Starting phenix.real_space_refine on Mon Jul 28 10:34:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sn2_25209/07_2025/7sn2_25209_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sn2_25209/07_2025/7sn2_25209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sn2_25209/07_2025/7sn2_25209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sn2_25209/07_2025/7sn2_25209.map" model { file = "/net/cci-nas-00/data/ceres_data/7sn2_25209/07_2025/7sn2_25209_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sn2_25209/07_2025/7sn2_25209_neut_trim.cif" } resolution = 4.3 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 3284 2.51 5 N 868 2.21 5 O 1016 1.98 5 H 4904 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10092 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3477 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 13, 'TRANS': 209} Chain: "H" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3236 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3251 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 89 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.30, per 1000 atoms: 0.53 Number of scatterers: 10092 At special positions: 0 Unit cell: (85.8, 113.85, 99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 O 1016 8.00 N 868 7.00 C 3284 6.00 H 4904 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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 ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 6 " BETA1-2 " MAN C 4 " - " NAG C 5 " " MAN C 6 " - " NAG C 7 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 1 " - " ASN A 331 " " NAG C 1 " - " ASN A 343 " Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 643.8 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: 1206 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 13 sheets defined 11.4% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 322 through 326 removed outlier: 4.062A pdb=" N SER A 325 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 326 " --> pdb=" O THR A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 326' Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 4.084A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.690A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.562A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 187 through 192 removed outlier: 4.389A pdb=" N THR H 191 " --> pdb=" O SER H 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.580A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 356 removed outlier: 4.211A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.914A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.410A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.410A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 120 through 122 removed outlier: 5.924A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 120 through 122 removed outlier: 5.924A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.457A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL H 198 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL H 207 " --> pdb=" O VAL H 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.507A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB3, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.746A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 145 through 149 178 hydrogen bonds defined for protein. 426 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: 3.51 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 4900 1.04 - 1.24: 685 1.24 - 1.44: 1708 1.44 - 1.64: 2905 1.64 - 1.85: 22 Bond restraints: 10220 Sorted by residual: bond pdb=" CA PHE A 329 " pdb=" CB PHE A 329 " ideal model delta sigma weight residual 1.530 1.569 -0.039 1.58e-02 4.01e+03 6.05e+00 bond pdb=" C2 MAN C 6 " pdb=" O2 MAN C 6 " ideal model delta sigma weight residual 1.407 1.454 -0.047 2.00e-02 2.50e+03 5.45e+00 bond pdb=" CB THR A 385 " pdb=" CG2 THR A 385 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.88e+00 bond pdb=" CA ALA A 435 " pdb=" C ALA A 435 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.31e-02 5.83e+03 4.69e+00 bond pdb=" C6 BMA C 3 " pdb=" O6 BMA C 3 " ideal model delta sigma weight residual 1.411 1.453 -0.042 2.00e-02 2.50e+03 4.37e+00 ... (remaining 10215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 18125 4.17 - 8.33: 159 8.33 - 12.50: 20 12.50 - 16.67: 1 16.67 - 20.84: 3 Bond angle restraints: 18308 Sorted by residual: angle pdb=" N LYS A 529 " pdb=" CA LYS A 529 " pdb=" C LYS A 529 " ideal model delta sigma weight residual 111.02 120.97 -9.95 1.22e+00 6.72e-01 6.65e+01 angle pdb=" N ASN A 437 " pdb=" CA ASN A 437 " pdb=" CB ASN A 437 " ideal model delta sigma weight residual 109.97 98.40 11.57 1.47e+00 4.63e-01 6.20e+01 angle pdb=" HB2 ASN A 437 " pdb=" CB ASN A 437 " pdb=" HB3 ASN A 437 " ideal model delta sigma weight residual 110.00 89.16 20.84 3.00e+00 1.11e-01 4.82e+01 angle pdb=" CG ASN A 437 " pdb=" CB ASN A 437 " pdb=" HB2 ASN A 437 " ideal model delta sigma weight residual 108.00 87.44 20.56 3.00e+00 1.11e-01 4.70e+01 angle pdb=" CA ASN A 437 " pdb=" CB ASN A 437 " pdb=" HB2 ASN A 437 " ideal model delta sigma weight residual 109.00 88.49 20.51 3.00e+00 1.11e-01 4.67e+01 ... (remaining 18303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.01: 4717 25.01 - 50.02: 278 50.02 - 75.03: 48 75.03 - 100.04: 17 100.04 - 125.05: 9 Dihedral angle restraints: 5069 sinusoidal: 2787 harmonic: 2282 Sorted by residual: dihedral pdb=" CA SER A 530 " pdb=" C SER A 530 " pdb=" N THR A 531 " pdb=" CA THR A 531 " ideal model delta harmonic sigma weight residual 180.00 136.70 43.30 0 5.00e+00 4.00e-02 7.50e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 17.59 75.41 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CA VAL A 395 " pdb=" C VAL A 395 " pdb=" N TYR A 396 " pdb=" CA TYR A 396 " ideal model delta harmonic sigma weight residual -180.00 -143.39 -36.61 0 5.00e+00 4.00e-02 5.36e+01 ... (remaining 5066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 756 0.118 - 0.237: 61 0.237 - 0.355: 8 0.355 - 0.474: 1 0.474 - 0.592: 1 Chirality restraints: 827 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.34e+02 chirality pdb=" C1 NAG C 7 " pdb=" O2 MAN C 6 " pdb=" C2 NAG C 7 " pdb=" O5 NAG C 7 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.05e+02 chirality pdb=" C1 NAG C 5 " pdb=" O2 MAN C 4 " pdb=" C2 NAG C 5 " pdb=" O5 NAG C 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 2.01e+02 ... (remaining 824 not shown) Planarity restraints: 1529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 91 " 0.527 9.50e-02 1.11e+02 1.76e-01 3.40e+01 pdb=" NE ARG L 91 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG L 91 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG L 91 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG L 91 " 0.017 2.00e-02 2.50e+03 pdb="HH11 ARG L 91 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG L 91 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG L 91 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG L 91 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 99 " 0.022 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C ARG H 99 " -0.075 2.00e-02 2.50e+03 pdb=" O ARG H 99 " 0.029 2.00e-02 2.50e+03 pdb=" N ASP H 100 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 94 " -0.371 9.50e-02 1.11e+02 1.24e-01 1.67e+01 pdb=" NE ARG H 94 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG H 94 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG H 94 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG H 94 " -0.010 2.00e-02 2.50e+03 pdb="HH11 ARG H 94 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG H 94 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG H 94 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 94 " -0.001 2.00e-02 2.50e+03 ... (remaining 1526 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 195 2.11 - 2.73: 16965 2.73 - 3.35: 27854 3.35 - 3.98: 35537 3.98 - 4.60: 53717 Nonbonded interactions: 134268 Sorted by model distance: nonbonded pdb=" O ALA A 372 " pdb="HH22 ARG H 100D" model vdw 1.482 2.450 nonbonded pdb="HD21 ASN A 370 " pdb=" HH TYR H 58 " model vdw 1.545 2.100 nonbonded pdb="HH22 ARG A 328 " pdb=" O LYS A 528 " model vdw 1.611 2.450 nonbonded pdb=" H SER H 156 " pdb=" OD1 ASN H 197 " model vdw 1.680 2.450 nonbonded pdb=" H LYS A 462 " pdb=" OE2 GLU A 465 " model vdw 1.686 2.450 ... (remaining 134263 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: 0.780 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: 0.170 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 25.540 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 5334 Z= 0.329 Angle : 1.350 15.901 7282 Z= 0.720 Chirality : 0.073 0.592 827 Planarity : 0.013 0.236 916 Dihedral : 17.661 125.050 2052 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.31 % Allowed : 0.78 % Favored : 98.91 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -1.92 (0.32), residues: 642 helix: -2.74 (0.79), residues: 32 sheet: -0.58 (0.35), residues: 222 loop : -1.61 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 436 HIS 0.009 0.003 HIS H 35 PHE 0.047 0.004 PHE A 329 TYR 0.052 0.004 TYR A 508 ARG 0.010 0.001 ARG H 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00753 ( 2) link_NAG-ASN : angle 4.37503 ( 6) link_ALPHA1-6 : bond 0.01257 ( 1) link_ALPHA1-6 : angle 5.46797 ( 3) link_BETA1-2 : bond 0.00930 ( 2) link_BETA1-2 : angle 5.10887 ( 6) link_BETA1-4 : bond 0.01310 ( 4) link_BETA1-4 : angle 5.86693 ( 12) link_ALPHA1-3 : bond 0.00432 ( 1) link_ALPHA1-3 : angle 3.77049 ( 3) hydrogen bonds : bond 0.17229 ( 156) hydrogen bonds : angle 10.40459 ( 426) SS BOND : bond 0.01193 ( 8) SS BOND : angle 2.19704 ( 16) covalent geometry : bond 0.00716 ( 5316) covalent geometry : angle 1.30779 ( 7236) *********************** 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 141 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7930 (m-30) cc_final: 0.7578 (m-30) REVERT: A 428 ASP cc_start: 0.8175 (t70) cc_final: 0.7963 (t70) REVERT: H 34 MET cc_start: 0.7390 (mmt) cc_final: 0.7137 (mmt) REVERT: H 46 GLU cc_start: 0.7527 (tt0) cc_final: 0.6900 (pt0) REVERT: L 13 LEU cc_start: 0.7664 (tp) cc_final: 0.7422 (tp) REVERT: L 189 HIS cc_start: 0.6327 (t-90) cc_final: 0.5910 (t70) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.3671 time to fit residues: 65.8787 Evaluate side-chains 117 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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: 5.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.119824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097547 restraints weight = 36982.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.101786 restraints weight = 16410.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.104511 restraints weight = 9610.057| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5334 Z= 0.170 Angle : 0.786 10.737 7282 Z= 0.402 Chirality : 0.050 0.438 827 Planarity : 0.007 0.118 916 Dihedral : 14.158 106.016 917 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.48 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.61 (0.32), residues: 642 helix: -3.44 (0.55), residues: 38 sheet: -0.10 (0.34), residues: 221 loop : -1.44 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 100C HIS 0.006 0.002 HIS L 189 PHE 0.024 0.002 PHE A 329 TYR 0.021 0.002 TYR A 396 ARG 0.004 0.001 ARG H 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00636 ( 2) link_NAG-ASN : angle 4.10035 ( 6) link_ALPHA1-6 : bond 0.01160 ( 1) link_ALPHA1-6 : angle 0.69457 ( 3) link_BETA1-2 : bond 0.00374 ( 2) link_BETA1-2 : angle 1.16411 ( 6) link_BETA1-4 : bond 0.01053 ( 4) link_BETA1-4 : angle 4.29310 ( 12) link_ALPHA1-3 : bond 0.01332 ( 1) link_ALPHA1-3 : angle 2.65576 ( 3) hydrogen bonds : bond 0.04677 ( 156) hydrogen bonds : angle 8.25768 ( 426) SS BOND : bond 0.00666 ( 8) SS BOND : angle 1.02196 ( 16) covalent geometry : bond 0.00371 ( 5316) covalent geometry : angle 0.75518 ( 7236) *********************** 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 138 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7935 (m-30) cc_final: 0.7599 (m-30) REVERT: H 86 ASP cc_start: 0.9035 (m-30) cc_final: 0.8216 (m-30) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.3476 time to fit residues: 61.6767 Evaluate side-chains 113 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.118852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.096097 restraints weight = 37671.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.100289 restraints weight = 16683.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.103025 restraints weight = 9843.849| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5334 Z= 0.174 Angle : 0.735 11.036 7282 Z= 0.372 Chirality : 0.048 0.329 827 Planarity : 0.007 0.094 916 Dihedral : 12.538 104.986 917 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.63 % Favored : 92.21 % Rotamer: Outliers : 0.18 % Allowed : 3.04 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.66 (0.32), residues: 642 helix: -3.15 (0.62), residues: 38 sheet: -0.27 (0.33), residues: 228 loop : -1.43 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 100C HIS 0.004 0.001 HIS H 35 PHE 0.026 0.002 PHE A 329 TYR 0.019 0.002 TYR A 396 ARG 0.004 0.000 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00767 ( 2) link_NAG-ASN : angle 3.23588 ( 6) link_ALPHA1-6 : bond 0.01832 ( 1) link_ALPHA1-6 : angle 2.11169 ( 3) link_BETA1-2 : bond 0.00584 ( 2) link_BETA1-2 : angle 1.33280 ( 6) link_BETA1-4 : bond 0.00900 ( 4) link_BETA1-4 : angle 4.10021 ( 12) link_ALPHA1-3 : bond 0.01205 ( 1) link_ALPHA1-3 : angle 2.34978 ( 3) hydrogen bonds : bond 0.04081 ( 156) hydrogen bonds : angle 7.52117 ( 426) SS BOND : bond 0.00875 ( 8) SS BOND : angle 0.98697 ( 16) covalent geometry : bond 0.00381 ( 5316) covalent geometry : angle 0.70666 ( 7236) *********************** 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 134 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7935 (m-30) cc_final: 0.7592 (m-30) REVERT: H 86 ASP cc_start: 0.9086 (m-30) cc_final: 0.8217 (m-30) REVERT: L 174 SER cc_start: 0.9392 (t) cc_final: 0.9177 (t) REVERT: L 185 ASP cc_start: 0.7810 (m-30) cc_final: 0.7462 (m-30) outliers start: 1 outliers final: 1 residues processed: 134 average time/residue: 0.3646 time to fit residues: 63.7342 Evaluate side-chains 111 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 61 optimal weight: 7.9990 chunk 16 optimal weight: 0.0000 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.0670 chunk 1 optimal weight: 0.0370 chunk 14 optimal weight: 0.0770 chunk 57 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 overall best weight: 0.1358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.121057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.098809 restraints weight = 36848.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.103085 restraints weight = 16122.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.105845 restraints weight = 9348.697| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5334 Z= 0.127 Angle : 0.687 9.663 7282 Z= 0.346 Chirality : 0.049 0.347 827 Planarity : 0.006 0.080 916 Dihedral : 10.973 99.128 917 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.70 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.33), residues: 642 helix: -3.23 (0.58), residues: 38 sheet: 0.03 (0.34), residues: 222 loop : -1.30 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 100C HIS 0.003 0.001 HIS L 189 PHE 0.021 0.001 PHE A 329 TYR 0.023 0.001 TYR A 508 ARG 0.002 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 2) link_NAG-ASN : angle 2.95739 ( 6) link_ALPHA1-6 : bond 0.02144 ( 1) link_ALPHA1-6 : angle 3.02881 ( 3) link_BETA1-2 : bond 0.00510 ( 2) link_BETA1-2 : angle 0.86990 ( 6) link_BETA1-4 : bond 0.00822 ( 4) link_BETA1-4 : angle 3.66074 ( 12) link_ALPHA1-3 : bond 0.01300 ( 1) link_ALPHA1-3 : angle 2.49982 ( 3) hydrogen bonds : bond 0.03659 ( 156) hydrogen bonds : angle 7.00762 ( 426) SS BOND : bond 0.00764 ( 8) SS BOND : angle 0.59665 ( 16) covalent geometry : bond 0.00280 ( 5316) covalent geometry : angle 0.66135 ( 7236) *********************** 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 132 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7922 (m-30) cc_final: 0.7602 (m-30) REVERT: H 86 ASP cc_start: 0.9107 (m-30) cc_final: 0.8252 (m-30) REVERT: H 206 LYS cc_start: 0.8405 (tptp) cc_final: 0.7957 (tptp) REVERT: L 174 SER cc_start: 0.9311 (t) cc_final: 0.9057 (t) REVERT: L 185 ASP cc_start: 0.7869 (m-30) cc_final: 0.7537 (m-30) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.3552 time to fit residues: 60.4033 Evaluate side-chains 110 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.118927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.096653 restraints weight = 37056.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.100822 restraints weight = 16421.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.103513 restraints weight = 9606.999| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5334 Z= 0.175 Angle : 0.697 9.599 7282 Z= 0.351 Chirality : 0.047 0.341 827 Planarity : 0.006 0.050 916 Dihedral : 10.720 95.252 917 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.63 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.50 (0.33), residues: 642 helix: -3.21 (0.59), residues: 38 sheet: -0.05 (0.34), residues: 223 loop : -1.37 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 100C HIS 0.010 0.002 HIS H 35 PHE 0.022 0.002 PHE A 329 TYR 0.023 0.002 TYR A 508 ARG 0.008 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 2) link_NAG-ASN : angle 2.93403 ( 6) link_ALPHA1-6 : bond 0.02045 ( 1) link_ALPHA1-6 : angle 2.61658 ( 3) link_BETA1-2 : bond 0.00330 ( 2) link_BETA1-2 : angle 0.86945 ( 6) link_BETA1-4 : bond 0.00574 ( 4) link_BETA1-4 : angle 3.69593 ( 12) link_ALPHA1-3 : bond 0.01253 ( 1) link_ALPHA1-3 : angle 2.59060 ( 3) hydrogen bonds : bond 0.03485 ( 156) hydrogen bonds : angle 6.88288 ( 426) SS BOND : bond 0.00604 ( 8) SS BOND : angle 0.81177 ( 16) covalent geometry : bond 0.00384 ( 5316) covalent geometry : angle 0.67143 ( 7236) *********************** 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 131 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7919 (m-30) cc_final: 0.7597 (m-30) REVERT: A 428 ASP cc_start: 0.8161 (t0) cc_final: 0.7953 (t0) REVERT: H 86 ASP cc_start: 0.9127 (m-30) cc_final: 0.8213 (m-30) REVERT: H 206 LYS cc_start: 0.8412 (tptp) cc_final: 0.7963 (tptp) REVERT: L 174 SER cc_start: 0.9360 (t) cc_final: 0.9109 (t) REVERT: L 185 ASP cc_start: 0.7883 (m-30) cc_final: 0.7574 (m-30) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.4814 time to fit residues: 79.8389 Evaluate side-chains 106 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.0570 chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.118468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095423 restraints weight = 37312.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.099644 restraints weight = 16723.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102444 restraints weight = 9835.705| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5334 Z= 0.141 Angle : 0.671 9.125 7282 Z= 0.336 Chirality : 0.046 0.332 827 Planarity : 0.006 0.050 916 Dihedral : 10.165 91.208 917 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.17 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.33), residues: 642 helix: -3.15 (0.60), residues: 38 sheet: 0.00 (0.34), residues: 222 loop : -1.34 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 100C HIS 0.002 0.001 HIS L 189 PHE 0.021 0.001 PHE A 329 TYR 0.022 0.001 TYR A 508 ARG 0.007 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 2) link_NAG-ASN : angle 2.79595 ( 6) link_ALPHA1-6 : bond 0.02181 ( 1) link_ALPHA1-6 : angle 3.06783 ( 3) link_BETA1-2 : bond 0.00440 ( 2) link_BETA1-2 : angle 0.81482 ( 6) link_BETA1-4 : bond 0.00575 ( 4) link_BETA1-4 : angle 3.48409 ( 12) link_ALPHA1-3 : bond 0.01443 ( 1) link_ALPHA1-3 : angle 2.66986 ( 3) hydrogen bonds : bond 0.03279 ( 156) hydrogen bonds : angle 6.61734 ( 426) SS BOND : bond 0.00621 ( 8) SS BOND : angle 0.67790 ( 16) covalent geometry : bond 0.00314 ( 5316) covalent geometry : angle 0.64664 ( 7236) *********************** 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 131 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7902 (m-30) cc_final: 0.7591 (m-30) REVERT: H 86 ASP cc_start: 0.9144 (m-30) cc_final: 0.8217 (m-30) REVERT: H 206 LYS cc_start: 0.8456 (tptp) cc_final: 0.8009 (tptp) REVERT: L 93 ASN cc_start: 0.8378 (p0) cc_final: 0.7691 (t0) REVERT: L 174 SER cc_start: 0.9341 (t) cc_final: 0.9076 (t) REVERT: L 185 ASP cc_start: 0.8111 (m-30) cc_final: 0.7803 (m-30) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.3984 time to fit residues: 65.6008 Evaluate side-chains 108 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 4 optimal weight: 0.0470 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.117015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.094067 restraints weight = 37783.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098220 restraints weight = 16933.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.100959 restraints weight = 9975.873| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5334 Z= 0.198 Angle : 0.711 8.873 7282 Z= 0.357 Chirality : 0.046 0.323 827 Planarity : 0.006 0.053 916 Dihedral : 10.009 81.352 917 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.03 % Favored : 90.81 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.33), residues: 642 helix: -3.19 (0.59), residues: 38 sheet: -0.20 (0.35), residues: 223 loop : -1.49 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 100C HIS 0.003 0.001 HIS H 35 PHE 0.022 0.002 PHE A 329 TYR 0.023 0.002 TYR A 508 ARG 0.015 0.001 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00492 ( 2) link_NAG-ASN : angle 2.85769 ( 6) link_ALPHA1-6 : bond 0.02048 ( 1) link_ALPHA1-6 : angle 2.76844 ( 3) link_BETA1-2 : bond 0.00334 ( 2) link_BETA1-2 : angle 0.89781 ( 6) link_BETA1-4 : bond 0.00391 ( 4) link_BETA1-4 : angle 3.48218 ( 12) link_ALPHA1-3 : bond 0.01490 ( 1) link_ALPHA1-3 : angle 2.93778 ( 3) hydrogen bonds : bond 0.03410 ( 156) hydrogen bonds : angle 6.72089 ( 426) SS BOND : bond 0.00480 ( 8) SS BOND : angle 0.90162 ( 16) covalent geometry : bond 0.00435 ( 5316) covalent geometry : angle 0.68756 ( 7236) *********************** 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 131 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7932 (m-30) cc_final: 0.7607 (m-30) REVERT: H 86 ASP cc_start: 0.9163 (m-30) cc_final: 0.8271 (m-30) REVERT: H 206 LYS cc_start: 0.8491 (tptp) cc_final: 0.8067 (tptp) REVERT: L 93 ASN cc_start: 0.8457 (p0) cc_final: 0.7673 (t0) REVERT: L 174 SER cc_start: 0.9373 (t) cc_final: 0.9125 (t) REVERT: L 185 ASP cc_start: 0.8054 (m-30) cc_final: 0.7783 (m-30) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.3910 time to fit residues: 64.6246 Evaluate side-chains 105 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 56 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.118497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095648 restraints weight = 37554.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.099946 restraints weight = 16644.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.102753 restraints weight = 9712.456| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5334 Z= 0.126 Angle : 0.673 8.593 7282 Z= 0.337 Chirality : 0.046 0.303 827 Planarity : 0.006 0.048 916 Dihedral : 9.220 72.380 917 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.33), residues: 642 helix: -2.88 (0.67), residues: 32 sheet: -0.05 (0.35), residues: 222 loop : -1.38 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 100C HIS 0.004 0.001 HIS A 519 PHE 0.022 0.002 PHE A 338 TYR 0.016 0.001 TYR A 508 ARG 0.006 0.000 ARG H 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 2) link_NAG-ASN : angle 2.56885 ( 6) link_ALPHA1-6 : bond 0.02248 ( 1) link_ALPHA1-6 : angle 3.50284 ( 3) link_BETA1-2 : bond 0.00469 ( 2) link_BETA1-2 : angle 0.75646 ( 6) link_BETA1-4 : bond 0.00531 ( 4) link_BETA1-4 : angle 3.27220 ( 12) link_ALPHA1-3 : bond 0.01707 ( 1) link_ALPHA1-3 : angle 3.06724 ( 3) hydrogen bonds : bond 0.03252 ( 156) hydrogen bonds : angle 6.51768 ( 426) SS BOND : bond 0.00566 ( 8) SS BOND : angle 0.73664 ( 16) covalent geometry : bond 0.00279 ( 5316) covalent geometry : angle 0.64998 ( 7236) *********************** 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 130 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7881 (m-30) cc_final: 0.7548 (m-30) REVERT: H 86 ASP cc_start: 0.9182 (m-30) cc_final: 0.8558 (m-30) REVERT: H 206 LYS cc_start: 0.8546 (tptp) cc_final: 0.8100 (tptp) REVERT: L 174 SER cc_start: 0.9307 (t) cc_final: 0.9039 (t) REVERT: L 185 ASP cc_start: 0.8018 (m-30) cc_final: 0.7747 (m-30) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.4060 time to fit residues: 67.2499 Evaluate side-chains 110 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 15 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.119020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.096173 restraints weight = 37227.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.100491 restraints weight = 16412.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.103330 restraints weight = 9562.768| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5334 Z= 0.128 Angle : 0.667 8.286 7282 Z= 0.334 Chirality : 0.046 0.307 827 Planarity : 0.006 0.047 916 Dihedral : 8.519 55.277 917 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.33), residues: 642 helix: -2.68 (0.72), residues: 32 sheet: 0.09 (0.35), residues: 222 loop : -1.38 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 100C HIS 0.003 0.001 HIS L 189 PHE 0.021 0.002 PHE A 329 TYR 0.023 0.001 TYR A 508 ARG 0.013 0.001 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 2) link_NAG-ASN : angle 2.48381 ( 6) link_ALPHA1-6 : bond 0.02364 ( 1) link_ALPHA1-6 : angle 3.48935 ( 3) link_BETA1-2 : bond 0.00334 ( 2) link_BETA1-2 : angle 0.81700 ( 6) link_BETA1-4 : bond 0.00423 ( 4) link_BETA1-4 : angle 3.21081 ( 12) link_ALPHA1-3 : bond 0.01971 ( 1) link_ALPHA1-3 : angle 3.65319 ( 3) hydrogen bonds : bond 0.03208 ( 156) hydrogen bonds : angle 6.36634 ( 426) SS BOND : bond 0.00544 ( 8) SS BOND : angle 0.75132 ( 16) covalent geometry : bond 0.00287 ( 5316) covalent geometry : angle 0.64305 ( 7236) *********************** 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 129 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7843 (m-30) cc_final: 0.7512 (m-30) REVERT: H 86 ASP cc_start: 0.9228 (m-30) cc_final: 0.8609 (m-30) REVERT: L 174 SER cc_start: 0.9266 (t) cc_final: 0.9004 (t) REVERT: L 185 ASP cc_start: 0.7999 (m-30) cc_final: 0.7727 (m-30) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.3959 time to fit residues: 64.2522 Evaluate side-chains 102 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.117923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095340 restraints weight = 37214.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.099580 restraints weight = 16550.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102341 restraints weight = 9707.374| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5334 Z= 0.149 Angle : 0.683 8.209 7282 Z= 0.342 Chirality : 0.047 0.303 827 Planarity : 0.006 0.068 916 Dihedral : 8.300 51.949 917 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.31 (0.34), residues: 642 helix: -2.74 (0.70), residues: 32 sheet: 0.17 (0.36), residues: 222 loop : -1.37 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 100C HIS 0.008 0.001 HIS H 35 PHE 0.021 0.001 PHE A 329 TYR 0.017 0.001 TYR L 36 ARG 0.006 0.001 ARG H 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 2) link_NAG-ASN : angle 2.48395 ( 6) link_ALPHA1-6 : bond 0.02313 ( 1) link_ALPHA1-6 : angle 3.43011 ( 3) link_BETA1-2 : bond 0.00287 ( 2) link_BETA1-2 : angle 1.05948 ( 6) link_BETA1-4 : bond 0.00408 ( 4) link_BETA1-4 : angle 3.24908 ( 12) link_ALPHA1-3 : bond 0.01927 ( 1) link_ALPHA1-3 : angle 3.86590 ( 3) hydrogen bonds : bond 0.03358 ( 156) hydrogen bonds : angle 6.33307 ( 426) SS BOND : bond 0.00607 ( 8) SS BOND : angle 0.79986 ( 16) covalent geometry : bond 0.00334 ( 5316) covalent geometry : angle 0.65877 ( 7236) ********************** 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 128 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7818 (m-30) cc_final: 0.7474 (m-30) REVERT: H 86 ASP cc_start: 0.9217 (m-30) cc_final: 0.8624 (m-30) REVERT: L 174 SER cc_start: 0.9243 (t) cc_final: 0.8923 (t) REVERT: L 185 ASP cc_start: 0.7983 (m-30) cc_final: 0.7709 (m-30) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.3712 time to fit residues: 60.3641 Evaluate side-chains 106 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 21 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 62 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.118876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.096025 restraints weight = 37055.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.100327 restraints weight = 16505.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.103107 restraints weight = 9673.470| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5334 Z= 0.121 Angle : 0.664 8.043 7282 Z= 0.333 Chirality : 0.047 0.286 827 Planarity : 0.006 0.048 916 Dihedral : 7.857 48.363 917 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.30 (0.34), residues: 642 helix: -2.81 (0.67), residues: 38 sheet: 0.19 (0.36), residues: 222 loop : -1.34 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 100C HIS 0.003 0.001 HIS L 189 PHE 0.020 0.001 PHE A 329 TYR 0.020 0.001 TYR A 508 ARG 0.008 0.001 ARG H 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 2) link_NAG-ASN : angle 2.32839 ( 6) link_ALPHA1-6 : bond 0.02362 ( 1) link_ALPHA1-6 : angle 3.76720 ( 3) link_BETA1-2 : bond 0.00340 ( 2) link_BETA1-2 : angle 1.16217 ( 6) link_BETA1-4 : bond 0.00476 ( 4) link_BETA1-4 : angle 3.13042 ( 12) link_ALPHA1-3 : bond 0.01859 ( 1) link_ALPHA1-3 : angle 4.00388 ( 3) hydrogen bonds : bond 0.03226 ( 156) hydrogen bonds : angle 6.25468 ( 426) SS BOND : bond 0.00531 ( 8) SS BOND : angle 0.69320 ( 16) covalent geometry : bond 0.00271 ( 5316) covalent geometry : angle 0.63914 ( 7236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4095.58 seconds wall clock time: 73 minutes 2.14 seconds (4382.14 seconds total)