101759 restraints weight = 5660.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.103588 restraints weight = 4013.269| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5079 Z= 0.176 Angle : 0.651 7.413 6910 Z= 0.344 Chirality : 0.046 0.188 754 Planarity : 0.005 0.044 871 Dihedral : 9.129 67.774 752 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.14 % Allowed : 18.85 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.90 (0.32), residues: 618 helix: -4.43 (0.52), residues: 12 sheet: -1.61 (0.34), residues: 243 loop : -2.09 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 90 HIS 0.004 0.002 HIS L 33 PHE 0.019 0.002 PHE D 71 TYR 0.024 0.002 TYR G 351 ARG 0.006 0.001 ARG G 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 1) link_NAG-ASN : angle 2.61548 ( 3) link_BETA1-4 : bond 0.00261 ( 2) link_BETA1-4 : angle 2.67908 ( 6) hydrogen bonds : bond 0.04408 ( 104) hydrogen bonds : angle 7.09204 ( 315) SS BOND : bond 0.00847 ( 7) SS BOND : angle 1.81810 ( 14) covalent geometry : bond 0.00387 ( 5069) covalent geometry : angle 0.63967 ( 6887) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: L 19 ILE cc_start: 0.8410 (tp) cc_final: 0.8117 (tp) REVERT: L 66 SER cc_start: 0.8942 (t) cc_final: 0.8721 (p) REVERT: D 17 ASP cc_start: 0.5013 (m-30) cc_final: 0.4671 (t70) REVERT: C 23 LYS cc_start: 0.8729 (ttmm) cc_final: 0.8222 (ttmm) outliers start: 17 outliers final: 10 residues processed: 152 average time/residue: 0.1705 time to fit residues: 32.8198 Evaluate side-chains 130 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 0.0970 chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.115823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.096536 restraints weight = 9928.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.099512 restraints weight = 5605.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.101491 restraints weight = 3870.972| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5079 Z= 0.178 Angle : 0.653 7.247 6910 Z= 0.341 Chirality : 0.045 0.180 754 Planarity : 0.005 0.090 871 Dihedral : 7.437 63.008 752 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.07 % Allowed : 20.33 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.62 (0.32), residues: 618 helix: -4.23 (0.60), residues: 13 sheet: -1.48 (0.34), residues: 245 loop : -1.84 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 102 HIS 0.004 0.002 HIS D 34 PHE 0.016 0.001 PHE H 68 TYR 0.022 0.002 TYR L 70 ARG 0.005 0.001 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 1) link_NAG-ASN : angle 2.57453 ( 3) link_BETA1-4 : bond 0.00458 ( 2) link_BETA1-4 : angle 2.55273 ( 6) hydrogen bonds : bond 0.03849 ( 104) hydrogen bonds : angle 6.21264 ( 315) SS BOND : bond 0.00409 ( 7) SS BOND : angle 2.25995 ( 14) covalent geometry : bond 0.00404 ( 5069) covalent geometry : angle 0.63904 ( 6887) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8372 (tm-30) REVERT: L 66 SER cc_start: 0.8801 (t) cc_final: 0.8403 (m) REVERT: G 389 ASP cc_start: 0.8020 (p0) cc_final: 0.7702 (p0) REVERT: G 461 LEU cc_start: 0.8788 (tp) cc_final: 0.8581 (tp) REVERT: D 17 ASP cc_start: 0.5370 (m-30) cc_final: 0.4871 (t70) REVERT: C 12 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7911 (mmtt) outliers start: 22 outliers final: 18 residues processed: 143 average time/residue: 0.2781 time to fit residues: 50.7696 Evaluate side-chains 130 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.0770 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 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 = 0.3394 r_free = 0.3394 target = 0.116517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.097142 restraints weight = 9974.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.100086 restraints weight = 5693.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.102027 restraints weight = 3941.075| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5079 Z= 0.145 Angle : 0.616 8.469 6910 Z= 0.318 Chirality : 0.044 0.169 754 Planarity : 0.004 0.035 871 Dihedral : 6.208 57.757 751 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.44 % Allowed : 21.26 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.37 (0.33), residues: 618 helix: -3.97 (0.72), residues: 13 sheet: -1.28 (0.34), residues: 247 loop : -1.69 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 104 HIS 0.003 0.001 HIS D 41 PHE 0.014 0.001 PHE H 68 TYR 0.020 0.001 TYR G 351 ARG 0.005 0.001 ARG G 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 1) link_NAG-ASN : angle 2.21254 ( 3) link_BETA1-4 : bond 0.00455 ( 2) link_BETA1-4 : angle 2.44088 ( 6) hydrogen bonds : bond 0.03426 ( 104) hydrogen bonds : angle 5.67743 ( 315) SS BOND : bond 0.00362 ( 7) SS BOND : angle 2.18289 ( 14) covalent geometry : bond 0.00329 ( 5069) covalent geometry : angle 0.60289 ( 6887) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8285 (tm-30) REVERT: L 66 SER cc_start: 0.8807 (t) cc_final: 0.8385 (m) REVERT: H 38 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8454 (ptt180) REVERT: H 74 LYS cc_start: 0.8312 (mptt) cc_final: 0.8082 (tptp) REVERT: H 87 ARG cc_start: 0.8076 (mmt180) cc_final: 0.7751 (mmt180) REVERT: H 93 MET cc_start: 0.8610 (tpp) cc_final: 0.8082 (ttt) REVERT: G 389 ASP cc_start: 0.8061 (p0) cc_final: 0.7737 (p0) REVERT: G 427 ASP cc_start: 0.8376 (m-30) cc_final: 0.7833 (t0) REVERT: D 17 ASP cc_start: 0.5459 (m-30) cc_final: 0.4895 (t70) REVERT: D 105 GLU cc_start: 0.6965 (tm-30) cc_final: 0.6419 (tt0) outliers start: 24 outliers final: 19 residues processed: 141 average time/residue: 0.2601 time to fit residues: 46.8272 Evaluate side-chains 135 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 366 SER Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 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 = 0.3352 r_free = 0.3352 target = 0.113195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.094158 restraints weight = 10022.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.096957 restraints weight = 5668.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.098849 restraints weight = 3955.829| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5079 Z= 0.239 Angle : 0.670 9.074 6910 Z= 0.347 Chirality : 0.045 0.165 754 Planarity : 0.005 0.035 871 Dihedral : 6.107 55.642 751 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 5.91 % Allowed : 21.07 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.28 (0.33), residues: 618 helix: -3.65 (0.95), residues: 13 sheet: -1.15 (0.34), residues: 252 loop : -1.69 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 90 HIS 0.004 0.002 HIS L 88 PHE 0.019 0.002 PHE H 29 TYR 0.024 0.002 TYR C 32 ARG 0.006 0.001 ARG G 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00090 ( 1) link_NAG-ASN : angle 2.77909 ( 3) link_BETA1-4 : bond 0.00429 ( 2) link_BETA1-4 : angle 2.28711 ( 6) hydrogen bonds : bond 0.03719 ( 104) hydrogen bonds : angle 5.53501 ( 315) SS BOND : bond 0.00548 ( 7) SS BOND : angle 2.55188 ( 14) covalent geometry : bond 0.00549 ( 5069) covalent geometry : angle 0.65505 ( 6887) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ILE cc_start: 0.8449 (mp) cc_final: 0.8209 (mm) REVERT: L 17 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8258 (tm-30) REVERT: L 66 SER cc_start: 0.8867 (t) cc_final: 0.8424 (m) REVERT: H 38 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8316 (ptt-90) REVERT: H 74 LYS cc_start: 0.8346 (mptt) cc_final: 0.8087 (tptp) REVERT: H 93 MET cc_start: 0.8662 (tpp) cc_final: 0.8161 (ttt) REVERT: G 389 ASP cc_start: 0.8085 (p0) cc_final: 0.7725 (p0) REVERT: G 403 ARG cc_start: 0.8664 (mtt-85) cc_final: 0.8384 (mtt180) REVERT: G 418 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.8936 (tt) REVERT: G 427 ASP cc_start: 0.8493 (m-30) cc_final: 0.7940 (t0) REVERT: G 467 ASP cc_start: 0.7529 (p0) cc_final: 0.7236 (p0) REVERT: D 17 ASP cc_start: 0.5692 (m-30) cc_final: 0.5025 (t70) REVERT: D 105 GLU cc_start: 0.7096 (tm-30) cc_final: 0.6508 (tt0) REVERT: C 12 LYS cc_start: 0.8357 (mmtt) cc_final: 0.8113 (tptm) outliers start: 32 outliers final: 21 residues processed: 138 average time/residue: 0.2093 time to fit residues: 37.3004 Evaluate side-chains 132 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 36 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 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 = 0.3373 r_free = 0.3373 target = 0.114701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.095178 restraints weight = 10017.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.097984 restraints weight = 5855.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.099879 restraints weight = 4126.706| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5079 Z= 0.170 Angle : 0.623 9.402 6910 Z= 0.323 Chirality : 0.044 0.156 754 Planarity : 0.004 0.037 871 Dihedral : 5.791 52.687 751 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 5.18 % Allowed : 22.18 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.18 (0.33), residues: 618 helix: -4.04 (0.69), residues: 19 sheet: -1.14 (0.34), residues: 251 loop : -1.50 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 104 HIS 0.003 0.001 HIS L 88 PHE 0.022 0.002 PHE H 29 TYR 0.024 0.001 TYR C 32 ARG 0.006 0.001 ARG G 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 1) link_NAG-ASN : angle 2.39038 ( 3) link_BETA1-4 : bond 0.00422 ( 2) link_BETA1-4 : angle 2.07459 ( 6) hydrogen bonds : bond 0.03326 ( 104) hydrogen bonds : angle 5.40194 ( 315) SS BOND : bond 0.00452 ( 7) SS BOND : angle 2.56130 ( 14) covalent geometry : bond 0.00392 ( 5069) covalent geometry : angle 0.60774 ( 6887) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.580 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: L 10 ILE cc_start: 0.8474 (mp) cc_final: 0.8247 (mm) REVERT: L 17 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8129 (tm-30) REVERT: L 66 SER cc_start: 0.8871 (t) cc_final: 0.8421 (m) REVERT: H 38 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8341 (ptt-90) REVERT: H 74 LYS cc_start: 0.8329 (mptt) cc_final: 0.8017 (tptp) REVERT: H 93 MET cc_start: 0.8672 (tpp) cc_final: 0.7856 (ttt) REVERT: G 389 ASP cc_start: 0.8077 (p0) cc_final: 0.7736 (p0) REVERT: G 427 ASP cc_start: 0.8475 (m-30) cc_final: 0.7936 (t0) REVERT: G 467 ASP cc_start: 0.7441 (p0) cc_final: 0.7150 (p0) REVERT: D 17 ASP cc_start: 0.5664 (m-30) cc_final: 0.5001 (t70) REVERT: D 105 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6544 (tt0) outliers start: 28 outliers final: 25 residues processed: 143 average time/residue: 0.1848 time to fit residues: 32.9273 Evaluate side-chains 142 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 366 SER Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 0.0570 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 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 = 0.3392 r_free = 0.3392 target = 0.115983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.096705 restraints weight = 9743.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.099566 restraints weight = 5609.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.101525 restraints weight = 3916.033| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5079 Z= 0.150 Angle : 0.624 9.046 6910 Z= 0.322 Chirality : 0.044 0.161 754 Planarity : 0.004 0.036 871 Dihedral : 5.573 50.173 751 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 5.18 % Allowed : 22.55 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 (0.34), residues: 618 helix: -3.56 (0.84), residues: 19 sheet: -1.07 (0.34), residues: 258 loop : -1.34 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 104 HIS 0.003 0.001 HIS D 41 PHE 0.024 0.002 PHE L 46 TYR 0.030 0.001 TYR G 351 ARG 0.006 0.001 ARG G 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 1) link_NAG-ASN : angle 2.19432 ( 3) link_BETA1-4 : bond 0.00304 ( 2) link_BETA1-4 : angle 1.92474 ( 6) hydrogen bonds : bond 0.03281 ( 104) hydrogen bonds : angle 5.28261 ( 315) SS BOND : bond 0.00386 ( 7) SS BOND : angle 2.60206 ( 14) covalent geometry : bond 0.00346 ( 5069) covalent geometry : angle 0.60923 ( 6887) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.535 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: L 10 ILE cc_start: 0.8491 (mp) cc_final: 0.8283 (mm) REVERT: L 17 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8101 (tm-30) REVERT: L 66 SER cc_start: 0.8847 (t) cc_final: 0.8400 (m) REVERT: H 38 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8409 (ptt180) REVERT: H 74 LYS cc_start: 0.8289 (mptt) cc_final: 0.8003 (tptp) REVERT: H 93 MET cc_start: 0.8666 (tpp) cc_final: 0.7855 (ttt) REVERT: G 389 ASP cc_start: 0.8057 (p0) cc_final: 0.7749 (p0) REVERT: G 403 ARG cc_start: 0.8532 (mtt-85) cc_final: 0.8200 (mtt180) REVERT: G 467 ASP cc_start: 0.7464 (p0) cc_final: 0.7150 (p0) REVERT: D 17 ASP cc_start: 0.5638 (m-30) cc_final: 0.5020 (t70) REVERT: D 89 GLN cc_start: 0.8639 (pp30) cc_final: 0.8292 (pp30) REVERT: D 90 GLN cc_start: 0.7866 (pt0) cc_final: 0.7662 (pt0) outliers start: 28 outliers final: 26 residues processed: 141 average time/residue: 0.1760 time to fit residues: 31.1076 Evaluate side-chains 143 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 366 SER Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 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 = 0.3387 r_free = 0.3387 target = 0.115409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.095664 restraints weight = 9896.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.098606 restraints weight = 5620.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.100640 restraints weight = 3902.305| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5079 Z= 0.162 Angle : 0.626 8.387 6910 Z= 0.324 Chirality : 0.044 0.163 754 Planarity : 0.004 0.039 871 Dihedral : 5.493 48.963 751 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 5.91 % Allowed : 23.11 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.91 (0.34), residues: 618 helix: -3.47 (0.93), residues: 19 sheet: -0.99 (0.34), residues: 258 loop : -1.30 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 104 HIS 0.003 0.001 HIS L 88 PHE 0.021 0.001 PHE L 46 TYR 0.029 0.001 TYR G 351 ARG 0.006 0.001 ARG G 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 1) link_NAG-ASN : angle 2.18774 ( 3) link_BETA1-4 : bond 0.00499 ( 2) link_BETA1-4 : angle 1.84544 ( 6) hydrogen bonds : bond 0.03241 ( 104) hydrogen bonds : angle 5.18984 ( 315) SS BOND : bond 0.00668 ( 7) SS BOND : angle 2.70656 ( 14) covalent geometry : bond 0.00372 ( 5069) covalent geometry : angle 0.61112 ( 6887) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ILE cc_start: 0.8472 (mp) cc_final: 0.8254 (mm) REVERT: L 17 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8268 (tm-30) REVERT: L 66 SER cc_start: 0.8867 (t) cc_final: 0.8416 (m) REVERT: H 38 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8343 (ptt-90) REVERT: H 74 LYS cc_start: 0.8275 (mptt) cc_final: 0.7968 (tptp) REVERT: H 93 MET cc_start: 0.8671 (tpp) cc_final: 0.7921 (ttt) REVERT: G 355 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7715 (ttt90) REVERT: G 389 ASP cc_start: 0.8051 (p0) cc_final: 0.7751 (p0) REVERT: G 417 LYS cc_start: 0.9165 (tppt) cc_final: 0.8949 (tppt) REVERT: G 467 ASP cc_start: 0.7378 (p0) cc_final: 0.7072 (p0) REVERT: D 17 ASP cc_start: 0.5719 (m-30) cc_final: 0.5020 (t70) REVERT: D 89 GLN cc_start: 0.8614 (pp30) cc_final: 0.8240 (pp30) REVERT: D 105 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6571 (tt0) REVERT: C 12 LYS cc_start: 0.8090 (mmmm) cc_final: 0.7512 (tptm) REVERT: C 94 TYR cc_start: 0.8458 (m-10) cc_final: 0.8130 (m-10) outliers start: 32 outliers final: 27 residues processed: 140 average time/residue: 0.1786 time to fit residues: 31.3701 Evaluate side-chains 144 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 0.0870 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN G 450 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.114491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.095042 restraints weight = 9770.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.097909 restraints weight = 5584.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.099923 restraints weight = 3885.341| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5079 Z= 0.184 Angle : 0.658 8.417 6910 Z= 0.340 Chirality : 0.044 0.168 754 Planarity : 0.004 0.052 871 Dihedral : 5.546 48.515 751 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 6.10 % Allowed : 23.11 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.90 (0.34), residues: 618 helix: -3.48 (0.95), residues: 19 sheet: -1.01 (0.34), residues: 252 loop : -1.28 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 104 HIS 0.004 0.001 HIS L 88 PHE 0.020 0.002 PHE H 29 TYR 0.030 0.002 TYR G 351 ARG 0.006 0.001 ARG G 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 1) link_NAG-ASN : angle 2.21457 ( 3) link_BETA1-4 : bond 0.00389 ( 2) link_BETA1-4 : angle 1.84548 ( 6) hydrogen bonds : bond 0.03386 ( 104) hydrogen bonds : angle 5.21898 ( 315) SS BOND : bond 0.00367 ( 7) SS BOND : angle 2.64754 ( 14) covalent geometry : bond 0.00424 ( 5069) covalent geometry : angle 0.64420 ( 6887) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ILE cc_start: 0.8555 (mp) cc_final: 0.8312 (mm) REVERT: L 17 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8332 (tm-30) REVERT: L 66 SER cc_start: 0.8871 (t) cc_final: 0.8423 (m) REVERT: H 38 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8327 (ptt-90) REVERT: H 74 LYS cc_start: 0.8276 (mptt) cc_final: 0.8019 (tptp) REVERT: H 93 MET cc_start: 0.8670 (tpp) cc_final: 0.8135 (ttt) REVERT: G 355 ARG cc_start: 0.8217 (ttm-80) cc_final: 0.7734 (ttt90) REVERT: G 389 ASP cc_start: 0.8042 (p0) cc_final: 0.7765 (p0) REVERT: G 403 ARG cc_start: 0.8563 (mtt-85) cc_final: 0.8216 (mtt180) REVERT: G 467 ASP cc_start: 0.7346 (p0) cc_final: 0.7065 (p0) REVERT: D 17 ASP cc_start: 0.5738 (m-30) cc_final: 0.5095 (t70) REVERT: D 89 GLN cc_start: 0.8642 (pp30) cc_final: 0.8273 (pp30) REVERT: D 90 GLN cc_start: 0.7949 (pt0) cc_final: 0.7695 (pt0) REVERT: D 105 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6573 (tt0) REVERT: C 12 LYS cc_start: 0.8137 (mmmm) cc_final: 0.7933 (tptm) REVERT: C 73 GLU cc_start: 0.8019 (pp20) cc_final: 0.7795 (pp20) REVERT: C 94 TYR cc_start: 0.8489 (m-10) cc_final: 0.8184 (m-10) outliers start: 33 outliers final: 30 residues processed: 141 average time/residue: 0.1835 time to fit residues: 32.4892 Evaluate side-chains 149 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.096535 restraints weight = 9880.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.099464 restraints weight = 5658.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.101405 restraints weight = 3928.458| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5079 Z= 0.152 Angle : 0.641 8.228 6910 Z= 0.333 Chirality : 0.044 0.169 754 Planarity : 0.005 0.066 871 Dihedral : 5.497 47.371 751 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 5.73 % Allowed : 23.84 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.77 (0.34), residues: 618 helix: -3.46 (0.97), residues: 19 sheet: -0.83 (0.35), residues: 245 loop : -1.27 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 104 HIS 0.004 0.001 HIS D 41 PHE 0.020 0.001 PHE H 29 TYR 0.030 0.002 TYR G 351 ARG 0.007 0.001 ARG G 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 1) link_NAG-ASN : angle 2.03971 ( 3) link_BETA1-4 : bond 0.00415 ( 2) link_BETA1-4 : angle 1.76865 ( 6) hydrogen bonds : bond 0.03235 ( 104) hydrogen bonds : angle 5.16657 ( 315) SS BOND : bond 0.00352 ( 7) SS BOND : angle 2.59222 ( 14) covalent geometry : bond 0.00354 ( 5069) covalent geometry : angle 0.62794 ( 6887) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8276 (tm-30) REVERT: L 66 SER cc_start: 0.8868 (t) cc_final: 0.8444 (m) REVERT: H 38 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8396 (ptt180) REVERT: H 74 LYS cc_start: 0.8257 (mptt) cc_final: 0.7955 (tptp) REVERT: G 355 ARG cc_start: 0.8205 (ttm-80) cc_final: 0.7757 (ttt90) REVERT: G 389 ASP cc_start: 0.8030 (p0) cc_final: 0.7773 (p0) REVERT: G 467 ASP cc_start: 0.7302 (p0) cc_final: 0.7003 (p0) REVERT: D 17 ASP cc_start: 0.5698 (m-30) cc_final: 0.5053 (t70) REVERT: D 89 GLN cc_start: 0.8594 (pp30) cc_final: 0.8241 (pp30) REVERT: D 90 GLN cc_start: 0.7913 (pt0) cc_final: 0.7672 (pt0) REVERT: D 105 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6521 (tt0) REVERT: C 73 GLU cc_start: 0.7992 (pp20) cc_final: 0.7764 (pp20) REVERT: C 94 TYR cc_start: 0.8456 (m-10) cc_final: 0.8164 (m-10) outliers start: 31 outliers final: 30 residues processed: 140 average time/residue: 0.1737 time to fit residues: 30.7146 Evaluate side-chains 147 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 5 optimal weight: 0.0270 chunk 44 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.0010 chunk 13 optimal weight: 2.9990 overall best weight: 0.6246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.115639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.097299 restraints weight = 9750.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.100073 restraints weight = 5578.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.101951 restraints weight = 3869.799| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5079 Z= 0.151 Angle : 0.645 7.951 6910 Z= 0.336 Chirality : 0.044 0.176 754 Planarity : 0.004 0.055 871 Dihedral : 5.448 46.436 751 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 5.55 % Allowed : 24.21 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.68 (0.34), residues: 618 helix: -3.42 (1.01), residues: 19 sheet: -0.79 (0.35), residues: 245 loop : -1.19 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.004 0.001 HIS D 41 PHE 0.025 0.001 PHE L 46 TYR 0.029 0.001 TYR G 351 ARG 0.006 0.001 ARG G 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 1) link_NAG-ASN : angle 1.96715 ( 3) link_BETA1-4 : bond 0.00440 ( 2) link_BETA1-4 : angle 1.70733 ( 6) hydrogen bonds : bond 0.03292 ( 104) hydrogen bonds : angle 5.12175 ( 315) SS BOND : bond 0.00344 ( 7) SS BOND : angle 2.53966 ( 14) covalent geometry : bond 0.00348 ( 5069) covalent geometry : angle 0.63286 ( 6887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5291.74 seconds wall clock time: 96 minutes 44.68 seconds (5804.68 seconds total)