Starting phenix.real_space_refine on Sun Apr 27 09:48:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1d_41810/04_2025/8u1d_41810.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1d_41810/04_2025/8u1d_41810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u1d_41810/04_2025/8u1d_41810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1d_41810/04_2025/8u1d_41810.map" model { file = "/net/cci-nas-00/data/ceres_data/8u1d_41810/04_2025/8u1d_41810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1d_41810/04_2025/8u1d_41810.cif" } resolution = 4.25 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= 0.012 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 35 5.16 5 C 3195 2.51 5 N 882 2.21 5 O 997 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5109 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3310 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 18, 'TRANS': 402} Chain breaks: 1 Chain: "I" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.06, per 1000 atoms: 0.79 Number of scatterers: 5109 At special positions: 0 Unit cell: (89.64, 84.24, 85.32, 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 35 16.00 O 997 8.00 N 882 7.00 C 3195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 386 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 616.3 milliseconds 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1212 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 14 sheets defined 13.8% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 99 through 115 removed outlier: 4.125A pdb=" N GLN A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.644A pdb=" N ILE A 141 " --> pdb=" O ASN A 138 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 138 through 142' Processing helix chain 'A' and resid 205 through 209 removed outlier: 3.518A pdb=" N VAL A 208 " --> pdb=" O CYS A 205 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 209 " --> pdb=" O PRO A 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 205 through 209' Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.826A pdb=" N THR A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 392 removed outlier: 3.571A pdb=" N PHE A 391 " --> pdb=" O SER A 388 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN A 392 " --> pdb=" O SER A 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 388 through 392' Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.220A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.967A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 86 removed outlier: 3.637A pdb=" N SER A 243 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL A 245 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 224 " --> pdb=" O VAL A 487 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.377A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.556A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.117A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.556A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.117A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 307 removed outlier: 6.898A pdb=" N ASN A 301 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N VAL A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 361 removed outlier: 6.928A pdb=" N ASN A 357 " --> pdb=" O GLU A 464 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N PHE A 466 " --> pdb=" O ASN A 357 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR A 359 " --> pdb=" O PHE A 466 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.527A pdb=" N LEU I 82 " --> pdb=" O VAL I 18 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 57 through 58 removed outlier: 6.056A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 57 through 58 removed outlier: 6.056A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.800A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER J 67 " --> pdb=" O ASP J 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.064A pdb=" N LEU J 11 " --> pdb=" O ASP J 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.542A pdb=" N ALA J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN J 37 " --> pdb=" O ALA J 46 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE J 48 " --> pdb=" O TRP J 35 " (cutoff:3.500A) 168 hydrogen bonds defined for protein. 420 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.81 Time building geometry restraints manager: 1.42 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: 1654 1.34 - 1.46: 1222 1.46 - 1.59: 2297 1.59 - 1.71: 0 1.71 - 1.83: 48 Bond restraints: 5221 Sorted by residual: bond pdb=" N ASP A 78 " pdb=" CA ASP A 78 " ideal model delta sigma weight residual 1.460 1.487 -0.027 7.10e-03 1.98e+04 1.46e+01 bond pdb=" N ILE A 271 " pdb=" CA ILE A 271 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.11e-02 8.12e+03 1.02e+01 bond pdb=" N VAL A 281 " pdb=" CA VAL A 281 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.00e+01 bond pdb=" N VAL A 65 " pdb=" CA VAL A 65 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.12e+00 bond pdb=" N VAL A 286 " pdb=" CA VAL A 286 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.24e-02 6.50e+03 8.07e+00 ... (remaining 5216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 6546 1.85 - 3.70: 447 3.70 - 5.55: 58 5.55 - 7.40: 24 7.40 - 9.25: 10 Bond angle restraints: 7085 Sorted by residual: angle pdb=" N LYS A 63 " pdb=" CA LYS A 63 " pdb=" C LYS A 63 " ideal model delta sigma weight residual 113.28 107.17 6.11 1.22e+00 6.72e-01 2.50e+01 angle pdb=" N ILE J 29 " pdb=" CA ILE J 29 " pdb=" C ILE J 29 " ideal model delta sigma weight residual 112.17 107.96 4.21 9.50e-01 1.11e+00 1.96e+01 angle pdb=" N VAL A 68 " pdb=" CA VAL A 68 " pdb=" C VAL A 68 " ideal model delta sigma weight residual 113.16 106.66 6.50 1.49e+00 4.50e-01 1.90e+01 angle pdb=" C PRO I 41 " pdb=" N ARG I 42 " pdb=" CA ARG I 42 " ideal model delta sigma weight residual 121.54 129.09 -7.55 1.91e+00 2.74e-01 1.56e+01 angle pdb=" CB GLN I 39 " pdb=" CG GLN I 39 " pdb=" CD GLN I 39 " ideal model delta sigma weight residual 112.60 119.26 -6.66 1.70e+00 3.46e-01 1.54e+01 ... (remaining 7080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 2836 17.29 - 34.58: 248 34.58 - 51.87: 59 51.87 - 69.16: 6 69.16 - 86.46: 4 Dihedral angle restraints: 3153 sinusoidal: 1264 harmonic: 1889 Sorted by residual: dihedral pdb=" CA GLU A 429 " pdb=" C GLU A 429 " pdb=" N VAL A 430 " pdb=" CA VAL A 430 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " pdb=" CB CYS J 88 " ideal model delta sinusoidal sigma weight residual 93.00 130.77 -37.77 1 1.00e+01 1.00e-02 2.01e+01 dihedral pdb=" CA MET A 434 " pdb=" C MET A 434 " pdb=" N TYR A 435 " pdb=" CA TYR A 435 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 3150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 617 0.071 - 0.143: 138 0.143 - 0.214: 30 0.214 - 0.285: 3 0.285 - 0.357: 1 Chirality restraints: 789 Sorted by residual: chirality pdb=" CB VAL A 208 " pdb=" CA VAL A 208 " pdb=" CG1 VAL A 208 " pdb=" CG2 VAL A 208 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CB ILE A 326 " pdb=" CA ILE A 326 " pdb=" CG1 ILE A 326 " pdb=" CG2 ILE A 326 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA GLU J 81 " pdb=" N GLU J 81 " pdb=" C GLU J 81 " pdb=" CB GLU J 81 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 786 not shown) Planarity restraints: 910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER J 94 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO J 95 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO J 95 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO J 95 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 103 " -0.015 2.00e-02 2.50e+03 1.54e-02 5.92e+00 pdb=" CG TRP I 103 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP I 103 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP I 103 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP I 103 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP I 103 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 103 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 103 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 103 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP I 103 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN J 79 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO J 80 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO J 80 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO J 80 " 0.031 5.00e-02 4.00e+02 ... (remaining 907 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1334 2.80 - 3.33: 4531 3.33 - 3.85: 8162 3.85 - 4.38: 8702 4.38 - 4.90: 15210 Nonbonded interactions: 37939 Sorted by model distance: nonbonded pdb=" NE2 GLN A 103 " pdb=" OD2 ASP A 107 " model vdw 2.280 3.120 nonbonded pdb=" OG SER J 14 " pdb=" OD2 ASP J 17 " model vdw 2.304 3.040 nonbonded pdb=" OG SER A 479 " pdb=" OE1 GLU A 480 " model vdw 2.334 3.040 nonbonded pdb=" O PHE I 100E" pdb=" OH TYR J 36 " model vdw 2.334 3.040 nonbonded pdb=" O GLN J 3 " pdb=" OG SER J 26 " model vdw 2.347 3.040 ... (remaining 37934 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.480 Find NCS groups from input model: 0.070 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 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 : 0.006 0.056 5230 Z= 0.359 Angle : 1.057 9.252 7104 Z= 0.611 Chirality : 0.064 0.357 789 Planarity : 0.007 0.071 909 Dihedral : 13.613 86.455 1917 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.94 % Favored : 91.74 % Rotamer: Outliers : 0.52 % Allowed : 1.22 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.32 (0.30), residues: 642 helix: -2.35 (0.52), residues: 57 sheet: -0.76 (0.36), residues: 189 loop : -1.87 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP I 103 HIS 0.016 0.002 HIS I 35 PHE 0.012 0.002 PHE A 210 TYR 0.033 0.003 TYR A 330 ARG 0.014 0.001 ARG J 42 Details of bonding type rmsd link_NAG-ASN : bond 0.01644 ( 1) link_NAG-ASN : angle 1.01020 ( 3) hydrogen bonds : bond 0.17849 ( 149) hydrogen bonds : angle 7.12534 ( 420) SS BOND : bond 0.00597 ( 8) SS BOND : angle 1.86133 ( 16) covalent geometry : bond 0.00586 ( 5221) covalent geometry : angle 1.05494 ( 7085) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 THR cc_start: 0.8241 (p) cc_final: 0.7914 (t) REVERT: A 396 MET cc_start: 0.6848 (ppp) cc_final: 0.6360 (ppp) REVERT: I 3 HIS cc_start: 0.8035 (t-90) cc_final: 0.7531 (t-90) REVERT: I 12 LYS cc_start: 0.8432 (mptt) cc_final: 0.8214 (mmtt) REVERT: I 80 MET cc_start: 0.8926 (ttt) cc_final: 0.8424 (ttp) REVERT: J 2 ILE cc_start: 0.7936 (mp) cc_final: 0.7267 (mp) REVERT: J 4 MET cc_start: 0.7089 (mpp) cc_final: 0.6819 (mpp) REVERT: J 58 VAL cc_start: 0.8674 (t) cc_final: 0.8212 (t) outliers start: 3 outliers final: 1 residues processed: 139 average time/residue: 0.1678 time to fit residues: 30.2402 Evaluate side-chains 97 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.0670 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.0670 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.145586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.122054 restraints weight = 11631.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.125756 restraints weight = 7349.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.128398 restraints weight = 5218.241| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5230 Z= 0.115 Angle : 0.592 6.818 7104 Z= 0.317 Chirality : 0.043 0.141 789 Planarity : 0.005 0.053 909 Dihedral : 6.039 52.745 725 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.98 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.60 (0.31), residues: 642 helix: -0.79 (0.68), residues: 52 sheet: -0.41 (0.38), residues: 169 loop : -1.43 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 50 HIS 0.004 0.001 HIS I 35 PHE 0.015 0.001 PHE A 233 TYR 0.014 0.001 TYR A 330 ARG 0.004 0.000 ARG J 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 1) link_NAG-ASN : angle 0.40828 ( 3) hydrogen bonds : bond 0.03990 ( 149) hydrogen bonds : angle 6.04769 ( 420) SS BOND : bond 0.00558 ( 8) SS BOND : angle 1.52469 ( 16) covalent geometry : bond 0.00250 ( 5221) covalent geometry : angle 0.58827 ( 7085) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 THR cc_start: 0.8650 (p) cc_final: 0.8371 (t) REVERT: A 122 LEU cc_start: 0.9138 (tp) cc_final: 0.8916 (tp) REVERT: A 145 MET cc_start: 0.2154 (mtt) cc_final: 0.1807 (mtt) REVERT: A 180 ASP cc_start: 0.7321 (t0) cc_final: 0.6545 (t0) REVERT: A 396 MET cc_start: 0.6726 (ppp) cc_final: 0.6306 (ppp) REVERT: A 426 MET cc_start: 0.7169 (tmm) cc_final: 0.6709 (tmm) REVERT: I 3 HIS cc_start: 0.8029 (t-90) cc_final: 0.7604 (t-90) REVERT: I 80 MET cc_start: 0.8976 (ttt) cc_final: 0.8524 (ttp) REVERT: J 2 ILE cc_start: 0.8042 (mp) cc_final: 0.7502 (mp) REVERT: J 79 GLN cc_start: 0.8070 (pp30) cc_final: 0.7831 (pp30) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1608 time to fit residues: 25.4638 Evaluate side-chains 89 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.142780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.118563 restraints weight = 12014.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.122082 restraints weight = 7813.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.124636 restraints weight = 5693.652| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5230 Z= 0.146 Angle : 0.599 7.058 7104 Z= 0.321 Chirality : 0.043 0.168 789 Planarity : 0.005 0.063 909 Dihedral : 5.953 53.518 725 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.54 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.36 (0.32), residues: 642 helix: 0.22 (0.76), residues: 46 sheet: -0.21 (0.38), residues: 186 loop : -1.43 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 50 HIS 0.003 0.001 HIS A 216 PHE 0.021 0.002 PHE J 83 TYR 0.015 0.002 TYR A 330 ARG 0.005 0.000 ARG I 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 1) link_NAG-ASN : angle 1.05749 ( 3) hydrogen bonds : bond 0.03753 ( 149) hydrogen bonds : angle 5.72648 ( 420) SS BOND : bond 0.00436 ( 8) SS BOND : angle 1.22835 ( 16) covalent geometry : bond 0.00329 ( 5221) covalent geometry : angle 0.59648 ( 7085) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: A 77 THR cc_start: 0.8680 (p) cc_final: 0.8404 (t) REVERT: A 104 MET cc_start: 0.8207 (tpp) cc_final: 0.7466 (tpt) REVERT: A 396 MET cc_start: 0.6834 (ppp) cc_final: 0.6435 (ppp) REVERT: A 426 MET cc_start: 0.7179 (tmm) cc_final: 0.6549 (tmm) REVERT: I 4 LEU cc_start: 0.8345 (mt) cc_final: 0.8114 (mt) REVERT: I 46 GLU cc_start: 0.7853 (tp30) cc_final: 0.7530 (tp30) REVERT: I 71 ARG cc_start: 0.9003 (ppt170) cc_final: 0.8542 (ptt90) REVERT: I 80 MET cc_start: 0.8961 (ttt) cc_final: 0.8521 (ttp) REVERT: J 2 ILE cc_start: 0.8229 (mp) cc_final: 0.7850 (mp) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1552 time to fit residues: 23.3248 Evaluate side-chains 86 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 56 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.140782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116379 restraints weight = 12097.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.119836 restraints weight = 7823.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.122340 restraints weight = 5700.439| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5230 Z= 0.163 Angle : 0.604 5.954 7104 Z= 0.322 Chirality : 0.043 0.173 789 Planarity : 0.004 0.059 909 Dihedral : 6.201 59.831 725 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.85 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.26 (0.32), residues: 642 helix: 0.62 (0.76), residues: 47 sheet: -0.17 (0.38), residues: 186 loop : -1.39 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 50 HIS 0.003 0.001 HIS I 58 PHE 0.013 0.002 PHE J 62 TYR 0.014 0.002 TYR I 32 ARG 0.004 0.000 ARG J 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 1) link_NAG-ASN : angle 1.07154 ( 3) hydrogen bonds : bond 0.03655 ( 149) hydrogen bonds : angle 5.77595 ( 420) SS BOND : bond 0.00474 ( 8) SS BOND : angle 1.15500 ( 16) covalent geometry : bond 0.00377 ( 5221) covalent geometry : angle 0.60144 ( 7085) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 77 THR cc_start: 0.8676 (p) cc_final: 0.8407 (t) REVERT: A 396 MET cc_start: 0.6797 (ppp) cc_final: 0.6408 (ppp) REVERT: A 426 MET cc_start: 0.7173 (tmm) cc_final: 0.6342 (tmm) REVERT: I 4 LEU cc_start: 0.8303 (mt) cc_final: 0.8065 (mt) REVERT: I 13 GLU cc_start: 0.8375 (mp0) cc_final: 0.8138 (mp0) REVERT: I 71 ARG cc_start: 0.9032 (ppt170) cc_final: 0.8492 (ptt90) REVERT: I 80 MET cc_start: 0.9079 (ttt) cc_final: 0.8550 (ttp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1555 time to fit residues: 22.3549 Evaluate side-chains 86 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 11 optimal weight: 0.0970 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 0.0370 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.142981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.118309 restraints weight = 11951.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121859 restraints weight = 7666.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.124394 restraints weight = 5558.887| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5230 Z= 0.114 Angle : 0.580 6.328 7104 Z= 0.309 Chirality : 0.043 0.138 789 Planarity : 0.004 0.057 909 Dihedral : 5.680 46.731 725 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.45 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.26 (0.32), residues: 642 helix: 0.31 (0.72), residues: 53 sheet: -0.05 (0.38), residues: 191 loop : -1.46 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 103 HIS 0.005 0.001 HIS J 90 PHE 0.023 0.001 PHE J 83 TYR 0.011 0.001 TYR A 330 ARG 0.005 0.000 ARG J 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 1) link_NAG-ASN : angle 1.04326 ( 3) hydrogen bonds : bond 0.03501 ( 149) hydrogen bonds : angle 5.54404 ( 420) SS BOND : bond 0.00402 ( 8) SS BOND : angle 1.05978 ( 16) covalent geometry : bond 0.00260 ( 5221) covalent geometry : angle 0.57813 ( 7085) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 77 THR cc_start: 0.8716 (p) cc_final: 0.8457 (t) REVERT: A 347 LYS cc_start: 0.8419 (pttt) cc_final: 0.8129 (tptp) REVERT: A 396 MET cc_start: 0.6740 (ppp) cc_final: 0.6361 (ppp) REVERT: A 426 MET cc_start: 0.7095 (tmm) cc_final: 0.6840 (tmm) REVERT: A 434 MET cc_start: 0.8146 (ttm) cc_final: 0.7589 (tpp) REVERT: I 4 LEU cc_start: 0.8284 (mt) cc_final: 0.8003 (mt) REVERT: I 71 ARG cc_start: 0.9019 (ppt170) cc_final: 0.8514 (ptt90) REVERT: I 80 MET cc_start: 0.9054 (ttt) cc_final: 0.8620 (ttp) REVERT: J 79 GLN cc_start: 0.7926 (pp30) cc_final: 0.7529 (pp30) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1570 time to fit residues: 22.1150 Evaluate side-chains 82 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 30 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 55 optimal weight: 0.0570 chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 195 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.143241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119578 restraints weight = 11629.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.123053 restraints weight = 7455.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.125471 restraints weight = 5399.446| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5230 Z= 0.110 Angle : 0.575 5.649 7104 Z= 0.303 Chirality : 0.042 0.154 789 Planarity : 0.004 0.054 909 Dihedral : 5.337 34.758 725 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.76 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.23 (0.32), residues: 642 helix: 0.38 (0.73), residues: 53 sheet: 0.06 (0.39), residues: 184 loop : -1.48 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 50 HIS 0.003 0.001 HIS A 249 PHE 0.013 0.001 PHE A 233 TYR 0.011 0.001 TYR J 91 ARG 0.006 0.000 ARG J 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 1) link_NAG-ASN : angle 0.96442 ( 3) hydrogen bonds : bond 0.03295 ( 149) hydrogen bonds : angle 5.46572 ( 420) SS BOND : bond 0.00383 ( 8) SS BOND : angle 1.03768 ( 16) covalent geometry : bond 0.00251 ( 5221) covalent geometry : angle 0.57358 ( 7085) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 77 THR cc_start: 0.8732 (p) cc_final: 0.8484 (t) REVERT: A 104 MET cc_start: 0.8790 (tpp) cc_final: 0.7695 (tpp) REVERT: A 321 GLN cc_start: 0.8523 (mp-120) cc_final: 0.8314 (pm20) REVERT: A 347 LYS cc_start: 0.8378 (pttt) cc_final: 0.8105 (tptp) REVERT: A 426 MET cc_start: 0.7073 (tmm) cc_final: 0.6867 (tmm) REVERT: A 434 MET cc_start: 0.8194 (ttm) cc_final: 0.7679 (tpp) REVERT: I 3 HIS cc_start: 0.8103 (t-90) cc_final: 0.7757 (t-90) REVERT: I 4 LEU cc_start: 0.8305 (mt) cc_final: 0.7987 (mt) REVERT: I 71 ARG cc_start: 0.8964 (ppt170) cc_final: 0.8532 (ptt90) REVERT: I 80 MET cc_start: 0.9121 (ttt) cc_final: 0.8702 (ttp) REVERT: J 79 GLN cc_start: 0.8148 (pp30) cc_final: 0.7742 (pp30) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1788 time to fit residues: 25.6054 Evaluate side-chains 86 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 40 optimal weight: 0.0770 chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 20 optimal weight: 0.0770 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 24 optimal weight: 0.0670 chunk 30 optimal weight: 0.9990 overall best weight: 0.1234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 195 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.144444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.119667 restraints weight = 11856.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123410 restraints weight = 7524.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.126100 restraints weight = 5389.375| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5230 Z= 0.100 Angle : 0.600 12.448 7104 Z= 0.305 Chirality : 0.042 0.153 789 Planarity : 0.004 0.052 909 Dihedral : 5.063 27.370 725 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.21 % Favored : 95.64 % Rotamer: Outliers : 0.17 % Allowed : 2.62 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.28 (0.32), residues: 642 helix: 0.41 (0.73), residues: 53 sheet: 0.06 (0.39), residues: 182 loop : -1.53 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 50 HIS 0.003 0.001 HIS I 35 PHE 0.013 0.001 PHE A 233 TYR 0.011 0.001 TYR J 49 ARG 0.008 0.000 ARG J 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 1) link_NAG-ASN : angle 0.94789 ( 3) hydrogen bonds : bond 0.03139 ( 149) hydrogen bonds : angle 5.32505 ( 420) SS BOND : bond 0.00323 ( 8) SS BOND : angle 0.94494 ( 16) covalent geometry : bond 0.00225 ( 5221) covalent geometry : angle 0.59895 ( 7085) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 77 THR cc_start: 0.8706 (p) cc_final: 0.8445 (t) REVERT: A 104 MET cc_start: 0.7928 (tpp) cc_final: 0.7459 (tpt) REVERT: A 116 LEU cc_start: 0.9579 (mm) cc_final: 0.9348 (mt) REVERT: A 321 GLN cc_start: 0.8595 (mp-120) cc_final: 0.8368 (pm20) REVERT: A 347 LYS cc_start: 0.8411 (pttt) cc_final: 0.8150 (tptp) REVERT: A 396 MET cc_start: 0.6562 (ppp) cc_final: 0.6189 (ppp) REVERT: I 3 HIS cc_start: 0.8021 (t-90) cc_final: 0.7641 (t-90) REVERT: I 12 LYS cc_start: 0.8671 (mmtm) cc_final: 0.7503 (tttt) REVERT: I 59 TYR cc_start: 0.8930 (m-10) cc_final: 0.8502 (m-10) REVERT: I 71 ARG cc_start: 0.8995 (ppt170) cc_final: 0.8580 (ptt90) REVERT: I 80 MET cc_start: 0.9067 (ttt) cc_final: 0.8420 (ttp) REVERT: J 79 GLN cc_start: 0.8194 (pp30) cc_final: 0.7815 (pp30) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.1610 time to fit residues: 23.5927 Evaluate side-chains 88 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 30 optimal weight: 0.0470 chunk 3 optimal weight: 0.0050 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.5092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 195 ASN ** A 300 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 = 0.3889 r_free = 0.3889 target = 0.145242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.121761 restraints weight = 11530.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.125202 restraints weight = 7408.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.127653 restraints weight = 5350.202| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5230 Z= 0.122 Angle : 0.624 13.479 7104 Z= 0.318 Chirality : 0.043 0.168 789 Planarity : 0.004 0.053 909 Dihedral : 5.127 28.148 725 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.14 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.33 (0.32), residues: 642 helix: 0.54 (0.75), residues: 53 sheet: -0.02 (0.38), residues: 182 loop : -1.58 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 50 HIS 0.003 0.001 HIS A 216 PHE 0.017 0.001 PHE J 62 TYR 0.011 0.001 TYR J 49 ARG 0.007 0.001 ARG J 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 1) link_NAG-ASN : angle 0.89650 ( 3) hydrogen bonds : bond 0.03393 ( 149) hydrogen bonds : angle 5.38572 ( 420) SS BOND : bond 0.00298 ( 8) SS BOND : angle 1.30251 ( 16) covalent geometry : bond 0.00282 ( 5221) covalent geometry : angle 0.62102 ( 7085) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 77 THR cc_start: 0.8753 (p) cc_final: 0.8521 (t) REVERT: A 116 LEU cc_start: 0.9583 (mm) cc_final: 0.9230 (mp) REVERT: A 347 LYS cc_start: 0.8336 (pttt) cc_final: 0.8093 (tptp) REVERT: A 396 MET cc_start: 0.6550 (ppp) cc_final: 0.6219 (ppp) REVERT: I 3 HIS cc_start: 0.8074 (t-90) cc_final: 0.7734 (t-90) REVERT: I 12 LYS cc_start: 0.8608 (mmtm) cc_final: 0.7542 (ttpt) REVERT: I 59 TYR cc_start: 0.8911 (m-10) cc_final: 0.8471 (m-10) REVERT: I 71 ARG cc_start: 0.8945 (ppt170) cc_final: 0.8640 (ptt90) REVERT: I 80 MET cc_start: 0.8775 (ttt) cc_final: 0.8183 (ttt) REVERT: J 79 GLN cc_start: 0.8153 (pp30) cc_final: 0.7858 (pp30) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1503 time to fit residues: 22.2226 Evaluate side-chains 85 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 0.0170 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 195 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.145126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.122223 restraints weight = 11512.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.125684 restraints weight = 7263.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.128167 restraints weight = 5166.628| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5230 Z= 0.112 Angle : 0.614 12.359 7104 Z= 0.314 Chirality : 0.043 0.164 789 Planarity : 0.004 0.048 909 Dihedral : 5.017 28.703 725 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.67 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.36 (0.32), residues: 642 helix: 0.53 (0.73), residues: 53 sheet: -0.07 (0.38), residues: 184 loop : -1.58 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 50 HIS 0.003 0.001 HIS A 374 PHE 0.014 0.001 PHE J 62 TYR 0.015 0.001 TYR J 49 ARG 0.008 0.001 ARG J 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 1) link_NAG-ASN : angle 0.89376 ( 3) hydrogen bonds : bond 0.03253 ( 149) hydrogen bonds : angle 5.30430 ( 420) SS BOND : bond 0.00318 ( 8) SS BOND : angle 1.16814 ( 16) covalent geometry : bond 0.00261 ( 5221) covalent geometry : angle 0.61202 ( 7085) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 77 THR cc_start: 0.8820 (p) cc_final: 0.8597 (t) REVERT: A 116 LEU cc_start: 0.9560 (mm) cc_final: 0.9211 (mp) REVERT: A 145 MET cc_start: 0.2522 (mtt) cc_final: 0.2180 (mtt) REVERT: A 347 LYS cc_start: 0.8333 (pttt) cc_final: 0.8071 (tptp) REVERT: A 396 MET cc_start: 0.6495 (ppp) cc_final: 0.6215 (ppp) REVERT: I 3 HIS cc_start: 0.8053 (t-90) cc_final: 0.7710 (t-90) REVERT: I 12 LYS cc_start: 0.8570 (mmtm) cc_final: 0.7493 (ttpt) REVERT: I 59 TYR cc_start: 0.8877 (m-10) cc_final: 0.8429 (m-10) REVERT: I 71 ARG cc_start: 0.8959 (ppt170) cc_final: 0.8679 (ptt90) REVERT: I 80 MET cc_start: 0.8785 (ttt) cc_final: 0.8120 (ttt) REVERT: J 79 GLN cc_start: 0.8156 (pp30) cc_final: 0.7913 (pp30) REVERT: J 104 VAL cc_start: 0.7786 (t) cc_final: 0.7571 (t) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1757 time to fit residues: 27.5186 Evaluate side-chains 92 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 43 optimal weight: 0.0050 chunk 39 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 195 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.142844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119667 restraints weight = 11572.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123161 restraints weight = 7268.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.125693 restraints weight = 5192.320| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5230 Z= 0.129 Angle : 0.622 11.525 7104 Z= 0.319 Chirality : 0.043 0.166 789 Planarity : 0.004 0.047 909 Dihedral : 5.110 29.231 725 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.54 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.37 (0.32), residues: 642 helix: 0.46 (0.71), residues: 53 sheet: -0.05 (0.38), residues: 184 loop : -1.59 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 47 HIS 0.003 0.001 HIS I 58 PHE 0.012 0.001 PHE A 233 TYR 0.012 0.001 TYR A 217 ARG 0.007 0.001 ARG J 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 1) link_NAG-ASN : angle 0.81734 ( 3) hydrogen bonds : bond 0.03364 ( 149) hydrogen bonds : angle 5.37505 ( 420) SS BOND : bond 0.00353 ( 8) SS BOND : angle 1.24096 ( 16) covalent geometry : bond 0.00298 ( 5221) covalent geometry : angle 0.61991 ( 7085) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: A 77 THR cc_start: 0.8841 (p) cc_final: 0.8597 (t) REVERT: A 116 LEU cc_start: 0.9554 (mm) cc_final: 0.9198 (mp) REVERT: A 145 MET cc_start: 0.2656 (mtt) cc_final: 0.2262 (mtt) REVERT: A 347 LYS cc_start: 0.8356 (pttt) cc_final: 0.8132 (tptp) REVERT: A 396 MET cc_start: 0.6571 (ppp) cc_final: 0.6298 (ppp) REVERT: I 3 HIS cc_start: 0.8124 (t-90) cc_final: 0.7754 (t-90) REVERT: I 47 TRP cc_start: 0.7503 (t-100) cc_final: 0.6810 (t-100) REVERT: I 51 ILE cc_start: 0.8900 (tt) cc_final: 0.8658 (tt) REVERT: I 71 ARG cc_start: 0.8962 (ppt170) cc_final: 0.8488 (ptt90) REVERT: I 80 MET cc_start: 0.8832 (ttt) cc_final: 0.8123 (ttt) REVERT: J 79 GLN cc_start: 0.8098 (pp30) cc_final: 0.7424 (pp30) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1580 time to fit residues: 23.5696 Evaluate side-chains 87 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 53 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.140802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116254 restraints weight = 12028.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119946 restraints weight = 7532.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.122515 restraints weight = 5369.592| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5230 Z= 0.148 Angle : 0.619 10.734 7104 Z= 0.319 Chirality : 0.043 0.165 789 Planarity : 0.004 0.047 909 Dihedral : 5.198 29.188 725 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.76 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.44 (0.32), residues: 642 helix: -0.18 (0.68), residues: 59 sheet: -0.17 (0.37), residues: 198 loop : -1.56 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 47 HIS 0.003 0.001 HIS A 374 PHE 0.012 0.001 PHE A 233 TYR 0.012 0.001 TYR I 91 ARG 0.006 0.001 ARG J 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 1) link_NAG-ASN : angle 0.80188 ( 3) hydrogen bonds : bond 0.03443 ( 149) hydrogen bonds : angle 5.41310 ( 420) SS BOND : bond 0.00402 ( 8) SS BOND : angle 1.00727 ( 16) covalent geometry : bond 0.00341 ( 5221) covalent geometry : angle 0.61746 ( 7085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2112.28 seconds wall clock time: 37 minutes 42.54 seconds (2262.54 seconds total)