Starting phenix.real_space_refine on Sun Apr 27 05:10:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2c_44103/04_2025/9b2c_44103.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2c_44103/04_2025/9b2c_44103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b2c_44103/04_2025/9b2c_44103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2c_44103/04_2025/9b2c_44103.map" model { file = "/net/cci-nas-00/data/ceres_data/9b2c_44103/04_2025/9b2c_44103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2c_44103/04_2025/9b2c_44103.cif" } resolution = 3.0 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= 0.118 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 26 5.16 5 C 2973 2.51 5 N 805 2.21 5 O 792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4596 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 761 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 1, 'TRANS': 108} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "L" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1535 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 57 Chain: "N" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 759 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 110 Chain: "H" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1488 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 49 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.81, per 1000 atoms: 0.83 Number of scatterers: 4596 At special positions: 0 Unit cell: (64, 81, 120, 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 26 16.00 O 792 8.00 N 805 7.00 C 2973 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 378 " distance=2.13 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 352 " distance=2.00 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 386 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.02 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.02 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 B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 501 " - " ASN A 331 " " NAG B 1 " - " ASN A 311 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 626.3 milliseconds 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 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: 11 helices and 16 sheets defined 8.1% alpha, 50.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.706A pdb=" N VAL A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 131 Processing helix chain 'L' and resid 188 through 192 Processing helix chain 'N' and resid 63 through 66 Processing helix chain 'N' and resid 88 through 92 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 100 through 104 Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 207 through 210 Processing sheet with id=AA1, first strand: chain 'A' and resid 320 through 328 removed outlier: 5.029A pdb=" N ALA A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASP A 317 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU A 323 " --> pdb=" O HIS A 315 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N HIS A 315 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 320 through 328 removed outlier: 5.029A pdb=" N ALA A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASP A 317 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU A 323 " --> pdb=" O HIS A 315 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N HIS A 315 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 333 through 335 removed outlier: 8.004A pdb=" N GLN A 376 " --> pdb=" O GLN A 412 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N GLN A 412 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 11.719A pdb=" N CYS A 378 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N GLU A 410 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 12.031A pdb=" N SER A 380 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N ALA A 408 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU A 400 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL A 392 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLN A 402 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE A 390 " --> pdb=" O GLN A 402 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 353 " --> pdb=" O THR A 393 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.591A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA7, first strand: chain 'L' and resid 119 through 123 removed outlier: 4.188A pdb=" N ALA L 135 " --> pdb=" O LEU L 186 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 158 through 159 Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.501A pdb=" N SER N 26 " --> pdb=" O GLN N 4 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 59 through 61 removed outlier: 6.520A pdb=" N TRP N 37 " --> pdb=" O VAL N 49 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL N 51 " --> pdb=" O MET N 35 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N MET N 35 " --> pdb=" O VAL N 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.848A pdb=" N THR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.669A pdb=" N PHE H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 126 through 130 removed outlier: 5.875A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 126 through 130 removed outlier: 5.875A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 157 through 160 removed outlier: 4.321A pdb=" N TYR H 200 " --> pdb=" O VAL H 217 " (cutoff:3.500A) 227 hydrogen bonds defined for protein. 552 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: 1.54 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 828 1.32 - 1.45: 1256 1.45 - 1.58: 2586 1.58 - 1.70: 2 1.70 - 1.83: 36 Bond restraints: 4708 Sorted by residual: bond pdb=" N PRO H 208 " pdb=" CD PRO H 208 " ideal model delta sigma weight residual 1.473 1.614 -0.141 1.40e-02 5.10e+03 1.01e+02 bond pdb=" N PRO L 45 " pdb=" CD PRO L 45 " ideal model delta sigma weight residual 1.473 1.403 0.070 1.40e-02 5.10e+03 2.49e+01 bond pdb=" CA SER N 36 " pdb=" CB SER N 36 " ideal model delta sigma weight residual 1.534 1.471 0.063 1.60e-02 3.91e+03 1.57e+01 bond pdb=" C CYS L 23 " pdb=" O CYS L 23 " ideal model delta sigma weight residual 1.234 1.194 0.040 1.18e-02 7.18e+03 1.17e+01 bond pdb=" N VAL A 395 " pdb=" CA VAL A 395 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.17e+01 ... (remaining 4703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 6027 2.96 - 5.92: 377 5.92 - 8.88: 46 8.88 - 11.85: 5 11.85 - 14.81: 1 Bond angle restraints: 6456 Sorted by residual: angle pdb=" C CYS H 202 " pdb=" CA CYS H 202 " pdb=" CB CYS H 202 " ideal model delta sigma weight residual 111.30 96.49 14.81 1.70e+00 3.46e-01 7.59e+01 angle pdb=" C GLY H 124 " pdb=" N PRO H 125 " pdb=" CA PRO H 125 " ideal model delta sigma weight residual 119.85 127.47 -7.62 1.01e+00 9.80e-01 5.70e+01 angle pdb=" C GLY L 104 " pdb=" N PRO L 105 " pdb=" CA PRO L 105 " ideal model delta sigma weight residual 119.32 127.54 -8.22 1.14e+00 7.69e-01 5.20e+01 angle pdb=" C GLN L 17 " pdb=" N PRO L 18 " pdb=" CA PRO L 18 " ideal model delta sigma weight residual 120.03 126.80 -6.77 9.90e-01 1.02e+00 4.67e+01 angle pdb=" C LYS A 338 " pdb=" N PRO A 339 " pdb=" CA PRO A 339 " ideal model delta sigma weight residual 119.56 126.53 -6.97 1.02e+00 9.61e-01 4.66e+01 ... (remaining 6451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.04: 2636 21.04 - 42.09: 84 42.09 - 63.13: 30 63.13 - 84.17: 11 84.17 - 105.21: 5 Dihedral angle restraints: 2766 sinusoidal: 880 harmonic: 1886 Sorted by residual: dihedral pdb=" CD ARG N 73 " pdb=" NE ARG N 73 " pdb=" CZ ARG N 73 " pdb=" NH1 ARG N 73 " ideal model delta sinusoidal sigma weight residual 0.00 82.47 -82.47 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS H 146 " pdb=" SG CYS H 146 " pdb=" SG CYS H 202 " pdb=" CB CYS H 202 " ideal model delta sinusoidal sigma weight residual 93.00 158.52 -65.52 1 1.00e+01 1.00e-02 5.62e+01 dihedral pdb=" C CYS H 202 " pdb=" N CYS H 202 " pdb=" CA CYS H 202 " pdb=" CB CYS H 202 " ideal model delta harmonic sigma weight residual -122.60 -104.12 -18.48 0 2.50e+00 1.60e-01 5.46e+01 ... (remaining 2763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 555 0.084 - 0.168: 150 0.168 - 0.252: 38 0.252 - 0.336: 5 0.336 - 0.421: 5 Chirality restraints: 753 Sorted by residual: chirality pdb=" C1 BMA B 3 " pdb=" O4 NAG B 2 " pdb=" C2 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.64e+01 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 -2.32 -0.08 2.00e-02 2.50e+03 1.42e+01 chirality pdb=" CA CYS H 202 " pdb=" N CYS H 202 " pdb=" C CYS H 202 " pdb=" CB CYS H 202 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.42e+00 ... (remaining 750 not shown) Planarity restraints: 839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 73 " -1.124 9.50e-02 1.11e+02 5.04e-01 1.53e+02 pdb=" NE ARG N 73 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG N 73 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG N 73 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG N 73 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 113 " 0.566 9.50e-02 1.11e+02 2.54e-01 3.93e+01 pdb=" NE ARG L 113 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG L 113 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG L 113 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG L 113 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 30 " -0.028 2.00e-02 2.50e+03 5.24e-02 2.75e+01 pdb=" C SER H 30 " 0.091 2.00e-02 2.50e+03 pdb=" O SER H 30 " -0.032 2.00e-02 2.50e+03 pdb=" N HIS H 31 " -0.031 2.00e-02 2.50e+03 ... (remaining 836 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1761 2.89 - 3.40: 3691 3.40 - 3.90: 7450 3.90 - 4.40: 8468 4.40 - 4.90: 14724 Nonbonded interactions: 36094 Sorted by model distance: nonbonded pdb=" O PRO L 8 " pdb=" CG2 THR L 107 " model vdw 2.392 3.460 nonbonded pdb=" O CYS H 202 " pdb=" CB CYS H 202 " model vdw 2.410 2.752 nonbonded pdb=" O LEU L 38 " pdb=" O TYR L 54 " model vdw 2.421 3.040 nonbonded pdb=" O TYR L 54 " pdb=" N VAL L 56 " model vdw 2.439 3.120 nonbonded pdb=" NH2 ARG L 51 " pdb=" O LEU H 103 " model vdw 2.441 3.120 ... (remaining 36089 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: 1.680 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.960 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.011 0.141 4720 Z= 0.720 Angle : 1.638 14.807 6484 Z= 1.106 Chirality : 0.087 0.421 753 Planarity : 0.025 0.504 837 Dihedral : 13.713 105.210 1536 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.77 % Allowed : 2.63 % Favored : 96.60 % Rotamer: Outliers : 3.41 % Allowed : 3.12 % Favored : 93.47 % Cbeta Deviations : 1.16 % Peptide Plane: Cis-proline : 13.79 % 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: -0.08 (0.32), residues: 647 helix: -2.74 (0.94), residues: 12 sheet: -0.09 (0.29), residues: 296 loop : 0.26 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP H 109 HIS 0.006 0.001 HIS H 31 PHE 0.015 0.003 PHE H 108 TYR 0.042 0.004 TYR L 54 ARG 0.006 0.001 ARG L 51 Details of bonding type rmsd link_NAG-ASN : bond 0.01055 ( 2) link_NAG-ASN : angle 2.96330 ( 6) link_BETA1-4 : bond 0.04683 ( 2) link_BETA1-4 : angle 7.43038 ( 6) hydrogen bonds : bond 0.18482 ( 196) hydrogen bonds : angle 9.28873 ( 552) SS BOND : bond 0.03775 ( 8) SS BOND : angle 4.83583 ( 16) covalent geometry : bond 0.01123 ( 4708) covalent geometry : angle 1.60574 ( 6456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.487 Fit side-chains REVERT: L 94 MET cc_start: 0.7619 (tmt) cc_final: 0.7122 (tmt) REVERT: L 148 GLU cc_start: 0.7866 (mp0) cc_final: 0.7258 (pp20) REVERT: L 165 GLN cc_start: 0.8031 (mt0) cc_final: 0.7822 (mt0) outliers start: 12 outliers final: 0 residues processed: 66 average time/residue: 1.0842 time to fit residues: 74.7258 Evaluate side-chains 40 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 0.0970 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.0470 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.159613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.125834 restraints weight = 4712.148| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.25 r_work: 0.3264 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 4720 Z= 0.141 Angle : 0.656 8.161 6484 Z= 0.337 Chirality : 0.047 0.165 753 Planarity : 0.005 0.043 837 Dihedral : 7.796 60.189 786 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.47 % Favored : 97.37 % Rotamer: Outliers : 1.70 % Allowed : 8.52 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: 0.14 (0.33), residues: 647 helix: -2.31 (0.76), residues: 20 sheet: 0.23 (0.29), residues: 301 loop : 0.29 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS L 194 PHE 0.015 0.002 PHE A 374 TYR 0.030 0.002 TYR L 54 ARG 0.004 0.001 ARG N 73 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 2) link_NAG-ASN : angle 1.08672 ( 6) link_BETA1-4 : bond 0.00570 ( 2) link_BETA1-4 : angle 2.81779 ( 6) hydrogen bonds : bond 0.03569 ( 196) hydrogen bonds : angle 6.63279 ( 552) SS BOND : bond 0.00434 ( 8) SS BOND : angle 1.57484 ( 16) covalent geometry : bond 0.00342 ( 4708) covalent geometry : angle 0.64593 ( 6456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.447 Fit side-chains REVERT: A 354 MET cc_start: 0.8809 (ttp) cc_final: 0.8596 (ttp) REVERT: L 27 GLN cc_start: 0.7836 (mt0) cc_final: 0.7634 (mm-40) REVERT: L 112 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7802 (ptpt) REVERT: L 152 GLN cc_start: 0.8437 (tt0) cc_final: 0.8156 (mt0) outliers start: 6 outliers final: 0 residues processed: 44 average time/residue: 1.0930 time to fit residues: 50.4821 Evaluate side-chains 34 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 112 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 163 ASN L 204 GLN H 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.150373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.115342 restraints weight = 4806.376| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.33 r_work: 0.3132 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 4720 Z= 0.261 Angle : 0.704 7.874 6484 Z= 0.364 Chirality : 0.049 0.164 753 Planarity : 0.005 0.049 837 Dihedral : 6.132 38.592 786 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.84 % Allowed : 9.94 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: -0.17 (0.33), residues: 647 helix: -2.05 (0.91), residues: 20 sheet: 0.07 (0.28), residues: 317 loop : 0.00 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 109 HIS 0.004 0.001 HIS L 194 PHE 0.023 0.002 PHE N 48 TYR 0.030 0.003 TYR L 54 ARG 0.004 0.001 ARG L 51 Details of bonding type rmsd link_NAG-ASN : bond 0.00128 ( 2) link_NAG-ASN : angle 0.90398 ( 6) link_BETA1-4 : bond 0.00318 ( 2) link_BETA1-4 : angle 2.96869 ( 6) hydrogen bonds : bond 0.03734 ( 196) hydrogen bonds : angle 6.40049 ( 552) SS BOND : bond 0.00430 ( 8) SS BOND : angle 2.01846 ( 16) covalent geometry : bond 0.00656 ( 4708) covalent geometry : angle 0.69194 ( 6456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.453 Fit side-chains REVERT: A 354 MET cc_start: 0.8914 (ttp) cc_final: 0.8617 (ttp) REVERT: A 372 MET cc_start: 0.6072 (ttp) cc_final: 0.5837 (ttm) REVERT: L 59 ARG cc_start: 0.8467 (mtm-85) cc_final: 0.8231 (mtm-85) REVERT: L 112 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7979 (ptpt) REVERT: L 152 GLN cc_start: 0.8518 (tt0) cc_final: 0.8305 (mt0) outliers start: 10 outliers final: 2 residues processed: 42 average time/residue: 1.1646 time to fit residues: 51.2057 Evaluate side-chains 35 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain H residue 5 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 43 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 152 GLN L 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.152112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.117042 restraints weight = 4819.978| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.33 r_work: 0.3150 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 4720 Z= 0.167 Angle : 0.615 6.648 6484 Z= 0.317 Chirality : 0.046 0.156 753 Planarity : 0.004 0.043 837 Dihedral : 5.365 34.825 786 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.69 % Allowed : 9.94 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: -0.22 (0.33), residues: 647 helix: -2.03 (0.90), residues: 21 sheet: 0.02 (0.28), residues: 306 loop : -0.03 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS L 194 PHE 0.015 0.002 PHE N 48 TYR 0.026 0.002 TYR L 54 ARG 0.003 0.001 ARG L 51 Details of bonding type rmsd link_NAG-ASN : bond 0.00091 ( 2) link_NAG-ASN : angle 0.82686 ( 6) link_BETA1-4 : bond 0.00514 ( 2) link_BETA1-4 : angle 2.61537 ( 6) hydrogen bonds : bond 0.03165 ( 196) hydrogen bonds : angle 6.02936 ( 552) SS BOND : bond 0.00343 ( 8) SS BOND : angle 1.50558 ( 16) covalent geometry : bond 0.00418 ( 4708) covalent geometry : angle 0.60553 ( 6456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 354 MET cc_start: 0.8898 (ttp) cc_final: 0.8653 (ttp) REVERT: A 357 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6578 (ptt180) REVERT: L 112 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8051 (ptpt) outliers start: 13 outliers final: 5 residues processed: 41 average time/residue: 1.1306 time to fit residues: 48.5996 Evaluate side-chains 41 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain H residue 5 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 9 optimal weight: 0.0010 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.151614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.116685 restraints weight = 4921.023| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.34 r_work: 0.3143 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 4720 Z= 0.190 Angle : 0.614 6.819 6484 Z= 0.318 Chirality : 0.046 0.158 753 Planarity : 0.005 0.043 837 Dihedral : 5.077 33.939 786 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.26 % Allowed : 10.23 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: -0.30 (0.33), residues: 647 helix: -1.99 (0.91), residues: 23 sheet: -0.00 (0.28), residues: 317 loop : -0.09 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.003 0.001 HIS L 98 PHE 0.015 0.002 PHE N 48 TYR 0.027 0.002 TYR L 54 ARG 0.006 0.001 ARG L 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 2) link_NAG-ASN : angle 0.82751 ( 6) link_BETA1-4 : bond 0.00317 ( 2) link_BETA1-4 : angle 2.22906 ( 6) hydrogen bonds : bond 0.03120 ( 196) hydrogen bonds : angle 5.93568 ( 552) SS BOND : bond 0.00326 ( 8) SS BOND : angle 1.47366 ( 16) covalent geometry : bond 0.00478 ( 4708) covalent geometry : angle 0.60634 ( 6456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 346 ASN cc_start: 0.7855 (m-40) cc_final: 0.7598 (m-40) REVERT: A 354 MET cc_start: 0.8874 (ttp) cc_final: 0.8659 (ttp) REVERT: A 357 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6548 (ptt180) REVERT: L 112 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8060 (ptpt) REVERT: L 160 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7384 (mm-40) outliers start: 15 outliers final: 7 residues processed: 42 average time/residue: 1.0432 time to fit residues: 46.1880 Evaluate side-chains 40 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 22 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.148523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.113595 restraints weight = 4835.278| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.32 r_work: 0.3114 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 4720 Z= 0.262 Angle : 0.671 7.615 6484 Z= 0.347 Chirality : 0.048 0.166 753 Planarity : 0.005 0.048 837 Dihedral : 5.218 34.622 786 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.69 % Allowed : 11.65 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: -0.50 (0.33), residues: 647 helix: -1.88 (0.98), residues: 22 sheet: -0.07 (0.28), residues: 310 loop : -0.35 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.004 0.001 HIS L 98 PHE 0.018 0.002 PHE N 48 TYR 0.028 0.003 TYR L 54 ARG 0.007 0.001 ARG L 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00084 ( 2) link_NAG-ASN : angle 0.85519 ( 6) link_BETA1-4 : bond 0.00258 ( 2) link_BETA1-4 : angle 1.99626 ( 6) hydrogen bonds : bond 0.03385 ( 196) hydrogen bonds : angle 6.16853 ( 552) SS BOND : bond 0.00425 ( 8) SS BOND : angle 1.58911 ( 16) covalent geometry : bond 0.00662 ( 4708) covalent geometry : angle 0.66441 ( 6456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 354 MET cc_start: 0.8926 (ttp) cc_final: 0.8667 (ttp) REVERT: A 357 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6647 (ptt180) REVERT: L 36 THR cc_start: 0.8096 (m) cc_final: 0.7843 (t) REVERT: L 112 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8057 (ptpt) REVERT: L 160 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7488 (mm-40) outliers start: 13 outliers final: 7 residues processed: 41 average time/residue: 1.2783 time to fit residues: 54.7683 Evaluate side-chains 40 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 46 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 chunk 56 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.151618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.116730 restraints weight = 4832.160| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.34 r_work: 0.3154 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4720 Z= 0.137 Angle : 0.573 6.225 6484 Z= 0.297 Chirality : 0.045 0.157 753 Planarity : 0.004 0.042 837 Dihedral : 4.870 32.704 786 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.78 % Favored : 97.06 % Rotamer: Outliers : 3.12 % Allowed : 12.78 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: -0.37 (0.34), residues: 647 helix: -1.74 (0.99), residues: 23 sheet: -0.04 (0.28), residues: 315 loop : -0.18 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS L 98 PHE 0.010 0.001 PHE L 214 TYR 0.025 0.002 TYR L 54 ARG 0.007 0.001 ARG L 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00069 ( 2) link_NAG-ASN : angle 0.80830 ( 6) link_BETA1-4 : bond 0.00341 ( 2) link_BETA1-4 : angle 1.73559 ( 6) hydrogen bonds : bond 0.02866 ( 196) hydrogen bonds : angle 5.82833 ( 552) SS BOND : bond 0.00276 ( 8) SS BOND : angle 1.17392 ( 16) covalent geometry : bond 0.00337 ( 4708) covalent geometry : angle 0.56779 ( 6456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 346 ASN cc_start: 0.7869 (m-40) cc_final: 0.7640 (m-40) REVERT: L 112 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8101 (ptpt) REVERT: L 160 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7511 (mm-40) outliers start: 11 outliers final: 7 residues processed: 45 average time/residue: 1.0598 time to fit residues: 50.1711 Evaluate side-chains 40 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 0.2980 chunk 44 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.153108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.118184 restraints weight = 4845.496| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.34 r_work: 0.3212 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4720 Z= 0.126 Angle : 0.560 5.781 6484 Z= 0.291 Chirality : 0.044 0.157 753 Planarity : 0.004 0.042 837 Dihedral : 4.702 30.764 786 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.78 % Favored : 97.06 % Rotamer: Outliers : 3.69 % Allowed : 13.07 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: -0.25 (0.34), residues: 647 helix: -1.33 (1.07), residues: 22 sheet: 0.04 (0.29), residues: 315 loop : -0.15 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS L 98 PHE 0.010 0.001 PHE L 214 TYR 0.025 0.002 TYR L 54 ARG 0.008 0.001 ARG L 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 2) link_NAG-ASN : angle 0.92218 ( 6) link_BETA1-4 : bond 0.00203 ( 2) link_BETA1-4 : angle 1.58749 ( 6) hydrogen bonds : bond 0.02782 ( 196) hydrogen bonds : angle 5.69451 ( 552) SS BOND : bond 0.00260 ( 8) SS BOND : angle 1.14394 ( 16) covalent geometry : bond 0.00311 ( 4708) covalent geometry : angle 0.55538 ( 6456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 346 ASN cc_start: 0.8042 (m-40) cc_final: 0.7826 (m-40) REVERT: A 357 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6684 (ptt180) REVERT: L 112 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8246 (ptpt) REVERT: H 35 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8640 (m110) outliers start: 13 outliers final: 6 residues processed: 45 average time/residue: 0.9184 time to fit residues: 43.8281 Evaluate side-chains 43 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 35 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 25 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 152 GLN L 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.151562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.117222 restraints weight = 4853.263| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.26 r_work: 0.3161 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4720 Z= 0.162 Angle : 0.586 5.819 6484 Z= 0.304 Chirality : 0.046 0.191 753 Planarity : 0.005 0.042 837 Dihedral : 4.739 31.665 786 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.12 % Allowed : 13.64 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: -0.30 (0.34), residues: 647 helix: -1.34 (1.08), residues: 22 sheet: 0.03 (0.29), residues: 310 loop : -0.21 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS L 98 PHE 0.011 0.001 PHE L 144 TYR 0.027 0.002 TYR L 54 ARG 0.007 0.001 ARG L 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 2) link_NAG-ASN : angle 0.87554 ( 6) link_BETA1-4 : bond 0.00367 ( 2) link_BETA1-4 : angle 1.52762 ( 6) hydrogen bonds : bond 0.02886 ( 196) hydrogen bonds : angle 5.71971 ( 552) SS BOND : bond 0.00291 ( 8) SS BOND : angle 1.27603 ( 16) covalent geometry : bond 0.00405 ( 4708) covalent geometry : angle 0.58138 ( 6456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 346 ASN cc_start: 0.7791 (m-40) cc_final: 0.7517 (m-40) REVERT: A 357 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6489 (ptt180) REVERT: L 112 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7975 (ptpt) outliers start: 11 outliers final: 6 residues processed: 44 average time/residue: 1.0259 time to fit residues: 47.6884 Evaluate side-chains 43 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 152 GLN L 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.150972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.116544 restraints weight = 4863.466| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.27 r_work: 0.3197 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 4720 Z= 0.177 Angle : 0.603 6.056 6484 Z= 0.312 Chirality : 0.046 0.219 753 Planarity : 0.005 0.043 837 Dihedral : 4.807 32.537 786 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.94 % Favored : 96.91 % Rotamer: Outliers : 2.56 % Allowed : 14.77 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: -0.36 (0.34), residues: 647 helix: -1.37 (1.07), residues: 22 sheet: 0.04 (0.29), residues: 305 loop : -0.32 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS L 98 PHE 0.012 0.002 PHE L 144 TYR 0.027 0.002 TYR L 54 ARG 0.008 0.001 ARG L 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 2) link_NAG-ASN : angle 0.87985 ( 6) link_BETA1-4 : bond 0.00301 ( 2) link_BETA1-4 : angle 1.49230 ( 6) hydrogen bonds : bond 0.02948 ( 196) hydrogen bonds : angle 5.75482 ( 552) SS BOND : bond 0.00308 ( 8) SS BOND : angle 1.28984 ( 16) covalent geometry : bond 0.00446 ( 4708) covalent geometry : angle 0.59869 ( 6456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 346 ASN cc_start: 0.7955 (m-40) cc_final: 0.7700 (m-40) REVERT: A 357 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6610 (ptt180) REVERT: A 403 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7171 (mtt90) REVERT: L 112 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8221 (ptpt) outliers start: 9 outliers final: 5 residues processed: 40 average time/residue: 1.1207 time to fit residues: 47.3015 Evaluate side-chains 41 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.151607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.117409 restraints weight = 4831.006| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.24 r_work: 0.3214 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4720 Z= 0.155 Angle : 0.585 6.000 6484 Z= 0.304 Chirality : 0.045 0.200 753 Planarity : 0.004 0.042 837 Dihedral : 4.725 32.516 786 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.78 % Favored : 97.06 % Rotamer: Outliers : 2.84 % Allowed : 14.20 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: -0.36 (0.34), residues: 647 helix: -1.34 (1.08), residues: 22 sheet: -0.02 (0.30), residues: 300 loop : -0.23 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS L 98 PHE 0.010 0.001 PHE L 144 TYR 0.026 0.002 TYR L 54 ARG 0.008 0.001 ARG L 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 2) link_NAG-ASN : angle 0.87208 ( 6) link_BETA1-4 : bond 0.00331 ( 2) link_BETA1-4 : angle 1.43491 ( 6) hydrogen bonds : bond 0.02818 ( 196) hydrogen bonds : angle 5.68414 ( 552) SS BOND : bond 0.00290 ( 8) SS BOND : angle 1.19113 ( 16) covalent geometry : bond 0.00390 ( 4708) covalent geometry : angle 0.58136 ( 6456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3436.06 seconds wall clock time: 59 minutes 5.61 seconds (3545.61 seconds total)