Starting phenix.real_space_refine on Thu Jun 5 03:08:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hgm_34742/06_2025/8hgm_34742.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgm_34742/06_2025/8hgm_34742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hgm_34742/06_2025/8hgm_34742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgm_34742/06_2025/8hgm_34742.map" model { file = "/net/cci-nas-00/data/ceres_data/8hgm_34742/06_2025/8hgm_34742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgm_34742/06_2025/8hgm_34742.cif" } resolution = 3.4 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= -0.001 sd= 0.014 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 22 5.16 5 C 3085 2.51 5 N 820 2.21 5 O 959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4886 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1532 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1668 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "D" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.02, per 1000 atoms: 1.03 Number of scatterers: 4886 At special positions: 0 Unit cell: (72.726, 70.38, 136.068, 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 22 16.00 O 959 8.00 N 820 7.00 C 3085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 204 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " 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 BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN B 343 " Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 577.7 milliseconds 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 12 sheets defined 12.7% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.976A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.801A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.574A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.277A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'C' and resid 26 through 29 removed outlier: 3.794A pdb=" N TYR C 29 " --> pdb=" O THR C 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 26 through 29' Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'D' and resid 80 through 84 removed outlier: 4.009A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.772A pdb=" N LYS D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 removed outlier: 3.860A pdb=" N GLU D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 184 through 189' Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.598A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.630A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA4, first strand: chain 'C' and resid 8 through 10 removed outlier: 3.827A pdb=" N GLY C 47 " --> pdb=" O TRP C 34 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG C 36 " --> pdb=" O TRP C 45 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TRP C 45 " --> pdb=" O ARG C 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 8 through 10 Processing sheet with id=AA6, first strand: chain 'C' and resid 128 through 132 removed outlier: 3.545A pdb=" N GLY C 147 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TYR C 184 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 128 through 132 removed outlier: 3.545A pdb=" N GLY C 147 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TYR C 184 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 159 through 162 removed outlier: 3.668A pdb=" N THR C 159 " --> pdb=" O ASN C 207 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS C 204 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.720A pdb=" N LEU D 74 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.823A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 115 through 119 removed outlier: 6.231A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 179 " --> pdb=" O GLN D 161 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN D 161 " --> pdb=" O THR D 179 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 154 through 155 removed outlier: 3.549A pdb=" N LYS D 146 " --> pdb=" O THR D 198 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 450 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: 1.64 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: 1.23 - 1.34: 1563 1.34 - 1.46: 1257 1.46 - 1.58: 2162 1.58 - 1.70: 0 1.70 - 1.81: 25 Bond restraints: 5007 Sorted by residual: bond pdb=" C THR C 173 " pdb=" N PHE C 174 " ideal model delta sigma weight residual 1.333 1.289 0.043 2.74e-02 1.33e+03 2.50e+00 bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.30e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.428 -0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" C5 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.11e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.425 -0.019 2.00e-02 2.50e+03 9.20e-01 ... (remaining 5002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 6769 2.86 - 5.73: 40 5.73 - 8.59: 2 8.59 - 11.45: 0 11.45 - 14.31: 1 Bond angle restraints: 6812 Sorted by residual: angle pdb=" C LYS C 151 " pdb=" N ASP C 152 " pdb=" CA ASP C 152 " ideal model delta sigma weight residual 122.82 126.84 -4.02 1.42e+00 4.96e-01 8.00e+00 angle pdb=" C THR C 173 " pdb=" N PHE C 174 " pdb=" CA PHE C 174 " ideal model delta sigma weight residual 122.15 113.71 8.44 3.47e+00 8.31e-02 5.91e+00 angle pdb=" C LYS C 10 " pdb=" N LYS C 11 " pdb=" CA LYS C 11 " ideal model delta sigma weight residual 120.71 135.02 -14.31 6.53e+00 2.35e-02 4.81e+00 angle pdb=" N TYR D 92 " pdb=" CA TYR D 92 " pdb=" C TYR D 92 " ideal model delta sigma weight residual 110.88 113.57 -2.69 1.28e+00 6.10e-01 4.41e+00 angle pdb=" C GLY D 51 " pdb=" N THR D 52 " pdb=" CA THR D 52 " ideal model delta sigma weight residual 121.54 125.34 -3.80 1.91e+00 2.74e-01 3.95e+00 ... (remaining 6807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 2753 17.76 - 35.51: 207 35.51 - 53.27: 42 53.27 - 71.03: 7 71.03 - 88.78: 3 Dihedral angle restraints: 3012 sinusoidal: 1184 harmonic: 1828 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -55.63 -30.37 1 1.00e+01 1.00e-02 1.32e+01 dihedral pdb=" CA CYS C 99 " pdb=" CB CYS C 99 " pdb=" SG CYS C 99 " pdb=" SG CYS C 104 " ideal model delta sinusoidal sigma weight residual -73.00 -10.05 -62.95 1 2.00e+01 2.50e-03 1.31e+01 dihedral pdb=" CA LEU B 461 " pdb=" C LEU B 461 " pdb=" N LYS B 462 " pdb=" CA LYS B 462 " ideal model delta harmonic sigma weight residual 180.00 163.75 16.25 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 3009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 473 0.033 - 0.066: 183 0.066 - 0.099: 58 0.099 - 0.132: 37 0.132 - 0.165: 1 Chirality restraints: 752 Sorted by residual: chirality pdb=" CA ASP C 152 " pdb=" N ASP C 152 " pdb=" C ASP C 152 " pdb=" CB ASP C 152 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA ILE B 358 " pdb=" N ILE B 358 " pdb=" C ILE B 358 " pdb=" CB ILE B 358 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA SER D 7 " pdb=" N SER D 7 " pdb=" C SER D 7 " pdb=" CB SER D 7 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 749 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO B 521 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 186 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.43e+00 pdb=" CG ASP D 186 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASP D 186 " 0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP D 186 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 462 " -0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO B 463 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " -0.015 5.00e-02 4.00e+02 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 230 2.72 - 3.27: 4720 3.27 - 3.81: 7543 3.81 - 4.36: 8788 4.36 - 4.90: 15508 Nonbonded interactions: 36789 Sorted by model distance: nonbonded pdb=" OG SER B 371 " pdb=" OG SER B 373 " model vdw 2.180 3.040 nonbonded pdb=" OG SER C 211 " pdb=" OG1 THR C 213 " model vdw 2.213 3.040 nonbonded pdb=" NE2 GLN C 179 " pdb=" O LEU C 183 " model vdw 2.229 3.120 nonbonded pdb=" OD2 ASP D 152 " pdb=" ND1 HIS D 190 " model vdw 2.256 3.120 nonbonded pdb=" OG SER B 375 " pdb=" O ALA B 435 " model vdw 2.289 3.040 ... (remaining 36784 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.950 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 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 : 0.004 0.043 5018 Z= 0.156 Angle : 0.590 14.314 6836 Z= 0.291 Chirality : 0.043 0.165 752 Planarity : 0.004 0.046 879 Dihedral : 13.086 88.784 1821 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: 0.29 (0.35), residues: 626 helix: -2.00 (0.80), residues: 33 sheet: 1.03 (0.35), residues: 243 loop : -0.14 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 149 HIS 0.002 0.001 HIS B 519 PHE 0.008 0.001 PHE D 140 TYR 0.016 0.001 TYR C 105 ARG 0.010 0.001 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 1) link_NAG-ASN : angle 1.72699 ( 3) link_BETA1-4 : bond 0.00139 ( 1) link_BETA1-4 : angle 1.22620 ( 3) hydrogen bonds : bond 0.27833 ( 158) hydrogen bonds : angle 10.08560 ( 450) SS BOND : bond 0.00400 ( 9) SS BOND : angle 0.68148 ( 18) covalent geometry : bond 0.00355 ( 5007) covalent geometry : angle 0.58837 ( 6812) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 ASP cc_start: 0.7749 (t0) cc_final: 0.7189 (t0) REVERT: D 43 GLN cc_start: 0.7679 (mp10) cc_final: 0.7350 (mp10) REVERT: D 82 GLU cc_start: 0.8272 (pm20) cc_final: 0.7946 (pm20) REVERT: D 107 ILE cc_start: 0.9195 (mt) cc_final: 0.8973 (tt) REVERT: D 125 GLN cc_start: 0.8415 (tp-100) cc_final: 0.7749 (tp-100) REVERT: D 150 LYS cc_start: 0.7857 (tppt) cc_final: 0.7629 (tmtt) REVERT: D 168 ASP cc_start: 0.9005 (t70) cc_final: 0.8672 (t70) REVERT: D 182 LEU cc_start: 0.9221 (tp) cc_final: 0.8930 (tt) REVERT: D 211 ASN cc_start: 0.8587 (t0) cc_final: 0.8235 (t0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2716 time to fit residues: 28.7948 Evaluate side-chains 57 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 18 optimal weight: 0.0980 chunk 29 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.082054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.061078 restraints weight = 13783.247| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 4.20 r_work: 0.2866 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5018 Z= 0.126 Angle : 0.601 13.331 6836 Z= 0.306 Chirality : 0.044 0.169 752 Planarity : 0.004 0.047 879 Dihedral : 4.950 34.971 732 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.11 % Allowed : 7.79 % Favored : 91.09 % 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: 0.18 (0.34), residues: 626 helix: -2.16 (0.67), residues: 39 sheet: 0.92 (0.34), residues: 238 loop : -0.10 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.003 0.001 HIS D 190 PHE 0.007 0.001 PHE B 400 TYR 0.025 0.001 TYR C 153 ARG 0.004 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00112 ( 1) link_NAG-ASN : angle 1.46235 ( 3) link_BETA1-4 : bond 0.00012 ( 1) link_BETA1-4 : angle 1.27392 ( 3) hydrogen bonds : bond 0.04234 ( 158) hydrogen bonds : angle 6.76757 ( 450) SS BOND : bond 0.00476 ( 9) SS BOND : angle 1.01168 ( 18) covalent geometry : bond 0.00283 ( 5007) covalent geometry : angle 0.59861 ( 6812) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: C 71 ASP cc_start: 0.7142 (t0) cc_final: 0.6471 (t0) REVERT: C 72 MET cc_start: 0.8981 (tpp) cc_final: 0.8765 (mpp) REVERT: C 105 TYR cc_start: 0.8957 (t80) cc_final: 0.8716 (t80) REVERT: D 43 GLN cc_start: 0.7544 (mp10) cc_final: 0.7168 (mp10) REVERT: D 82 GLU cc_start: 0.8731 (pm20) cc_final: 0.8415 (pm20) REVERT: D 139 ASN cc_start: 0.8183 (t0) cc_final: 0.7873 (m-40) outliers start: 6 outliers final: 5 residues processed: 69 average time/residue: 0.1925 time to fit residues: 16.9611 Evaluate side-chains 63 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain D residue 170 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 57 optimal weight: 0.0980 chunk 14 optimal weight: 0.0670 chunk 43 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN D 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.082724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.061608 restraints weight = 13905.199| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 4.25 r_work: 0.2884 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5018 Z= 0.106 Angle : 0.575 12.862 6836 Z= 0.285 Chirality : 0.043 0.190 752 Planarity : 0.004 0.048 879 Dihedral : 4.594 32.907 732 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.67 % Allowed : 9.09 % Favored : 89.24 % 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: 0.42 (0.34), residues: 626 helix: -1.98 (0.70), residues: 39 sheet: 1.13 (0.35), residues: 235 loop : 0.02 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.003 0.001 HIS D 190 PHE 0.015 0.001 PHE C 130 TYR 0.025 0.001 TYR C 153 ARG 0.004 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00022 ( 1) link_NAG-ASN : angle 1.36677 ( 3) link_BETA1-4 : bond 0.00093 ( 1) link_BETA1-4 : angle 1.05345 ( 3) hydrogen bonds : bond 0.03432 ( 158) hydrogen bonds : angle 5.97721 ( 450) SS BOND : bond 0.00509 ( 9) SS BOND : angle 0.90133 ( 18) covalent geometry : bond 0.00239 ( 5007) covalent geometry : angle 0.57328 ( 6812) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8911 (tp30) cc_final: 0.8467 (mm-30) REVERT: B 465 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6760 (pm20) REVERT: B 471 GLU cc_start: 0.8701 (tp30) cc_final: 0.8489 (tp30) REVERT: C 71 ASP cc_start: 0.7042 (t0) cc_final: 0.6380 (t0) REVERT: C 72 MET cc_start: 0.8874 (tpp) cc_final: 0.8670 (mpp) REVERT: C 105 TYR cc_start: 0.8922 (t80) cc_final: 0.7984 (t80) REVERT: C 106 ASP cc_start: 0.9397 (t0) cc_final: 0.9094 (t0) REVERT: D 43 GLN cc_start: 0.7536 (mp10) cc_final: 0.7144 (mp10) REVERT: D 80 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8335 (mm-30) REVERT: D 82 GLU cc_start: 0.8761 (pm20) cc_final: 0.8414 (pm20) REVERT: D 125 GLN cc_start: 0.8241 (tp40) cc_final: 0.7763 (mm-40) REVERT: D 189 LYS cc_start: 0.8905 (pptt) cc_final: 0.8657 (ptmm) outliers start: 9 outliers final: 3 residues processed: 72 average time/residue: 0.2639 time to fit residues: 24.4762 Evaluate side-chains 64 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain D residue 170 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 42 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.080201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.059637 restraints weight = 14179.950| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.13 r_work: 0.2812 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5018 Z= 0.221 Angle : 0.650 14.614 6836 Z= 0.326 Chirality : 0.045 0.183 752 Planarity : 0.004 0.048 879 Dihedral : 5.034 35.163 732 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.23 % Allowed : 11.50 % Favored : 86.27 % 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: 0.27 (0.35), residues: 626 helix: -2.61 (0.64), residues: 39 sheet: 1.07 (0.35), residues: 237 loop : -0.05 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 162 HIS 0.003 0.001 HIS D 199 PHE 0.014 0.001 PHE D 140 TYR 0.026 0.002 TYR C 153 ARG 0.006 0.001 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00741 ( 1) link_NAG-ASN : angle 2.06625 ( 3) link_BETA1-4 : bond 0.00685 ( 1) link_BETA1-4 : angle 1.54974 ( 3) hydrogen bonds : bond 0.03949 ( 158) hydrogen bonds : angle 5.85985 ( 450) SS BOND : bond 0.00667 ( 9) SS BOND : angle 1.05105 ( 18) covalent geometry : bond 0.00512 ( 5007) covalent geometry : angle 0.64693 ( 6812) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: B 462 LYS cc_start: 0.8654 (mtmm) cc_final: 0.8187 (mtmm) REVERT: B 465 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7158 (pm20) REVERT: B 471 GLU cc_start: 0.8734 (tp30) cc_final: 0.8489 (tp30) REVERT: C 71 ASP cc_start: 0.7227 (t0) cc_final: 0.6637 (t0) REVERT: C 105 TYR cc_start: 0.8903 (t80) cc_final: 0.8108 (t80) REVERT: C 106 ASP cc_start: 0.9484 (t0) cc_final: 0.9152 (t0) REVERT: C 179 GLN cc_start: 0.6867 (mm-40) cc_final: 0.6649 (mm-40) REVERT: D 43 GLN cc_start: 0.7671 (mp10) cc_final: 0.7242 (mp10) REVERT: D 80 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8455 (mm-30) REVERT: D 82 GLU cc_start: 0.8784 (pm20) cc_final: 0.8404 (pm20) REVERT: D 189 LYS cc_start: 0.8894 (pptt) cc_final: 0.8652 (ptmm) outliers start: 12 outliers final: 7 residues processed: 68 average time/residue: 0.2303 time to fit residues: 19.9056 Evaluate side-chains 61 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain D residue 170 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.081224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.060349 restraints weight = 14182.984| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 4.21 r_work: 0.2828 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5018 Z= 0.162 Angle : 0.608 14.412 6836 Z= 0.300 Chirality : 0.044 0.183 752 Planarity : 0.004 0.047 879 Dihedral : 4.892 34.152 732 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.60 % Allowed : 12.43 % Favored : 84.97 % 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: 0.26 (0.35), residues: 626 helix: -2.52 (0.72), residues: 33 sheet: 0.99 (0.34), residues: 241 loop : -0.07 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.002 0.001 HIS D 190 PHE 0.009 0.001 PHE D 140 TYR 0.027 0.001 TYR C 153 ARG 0.005 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 1) link_NAG-ASN : angle 1.64405 ( 3) link_BETA1-4 : bond 0.00167 ( 1) link_BETA1-4 : angle 1.26558 ( 3) hydrogen bonds : bond 0.03439 ( 158) hydrogen bonds : angle 5.62000 ( 450) SS BOND : bond 0.00485 ( 9) SS BOND : angle 1.02457 ( 18) covalent geometry : bond 0.00380 ( 5007) covalent geometry : angle 0.60478 ( 6812) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8366 (mt-10) REVERT: B 462 LYS cc_start: 0.8718 (mtmm) cc_final: 0.8240 (mtmm) REVERT: B 465 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7125 (pm20) REVERT: B 467 ASP cc_start: 0.8350 (m-30) cc_final: 0.7851 (m-30) REVERT: C 71 ASP cc_start: 0.7188 (t0) cc_final: 0.6588 (t0) REVERT: C 105 TYR cc_start: 0.8908 (t80) cc_final: 0.8127 (t80) REVERT: C 106 ASP cc_start: 0.9452 (t0) cc_final: 0.9083 (t0) REVERT: C 179 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6966 (mm-40) REVERT: D 43 GLN cc_start: 0.7628 (mp10) cc_final: 0.7190 (mp10) REVERT: D 189 LYS cc_start: 0.8895 (pptt) cc_final: 0.8643 (ptmm) outliers start: 14 outliers final: 10 residues processed: 65 average time/residue: 0.2123 time to fit residues: 17.9041 Evaluate side-chains 65 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 170 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 47 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.0040 chunk 24 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.082384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.061398 restraints weight = 14108.192| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 4.24 r_work: 0.2851 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5018 Z= 0.116 Angle : 0.576 13.952 6836 Z= 0.283 Chirality : 0.043 0.173 752 Planarity : 0.004 0.048 879 Dihedral : 4.635 32.555 732 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.60 % Allowed : 13.73 % Favored : 83.67 % 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: 0.39 (0.35), residues: 626 helix: -2.36 (0.73), residues: 33 sheet: 1.02 (0.35), residues: 236 loop : 0.07 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.002 0.000 HIS D 190 PHE 0.007 0.001 PHE C 130 TYR 0.029 0.001 TYR C 153 ARG 0.006 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00061 ( 1) link_NAG-ASN : angle 1.40629 ( 3) link_BETA1-4 : bond 0.00043 ( 1) link_BETA1-4 : angle 1.09048 ( 3) hydrogen bonds : bond 0.03007 ( 158) hydrogen bonds : angle 5.41466 ( 450) SS BOND : bond 0.00416 ( 9) SS BOND : angle 0.92987 ( 18) covalent geometry : bond 0.00274 ( 5007) covalent geometry : angle 0.57426 ( 6812) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8395 (mt-10) REVERT: B 462 LYS cc_start: 0.8708 (mtmm) cc_final: 0.8199 (mtmm) REVERT: B 465 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7102 (pm20) REVERT: B 471 GLU cc_start: 0.8781 (tp30) cc_final: 0.8522 (tp30) REVERT: C 71 ASP cc_start: 0.7118 (t0) cc_final: 0.6515 (t0) REVERT: C 105 TYR cc_start: 0.8899 (t80) cc_final: 0.8146 (t80) REVERT: C 106 ASP cc_start: 0.9439 (t0) cc_final: 0.9073 (t0) REVERT: C 179 GLN cc_start: 0.7191 (mm-40) cc_final: 0.6954 (mm-40) REVERT: D 43 GLN cc_start: 0.7523 (mp10) cc_final: 0.6901 (mp10) REVERT: D 189 LYS cc_start: 0.8873 (pptt) cc_final: 0.8588 (ptmm) outliers start: 14 outliers final: 8 residues processed: 66 average time/residue: 0.2335 time to fit residues: 20.0609 Evaluate side-chains 64 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 170 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.081247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.059890 restraints weight = 13815.965| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 4.26 r_work: 0.2848 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5018 Z= 0.123 Angle : 0.583 13.856 6836 Z= 0.284 Chirality : 0.043 0.176 752 Planarity : 0.004 0.048 879 Dihedral : 4.550 32.165 732 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.41 % Allowed : 14.29 % Favored : 83.30 % 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: 0.38 (0.35), residues: 626 helix: -2.28 (0.76), residues: 33 sheet: 0.92 (0.34), residues: 243 loop : 0.12 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.002 0.001 HIS C 208 PHE 0.008 0.001 PHE D 140 TYR 0.029 0.001 TYR C 153 ARG 0.009 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00101 ( 1) link_NAG-ASN : angle 1.44277 ( 3) link_BETA1-4 : bond 0.00048 ( 1) link_BETA1-4 : angle 1.15124 ( 3) hydrogen bonds : bond 0.02949 ( 158) hydrogen bonds : angle 5.30102 ( 450) SS BOND : bond 0.00404 ( 9) SS BOND : angle 0.93612 ( 18) covalent geometry : bond 0.00292 ( 5007) covalent geometry : angle 0.58081 ( 6812) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 1.645 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8387 (mt-10) REVERT: B 462 LYS cc_start: 0.8710 (mtmm) cc_final: 0.8197 (mtmm) REVERT: B 465 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7104 (pm20) REVERT: B 471 GLU cc_start: 0.8793 (tp30) cc_final: 0.8472 (tp30) REVERT: C 105 TYR cc_start: 0.8949 (t80) cc_final: 0.8257 (t80) REVERT: C 106 ASP cc_start: 0.9455 (t0) cc_final: 0.9086 (t0) REVERT: C 179 GLN cc_start: 0.7419 (mm-40) cc_final: 0.7184 (mm-40) REVERT: C 220 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7088 (mm-30) REVERT: D 43 GLN cc_start: 0.7472 (mp10) cc_final: 0.6887 (mp10) REVERT: D 189 LYS cc_start: 0.8875 (pptt) cc_final: 0.8570 (ptmm) outliers start: 13 outliers final: 9 residues processed: 68 average time/residue: 0.4623 time to fit residues: 43.7595 Evaluate side-chains 67 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 170 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 0.0870 chunk 49 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.081159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.059938 restraints weight = 14100.881| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 4.28 r_work: 0.2814 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5018 Z= 0.128 Angle : 0.591 13.722 6836 Z= 0.286 Chirality : 0.043 0.183 752 Planarity : 0.004 0.048 879 Dihedral : 4.525 32.226 732 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.04 % Allowed : 15.58 % Favored : 82.37 % 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: 0.37 (0.35), residues: 626 helix: -2.28 (0.77), residues: 33 sheet: 0.95 (0.34), residues: 248 loop : 0.06 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.001 0.000 HIS D 199 PHE 0.007 0.001 PHE D 140 TYR 0.030 0.001 TYR C 153 ARG 0.008 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 1) link_NAG-ASN : angle 1.44262 ( 3) link_BETA1-4 : bond 0.00065 ( 1) link_BETA1-4 : angle 1.13934 ( 3) hydrogen bonds : bond 0.02959 ( 158) hydrogen bonds : angle 5.23131 ( 450) SS BOND : bond 0.00402 ( 9) SS BOND : angle 0.91338 ( 18) covalent geometry : bond 0.00303 ( 5007) covalent geometry : angle 0.58848 ( 6812) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8461 (mt-10) REVERT: B 462 LYS cc_start: 0.8659 (mtmm) cc_final: 0.8160 (mtmm) REVERT: B 465 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7029 (pm20) REVERT: C 105 TYR cc_start: 0.8942 (t80) cc_final: 0.8283 (t80) REVERT: C 179 GLN cc_start: 0.7320 (mm-40) cc_final: 0.7067 (mm-40) REVERT: C 220 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7155 (mm-30) REVERT: D 43 GLN cc_start: 0.7435 (mp10) cc_final: 0.6881 (mp10) REVERT: D 189 LYS cc_start: 0.8876 (pptt) cc_final: 0.8563 (ptmm) outliers start: 11 outliers final: 8 residues processed: 68 average time/residue: 0.4400 time to fit residues: 39.2598 Evaluate side-chains 67 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 170 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.081195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.059944 restraints weight = 13893.045| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 4.26 r_work: 0.2815 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5018 Z= 0.129 Angle : 0.601 13.653 6836 Z= 0.290 Chirality : 0.043 0.180 752 Planarity : 0.004 0.048 879 Dihedral : 4.502 32.132 732 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.41 % Allowed : 15.03 % Favored : 82.56 % 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: 0.39 (0.35), residues: 626 helix: -2.45 (0.68), residues: 39 sheet: 1.09 (0.35), residues: 241 loop : 0.07 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.001 0.000 HIS C 208 PHE 0.008 0.001 PHE D 140 TYR 0.030 0.001 TYR C 153 ARG 0.009 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 1) link_NAG-ASN : angle 1.42200 ( 3) link_BETA1-4 : bond 0.00017 ( 1) link_BETA1-4 : angle 1.13814 ( 3) hydrogen bonds : bond 0.02937 ( 158) hydrogen bonds : angle 5.19004 ( 450) SS BOND : bond 0.00406 ( 9) SS BOND : angle 0.92415 ( 18) covalent geometry : bond 0.00306 ( 5007) covalent geometry : angle 0.59873 ( 6812) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8517 (mt-10) REVERT: B 462 LYS cc_start: 0.8656 (mtmm) cc_final: 0.8130 (mtmm) REVERT: B 465 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7096 (pm20) REVERT: B 467 ASP cc_start: 0.8406 (m-30) cc_final: 0.7969 (m-30) REVERT: B 471 GLU cc_start: 0.8803 (tp30) cc_final: 0.8493 (tp30) REVERT: C 105 TYR cc_start: 0.8979 (t80) cc_final: 0.8356 (t80) REVERT: C 179 GLN cc_start: 0.7380 (mm-40) cc_final: 0.7110 (mm-40) REVERT: C 220 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7116 (mm-30) REVERT: D 43 GLN cc_start: 0.7478 (mp10) cc_final: 0.6934 (mp10) outliers start: 13 outliers final: 10 residues processed: 70 average time/residue: 0.1800 time to fit residues: 16.1855 Evaluate side-chains 67 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 170 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.080619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.059480 restraints weight = 13960.914| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 4.27 r_work: 0.2836 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5018 Z= 0.151 Angle : 0.621 13.687 6836 Z= 0.302 Chirality : 0.043 0.181 752 Planarity : 0.004 0.048 879 Dihedral : 4.594 32.791 732 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.86 % Allowed : 15.58 % Favored : 82.56 % 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: 0.36 (0.35), residues: 626 helix: -2.55 (0.67), residues: 39 sheet: 1.07 (0.35), residues: 241 loop : 0.05 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.002 0.001 HIS C 208 PHE 0.009 0.001 PHE D 140 TYR 0.030 0.001 TYR C 153 ARG 0.009 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 1) link_NAG-ASN : angle 1.56227 ( 3) link_BETA1-4 : bond 0.00122 ( 1) link_BETA1-4 : angle 1.19234 ( 3) hydrogen bonds : bond 0.03070 ( 158) hydrogen bonds : angle 5.18722 ( 450) SS BOND : bond 0.00596 ( 9) SS BOND : angle 0.98275 ( 18) covalent geometry : bond 0.00360 ( 5007) covalent geometry : angle 0.61915 ( 6812) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8524 (mt-10) REVERT: B 462 LYS cc_start: 0.8686 (mtmm) cc_final: 0.8154 (mtmm) REVERT: B 465 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7155 (pm20) REVERT: B 467 ASP cc_start: 0.8421 (m-30) cc_final: 0.8176 (m-30) REVERT: B 471 GLU cc_start: 0.8778 (tp30) cc_final: 0.8498 (tp30) REVERT: C 105 TYR cc_start: 0.9015 (t80) cc_final: 0.8426 (t80) REVERT: C 179 GLN cc_start: 0.7451 (mm-40) cc_final: 0.7166 (mm-40) REVERT: C 220 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7101 (mm-30) REVERT: D 43 GLN cc_start: 0.7512 (mp10) cc_final: 0.6957 (mp10) REVERT: D 82 GLU cc_start: 0.8709 (pm20) cc_final: 0.8325 (pm20) REVERT: D 162 GLU cc_start: 0.8827 (tp30) cc_final: 0.8564 (tp30) outliers start: 10 outliers final: 9 residues processed: 68 average time/residue: 0.1910 time to fit residues: 16.8089 Evaluate side-chains 66 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 170 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 59 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 41 optimal weight: 0.0470 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.081470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.060156 restraints weight = 14059.647| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 4.30 r_work: 0.2851 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5018 Z= 0.123 Angle : 0.598 13.587 6836 Z= 0.292 Chirality : 0.043 0.179 752 Planarity : 0.004 0.048 879 Dihedral : 4.472 31.936 732 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.86 % Allowed : 15.58 % Favored : 82.56 % 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: 0.40 (0.35), residues: 626 helix: -2.40 (0.68), residues: 39 sheet: 1.09 (0.35), residues: 241 loop : 0.06 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.000 HIS D 190 PHE 0.007 0.001 PHE D 140 TYR 0.028 0.001 TYR C 153 ARG 0.009 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00034 ( 1) link_NAG-ASN : angle 1.32786 ( 3) link_BETA1-4 : bond 0.00053 ( 1) link_BETA1-4 : angle 1.03870 ( 3) hydrogen bonds : bond 0.02830 ( 158) hydrogen bonds : angle 5.09583 ( 450) SS BOND : bond 0.00416 ( 9) SS BOND : angle 0.93882 ( 18) covalent geometry : bond 0.00297 ( 5007) covalent geometry : angle 0.59638 ( 6812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4144.61 seconds wall clock time: 75 minutes 46.25 seconds (4546.25 seconds total)