Starting phenix.real_space_refine on Sat May 10 05:54:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1d_41810/05_2025/8u1d_41810.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1d_41810/05_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_41810/05_2025/8u1d_41810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1d_41810/05_2025/8u1d_41810.map" model { file = "/net/cci-nas-00/data/ceres_data/8u1d_41810/05_2025/8u1d_41810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1d_41810/05_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-5687/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: 3.80, per 1000 atoms: 0.74 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: 1.23 Conformation dependent library (CDL) restraints added in 607.7 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: 0.66 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: 1.61 Time building geometry restraints manager: 1.40 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: 0.010 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.130 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.640 ------------------------------------------------------------------------------- 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 : 0.539 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: 0.1530 time to fit residues: 27.5400 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 : 0.525 ------------------------------------------------------------------------------- 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: 0.0170 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.0670 overall best weight: 0.3556 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.145690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122129 restraints weight = 11639.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.125832 restraints weight = 7356.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.128502 restraints weight = 5214.591| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5230 Z= 0.110 Angle : 0.584 6.716 7104 Z= 0.313 Chirality : 0.043 0.143 789 Planarity : 0.005 0.053 909 Dihedral : 6.048 52.951 725 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.67 % Favored : 95.17 % 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: -1.58 (0.31), residues: 642 helix: -0.73 (0.68), residues: 52 sheet: -0.40 (0.38), residues: 169 loop : -1.43 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 50 HIS 0.005 0.001 HIS I 35 PHE 0.014 0.001 PHE A 233 TYR 0.014 0.001 TYR A 330 ARG 0.005 0.000 ARG J 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 1) link_NAG-ASN : angle 0.52990 ( 3) hydrogen bonds : bond 0.03823 ( 149) hydrogen bonds : angle 6.01278 ( 420) SS BOND : bond 0.00434 ( 8) SS BOND : angle 1.44018 ( 16) covalent geometry : bond 0.00240 ( 5221) covalent geometry : angle 0.58081 ( 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 : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 THR cc_start: 0.8659 (p) cc_final: 0.8380 (t) REVERT: A 122 LEU cc_start: 0.9139 (tp) cc_final: 0.8924 (tp) REVERT: A 145 MET cc_start: 0.2189 (mtt) cc_final: 0.1832 (mtt) REVERT: A 396 MET cc_start: 0.6720 (ppp) cc_final: 0.6304 (ppp) REVERT: A 426 MET cc_start: 0.7171 (tmm) cc_final: 0.6699 (tmm) REVERT: I 3 HIS cc_start: 0.8034 (t-90) cc_final: 0.7615 (t-90) REVERT: I 80 MET cc_start: 0.8953 (ttt) cc_final: 0.8529 (ttp) REVERT: J 2 ILE cc_start: 0.8051 (mp) cc_final: 0.7498 (mp) REVERT: J 79 GLN cc_start: 0.8066 (pp30) cc_final: 0.7646 (pp30) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1501 time to fit residues: 23.9096 Evaluate side-chains 90 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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: 4.9990 chunk 2 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 42 optimal weight: 0.0970 chunk 11 optimal weight: 0.0980 chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 0.0770 chunk 53 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 overall best weight: 0.3136 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.146186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.122462 restraints weight = 11819.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.126096 restraints weight = 7656.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.128795 restraints weight = 5521.682| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5230 Z= 0.104 Angle : 0.570 6.027 7104 Z= 0.306 Chirality : 0.043 0.177 789 Planarity : 0.004 0.059 909 Dihedral : 5.892 59.278 725 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.45 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % 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: -1.40 (0.32), residues: 642 helix: -0.26 (0.73), residues: 52 sheet: -0.17 (0.38), residues: 184 loop : -1.45 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 50 HIS 0.003 0.001 HIS I 35 PHE 0.031 0.001 PHE J 83 TYR 0.015 0.001 TYR A 330 ARG 0.005 0.000 ARG J 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 1) link_NAG-ASN : angle 0.80603 ( 3) hydrogen bonds : bond 0.03528 ( 149) hydrogen bonds : angle 5.62985 ( 420) SS BOND : bond 0.00398 ( 8) SS BOND : angle 1.11066 ( 16) covalent geometry : bond 0.00227 ( 5221) covalent geometry : angle 0.56780 ( 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 114 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 77 THR cc_start: 0.8693 (p) cc_final: 0.8413 (t) REVERT: A 104 MET cc_start: 0.8092 (tpp) cc_final: 0.7293 (tpp) REVERT: A 321 GLN cc_start: 0.8354 (mp-120) cc_final: 0.8071 (pm20) REVERT: A 396 MET cc_start: 0.6820 (ppp) cc_final: 0.6421 (ppp) REVERT: A 426 MET cc_start: 0.7053 (tmm) cc_final: 0.6535 (tmm) REVERT: A 434 MET cc_start: 0.8180 (ttm) cc_final: 0.7765 (tpp) REVERT: I 3 HIS cc_start: 0.8028 (t-90) cc_final: 0.7600 (t-90) REVERT: I 71 ARG cc_start: 0.8941 (ppt170) cc_final: 0.8579 (ptt90) REVERT: I 80 MET cc_start: 0.8975 (ttt) cc_final: 0.8738 (ttp) REVERT: I 100 SER cc_start: 0.7972 (p) cc_final: 0.7655 (p) REVERT: J 2 ILE cc_start: 0.8139 (mp) cc_final: 0.7820 (mp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1508 time to fit residues: 22.6267 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 : 0.515 ------------------------------------------------------------------------------- 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: 0.6980 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.137705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.112693 restraints weight = 12399.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116165 restraints weight = 8045.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.118627 restraints weight = 5879.118| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5230 Z= 0.227 Angle : 0.671 5.621 7104 Z= 0.359 Chirality : 0.044 0.187 789 Planarity : 0.005 0.056 909 Dihedral : 6.466 59.942 725 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.26 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % 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: 0.51 (0.74), residues: 47 sheet: -0.35 (0.37), residues: 198 loop : -1.32 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 47 HIS 0.005 0.001 HIS I 58 PHE 0.016 0.002 PHE A 233 TYR 0.021 0.002 TYR I 32 ARG 0.005 0.001 ARG J 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 1) link_NAG-ASN : angle 1.29551 ( 3) hydrogen bonds : bond 0.04045 ( 149) hydrogen bonds : angle 5.99029 ( 420) SS BOND : bond 0.00695 ( 8) SS BOND : angle 1.59859 ( 16) covalent geometry : bond 0.00519 ( 5221) covalent geometry : angle 0.66737 ( 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 108 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 77 THR cc_start: 0.8702 (p) cc_final: 0.8427 (t) REVERT: A 93 PHE cc_start: 0.7034 (m-80) cc_final: 0.6753 (m-80) REVERT: A 100 MET cc_start: 0.6035 (ptp) cc_final: 0.5780 (ptp) REVERT: A 122 LEU cc_start: 0.9321 (tp) cc_final: 0.9069 (tp) REVERT: A 426 MET cc_start: 0.7130 (tmm) cc_final: 0.6819 (tmm) REVERT: I 3 HIS cc_start: 0.8172 (t-90) cc_final: 0.7716 (t-90) REVERT: I 4 LEU cc_start: 0.8395 (mt) cc_final: 0.7998 (mt) REVERT: I 71 ARG cc_start: 0.9047 (ppt170) cc_final: 0.8510 (ptt90) REVERT: I 80 MET cc_start: 0.9015 (ttt) cc_final: 0.8440 (ttp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1556 time to fit residues: 22.0851 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 : 0.604 ------------------------------------------------------------------------------- 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: 4.9990 chunk 12 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 7 optimal weight: 0.0020 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 ** 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 = 0.3846 r_free = 0.3846 target = 0.141660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118713 restraints weight = 11774.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122252 restraints weight = 7395.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.124710 restraints weight = 5270.695| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2534 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= 0.121 Angle : 0.597 5.780 7104 Z= 0.316 Chirality : 0.043 0.157 789 Planarity : 0.004 0.052 909 Dihedral : 5.659 42.431 725 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.14 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: -1.15 (0.33), residues: 642 helix: 0.82 (0.77), residues: 47 sheet: -0.18 (0.37), residues: 203 loop : -1.33 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 50 HIS 0.004 0.001 HIS A 249 PHE 0.027 0.001 PHE J 83 TYR 0.011 0.001 TYR J 91 ARG 0.003 0.000 ARG J 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 1) link_NAG-ASN : angle 0.97473 ( 3) hydrogen bonds : bond 0.03399 ( 149) hydrogen bonds : angle 5.62187 ( 420) SS BOND : bond 0.00537 ( 8) SS BOND : angle 1.02739 ( 16) covalent geometry : bond 0.00276 ( 5221) covalent geometry : angle 0.59526 ( 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 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: 0.8747 (p) cc_final: 0.8517 (t) REVERT: A 104 MET cc_start: 0.8777 (tpp) cc_final: 0.7763 (tpt) REVERT: A 321 GLN cc_start: 0.8495 (mp-120) cc_final: 0.8154 (pm20) REVERT: A 347 LYS cc_start: 0.8329 (pttt) cc_final: 0.8052 (tptp) REVERT: A 396 MET cc_start: 0.6499 (ppp) cc_final: 0.6198 (ppp) REVERT: A 426 MET cc_start: 0.7114 (tmm) cc_final: 0.6792 (tmm) REVERT: I 3 HIS cc_start: 0.8162 (t-90) cc_final: 0.7831 (t-90) REVERT: I 4 LEU cc_start: 0.8371 (mt) cc_final: 0.8090 (mt) REVERT: I 71 ARG cc_start: 0.8979 (ppt170) cc_final: 0.8548 (ptt90) REVERT: I 80 MET cc_start: 0.9103 (ttt) cc_final: 0.8602 (ttp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1588 time to fit residues: 22.8425 Evaluate side-chains 91 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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: 0.4980 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 0.0050 chunk 47 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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 ** 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 = 0.3864 r_free = 0.3864 target = 0.143229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119742 restraints weight = 11656.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.123294 restraints weight = 7434.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.125731 restraints weight = 5351.763| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5230 Z= 0.118 Angle : 0.595 8.598 7104 Z= 0.311 Chirality : 0.042 0.155 789 Planarity : 0.004 0.049 909 Dihedral : 5.493 33.405 725 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.23 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 0.39 (0.74), residues: 52 sheet: -0.07 (0.38), residues: 196 loop : -1.47 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 50 HIS 0.004 0.001 HIS A 249 PHE 0.007 0.001 PHE I 63 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 0.00448 ( 1) link_NAG-ASN : angle 1.02132 ( 3) hydrogen bonds : bond 0.03407 ( 149) hydrogen bonds : angle 5.55266 ( 420) SS BOND : bond 0.00349 ( 8) SS BOND : angle 1.02341 ( 16) covalent geometry : bond 0.00275 ( 5221) covalent geometry : angle 0.59385 ( 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 108 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 77 THR cc_start: 0.8749 (p) cc_final: 0.8505 (t) REVERT: A 104 MET cc_start: 0.7968 (tpp) cc_final: 0.7366 (tpt) REVERT: A 321 GLN cc_start: 0.8505 (mp-120) cc_final: 0.8277 (pm20) REVERT: A 347 LYS cc_start: 0.8386 (pttt) cc_final: 0.8117 (tptp) REVERT: A 396 MET cc_start: 0.6453 (ppp) cc_final: 0.6143 (ppp) REVERT: A 426 MET cc_start: 0.7023 (tmm) cc_final: 0.6795 (tmm) REVERT: A 434 MET cc_start: 0.8137 (ttm) cc_final: 0.7853 (tpp) REVERT: I 4 LEU cc_start: 0.8344 (mt) cc_final: 0.8112 (mt) REVERT: I 13 GLU cc_start: 0.8264 (mp0) cc_final: 0.8008 (mp0) REVERT: I 71 ARG cc_start: 0.8954 (ppt170) cc_final: 0.8516 (ptt90) REVERT: I 80 MET cc_start: 0.9124 (ttt) cc_final: 0.8681 (ttp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1870 time to fit residues: 25.7298 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 : 0.653 ------------------------------------------------------------------------------- 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: 2.9990 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 chunk 28 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 0.0060 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 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 ** 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 = 0.3847 r_free = 0.3847 target = 0.140781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.115383 restraints weight = 12295.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119193 restraints weight = 7786.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121802 restraints weight = 5604.245| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5230 Z= 0.127 Angle : 0.591 10.821 7104 Z= 0.309 Chirality : 0.042 0.150 789 Planarity : 0.004 0.047 909 Dihedral : 5.381 27.141 725 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.07 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: -1.29 (0.32), residues: 642 helix: 0.36 (0.73), residues: 54 sheet: -0.20 (0.38), residues: 198 loop : -1.43 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 50 HIS 0.004 0.001 HIS I 35 PHE 0.015 0.001 PHE A 233 TYR 0.010 0.001 TYR I 91 ARG 0.008 0.001 ARG J 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 1) link_NAG-ASN : angle 0.98476 ( 3) hydrogen bonds : bond 0.03351 ( 149) hydrogen bonds : angle 5.47683 ( 420) SS BOND : bond 0.00358 ( 8) SS BOND : angle 1.01107 ( 16) covalent geometry : bond 0.00296 ( 5221) covalent geometry : angle 0.58988 ( 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 104 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 77 THR cc_start: 0.8766 (p) cc_final: 0.8490 (t) REVERT: A 321 GLN cc_start: 0.8733 (mp-120) cc_final: 0.8351 (pm20) REVERT: A 347 LYS cc_start: 0.8467 (pttt) cc_final: 0.8201 (tptp) REVERT: A 396 MET cc_start: 0.6667 (ppp) cc_final: 0.6331 (ppp) REVERT: A 434 MET cc_start: 0.8109 (ttm) cc_final: 0.7794 (tpp) REVERT: I 4 LEU cc_start: 0.8189 (mt) cc_final: 0.7945 (mt) REVERT: I 47 TRP cc_start: 0.7598 (t-100) cc_final: 0.7113 (t-100) REVERT: I 71 ARG cc_start: 0.9001 (ppt170) cc_final: 0.8453 (ptt90) REVERT: I 80 MET cc_start: 0.9019 (ttt) cc_final: 0.8487 (ttp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1508 time to fit residues: 20.8478 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 : 0.530 ------------------------------------------------------------------------------- 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: 0.9980 chunk 4 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 30 optimal weight: 0.0980 chunk 3 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** J 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.142009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.118763 restraints weight = 11550.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.122205 restraints weight = 7308.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.124676 restraints weight = 5244.521| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2904 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= 0.121 Angle : 0.611 12.128 7104 Z= 0.315 Chirality : 0.042 0.147 789 Planarity : 0.004 0.047 909 Dihedral : 5.259 27.506 725 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.07 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: 0.57 (0.73), residues: 53 sheet: -0.18 (0.38), residues: 198 loop : -1.53 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 50 HIS 0.004 0.001 HIS I 35 PHE 0.012 0.001 PHE A 233 TYR 0.019 0.001 TYR A 435 ARG 0.007 0.001 ARG J 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 1) link_NAG-ASN : angle 0.97128 ( 3) hydrogen bonds : bond 0.03283 ( 149) hydrogen bonds : angle 5.45560 ( 420) SS BOND : bond 0.00333 ( 8) SS BOND : angle 0.98944 ( 16) covalent geometry : bond 0.00281 ( 5221) covalent geometry : angle 0.61016 ( 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 105 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 77 THR cc_start: 0.8780 (p) cc_final: 0.8551 (t) REVERT: A 347 LYS cc_start: 0.8333 (pttt) cc_final: 0.8091 (tptp) REVERT: A 396 MET cc_start: 0.6568 (ppp) cc_final: 0.6288 (ppp) REVERT: A 426 MET cc_start: 0.6825 (tmm) cc_final: 0.6349 (tmm) REVERT: A 434 MET cc_start: 0.8141 (ttm) cc_final: 0.7868 (tpp) REVERT: I 4 LEU cc_start: 0.8384 (mt) cc_final: 0.8097 (mt) REVERT: I 47 TRP cc_start: 0.7703 (t-100) cc_final: 0.7326 (t-100) REVERT: I 71 ARG cc_start: 0.8994 (ppt170) cc_final: 0.8514 (ptt90) REVERT: I 80 MET cc_start: 0.9132 (ttt) cc_final: 0.8655 (ttp) REVERT: J 79 GLN cc_start: 0.8090 (pp30) cc_final: 0.7812 (pp30) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1580 time to fit residues: 21.9956 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 : 0.600 ------------------------------------------------------------------------------- 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: 0.7980 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.0170 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 43 optimal weight: 0.0270 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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** ** A 374 HIS ** 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 = 0.3858 r_free = 0.3858 target = 0.142555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.119375 restraints weight = 12073.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.122867 restraints weight = 7688.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.125281 restraints weight = 5552.979| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5230 Z= 0.113 Angle : 0.607 11.165 7104 Z= 0.314 Chirality : 0.042 0.148 789 Planarity : 0.004 0.048 909 Dihedral : 5.107 27.975 725 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.76 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: -1.32 (0.32), residues: 642 helix: 0.82 (0.75), residues: 53 sheet: -0.22 (0.37), residues: 196 loop : -1.53 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 50 HIS 0.003 0.001 HIS A 249 PHE 0.016 0.001 PHE I 63 TYR 0.010 0.001 TYR J 49 ARG 0.006 0.000 ARG J 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 1) link_NAG-ASN : angle 0.95280 ( 3) hydrogen bonds : bond 0.03345 ( 149) hydrogen bonds : angle 5.36845 ( 420) SS BOND : bond 0.00327 ( 8) SS BOND : angle 0.97120 ( 16) covalent geometry : bond 0.00264 ( 5221) covalent geometry : angle 0.60566 ( 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 111 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 77 THR cc_start: 0.8805 (p) cc_final: 0.8570 (t) REVERT: A 116 LEU cc_start: 0.9584 (mm) cc_final: 0.9257 (mt) REVERT: A 347 LYS cc_start: 0.8342 (pttt) cc_final: 0.8101 (tptp) REVERT: A 396 MET cc_start: 0.6626 (ppp) cc_final: 0.6361 (ppp) REVERT: A 434 MET cc_start: 0.8112 (ttm) cc_final: 0.7786 (tpp) REVERT: I 3 HIS cc_start: 0.8115 (t-90) cc_final: 0.7762 (t-90) REVERT: I 4 LEU cc_start: 0.8341 (mt) cc_final: 0.8026 (mt) REVERT: I 12 LYS cc_start: 0.8579 (mmtm) cc_final: 0.8105 (mmmm) REVERT: I 47 TRP cc_start: 0.7604 (t-100) cc_final: 0.7345 (t-100) REVERT: I 53 TYR cc_start: 0.8238 (t80) cc_final: 0.7874 (t80) REVERT: I 59 TYR cc_start: 0.8906 (m-10) cc_final: 0.8452 (m-10) REVERT: I 71 ARG cc_start: 0.9000 (ppt170) cc_final: 0.8605 (ptt90) REVERT: I 80 MET cc_start: 0.9113 (ttt) cc_final: 0.8747 (ttp) REVERT: I 89 VAL cc_start: 0.8002 (p) cc_final: 0.7793 (p) REVERT: I 96 GLU cc_start: 0.7450 (tt0) cc_final: 0.6929 (mt-10) REVERT: J 79 GLN cc_start: 0.8086 (pp30) cc_final: 0.7817 (pp30) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1550 time to fit residues: 22.7394 Evaluate side-chains 90 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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: 0.0370 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 39 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.1980 overall best weight: 0.3858 ------------------------------------------------------------------------------- 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** ** A 374 HIS ** 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 = 0.3869 r_free = 0.3869 target = 0.143482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.120675 restraints weight = 11479.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.124216 restraints weight = 7214.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.126679 restraints weight = 5114.669| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5230 Z= 0.109 Angle : 0.604 11.035 7104 Z= 0.311 Chirality : 0.043 0.148 789 Planarity : 0.004 0.048 909 Dihedral : 5.047 28.504 725 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.45 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: -1.35 (0.32), residues: 642 helix: 0.16 (0.70), residues: 59 sheet: -0.20 (0.37), residues: 196 loop : -1.48 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 50 HIS 0.012 0.001 HIS I 35 PHE 0.015 0.001 PHE I 100E TYR 0.016 0.001 TYR A 435 ARG 0.006 0.000 ARG J 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 1) link_NAG-ASN : angle 0.88549 ( 3) hydrogen bonds : bond 0.03349 ( 149) hydrogen bonds : angle 5.36223 ( 420) SS BOND : bond 0.00313 ( 8) SS BOND : angle 0.98162 ( 16) covalent geometry : bond 0.00252 ( 5221) covalent geometry : angle 0.60311 ( 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 : 0.542 Fit side-chains revert: symmetry clash REVERT: A 77 THR cc_start: 0.8832 (p) cc_final: 0.8603 (t) REVERT: A 116 LEU cc_start: 0.9591 (mm) cc_final: 0.9250 (mt) REVERT: A 347 LYS cc_start: 0.8342 (pttt) cc_final: 0.8123 (tptp) REVERT: A 396 MET cc_start: 0.6592 (ppp) cc_final: 0.6333 (ppp) REVERT: A 434 MET cc_start: 0.8052 (ttm) cc_final: 0.7768 (tpp) REVERT: I 3 HIS cc_start: 0.8133 (t-90) cc_final: 0.7777 (t-90) REVERT: I 4 LEU cc_start: 0.8319 (mt) cc_final: 0.8007 (mt) REVERT: I 12 LYS cc_start: 0.8536 (mmtm) cc_final: 0.8147 (mmmm) REVERT: I 47 TRP cc_start: 0.7938 (t-100) cc_final: 0.7620 (t-100) REVERT: I 51 ILE cc_start: 0.8840 (tt) cc_final: 0.8632 (tt) REVERT: I 59 TYR cc_start: 0.8902 (m-10) cc_final: 0.8383 (m-10) REVERT: I 71 ARG cc_start: 0.8982 (ppt170) cc_final: 0.8650 (ptt90) REVERT: I 80 MET cc_start: 0.9151 (ttt) cc_final: 0.8831 (ttp) REVERT: J 79 GLN cc_start: 0.8096 (pp30) cc_final: 0.7033 (pp30) REVERT: J 81 GLU cc_start: 0.8957 (pp20) cc_final: 0.8746 (pp20) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1559 time to fit residues: 23.0424 Evaluate side-chains 93 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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: 3.9990 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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 = 0.3804 r_free = 0.3804 target = 0.138333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114229 restraints weight = 12127.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.117635 restraints weight = 7868.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.120013 restraints weight = 5762.288| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5230 Z= 0.182 Angle : 0.639 10.162 7104 Z= 0.333 Chirality : 0.044 0.220 789 Planarity : 0.004 0.046 909 Dihedral : 5.369 28.970 725 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.17 % Favored : 92.68 % 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: -1.46 (0.32), residues: 642 helix: -0.08 (0.67), residues: 59 sheet: -0.22 (0.38), residues: 198 loop : -1.58 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 50 HIS 0.009 0.001 HIS I 35 PHE 0.017 0.002 PHE I 63 TYR 0.018 0.002 TYR I 91 ARG 0.006 0.001 ARG J 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00643 ( 1) link_NAG-ASN : angle 0.83602 ( 3) hydrogen bonds : bond 0.03625 ( 149) hydrogen bonds : angle 5.52244 ( 420) SS BOND : bond 0.00487 ( 8) SS BOND : angle 1.32801 ( 16) covalent geometry : bond 0.00419 ( 5221) covalent geometry : angle 0.63636 ( 7085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1941.92 seconds wall clock time: 34 minutes 42.37 seconds (2082.37 seconds total)