Starting phenix.real_space_refine on Wed Sep 17 04:55:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2c_44103/09_2025/9b2c_44103.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2c_44103/09_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_44103/09_2025/9b2c_44103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2c_44103/09_2025/9b2c_44103.map" model { file = "/net/cci-nas-00/data/ceres_data/9b2c_44103/09_2025/9b2c_44103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2c_44103/09_2025/9b2c_44103.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 3, 'ASN:plan1': 3, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 2} 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: {'ARG:plan': 2, 'ASP:plan': 7, 'GLU:plan': 5, 'ASN:plan1': 2} 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, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 8, 'ASN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 5, 'ASN:plan1': 4, 'GLN:plan1': 1} 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: 1.38, per 1000 atoms: 0.30 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: 0.43 Conformation dependent library (CDL) restraints added in 172.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.32 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: 0.72 Time building geometry restraints manager: 0.58 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.630 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.280 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG L 51 TYR 0.042 0.004 TYR L 54 PHE 0.015 0.003 PHE H 108 TRP 0.026 0.005 TRP H 109 HIS 0.006 0.001 HIS H 31 Details of bonding type rmsd covalent geometry : bond 0.01123 ( 4708) covalent geometry : angle 1.60574 ( 6456) SS BOND : bond 0.03775 ( 8) SS BOND : angle 4.83583 ( 16) hydrogen bonds : bond 0.18482 ( 196) hydrogen bonds : angle 9.28873 ( 552) link_BETA1-4 : bond 0.04683 ( 2) link_BETA1-4 : angle 7.43038 ( 6) link_NAG-ASN : bond 0.01055 ( 2) link_NAG-ASN : angle 2.96330 ( 6) *********************** 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 : 0.176 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: 0.5341 time to fit residues: 36.6528 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 : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.158178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.124655 restraints weight = 4765.791| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.21 r_work: 0.3246 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 4720 Z= 0.160 Angle : 0.670 7.375 6484 Z= 0.350 Chirality : 0.047 0.161 753 Planarity : 0.005 0.053 837 Dihedral : 8.036 62.955 786 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.47 % Favored : 97.37 % Rotamer: Outliers : 1.42 % Allowed : 8.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.33), residues: 647 helix: -2.41 (0.74), residues: 20 sheet: 0.22 (0.29), residues: 301 loop : 0.27 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 73 TYR 0.030 0.002 TYR L 54 PHE 0.016 0.002 PHE A 374 TRP 0.013 0.001 TRP H 47 HIS 0.004 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 4708) covalent geometry : angle 0.65632 ( 6456) SS BOND : bond 0.00350 ( 8) SS BOND : angle 2.07719 ( 16) hydrogen bonds : bond 0.03996 ( 196) hydrogen bonds : angle 6.74921 ( 552) link_BETA1-4 : bond 0.00348 ( 2) link_BETA1-4 : angle 3.03555 ( 6) link_NAG-ASN : bond 0.00138 ( 2) link_NAG-ASN : angle 1.04088 ( 6) *********************** 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: 5 poor density : 40 time to evaluate : 0.156 Fit side-chains REVERT: L 27 GLN cc_start: 0.7989 (mt0) cc_final: 0.7750 (mm-40) REVERT: L 112 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7788 (ptpt) REVERT: L 152 GLN cc_start: 0.8490 (tt0) cc_final: 0.8214 (mt0) outliers start: 5 outliers final: 0 residues processed: 44 average time/residue: 0.5957 time to fit residues: 27.3228 Evaluate side-chains 35 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 12 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3696 r_free = 0.3696 target = 0.153470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118814 restraints weight = 4751.501| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.28 r_work: 0.3163 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 4720 Z= 0.197 Angle : 0.655 7.068 6484 Z= 0.338 Chirality : 0.047 0.162 753 Planarity : 0.005 0.044 837 Dihedral : 5.868 37.981 786 Min Nonbonded Distance : 2.512 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.33), residues: 647 helix: -1.68 (0.97), residues: 19 sheet: 0.10 (0.28), residues: 316 loop : 0.09 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 51 TYR 0.030 0.002 TYR L 54 PHE 0.020 0.002 PHE N 48 TRP 0.013 0.001 TRP H 47 HIS 0.004 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 4708) covalent geometry : angle 0.64345 ( 6456) SS BOND : bond 0.00367 ( 8) SS BOND : angle 1.79652 ( 16) hydrogen bonds : bond 0.03469 ( 196) hydrogen bonds : angle 6.18245 ( 552) link_BETA1-4 : bond 0.00579 ( 2) link_BETA1-4 : angle 2.95981 ( 6) link_NAG-ASN : bond 0.00207 ( 2) link_NAG-ASN : angle 0.99681 ( 6) *********************** 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 49 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.186 Fit side-chains REVERT: A 346 ASN cc_start: 0.7588 (m-40) cc_final: 0.7312 (m-40) REVERT: L 112 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7904 (ptpt) REVERT: L 152 GLN cc_start: 0.8449 (tt0) cc_final: 0.8215 (mt0) outliers start: 10 outliers final: 2 residues processed: 46 average time/residue: 0.5380 time to fit residues: 25.8670 Evaluate side-chains 39 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 54 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 chunk 60 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.154144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.119518 restraints weight = 4791.037| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.28 r_work: 0.3186 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4720 Z= 0.143 Angle : 0.591 6.153 6484 Z= 0.305 Chirality : 0.045 0.148 753 Planarity : 0.004 0.044 837 Dihedral : 5.142 33.991 786 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.33), residues: 647 helix: -1.94 (0.89), residues: 22 sheet: 0.10 (0.29), residues: 306 loop : 0.06 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 79 TYR 0.025 0.002 TYR L 54 PHE 0.012 0.001 PHE N 48 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 4708) covalent geometry : angle 0.58235 ( 6456) SS BOND : bond 0.00270 ( 8) SS BOND : angle 1.36627 ( 16) hydrogen bonds : bond 0.02996 ( 196) hydrogen bonds : angle 5.84668 ( 552) link_BETA1-4 : bond 0.00379 ( 2) link_BETA1-4 : angle 2.48135 ( 6) link_NAG-ASN : bond 0.00134 ( 2) link_NAG-ASN : angle 0.90535 ( 6) *********************** 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 51 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.102 Fit side-chains REVERT: A 346 ASN cc_start: 0.7507 (m-40) cc_final: 0.7238 (m-40) REVERT: A 357 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6471 (ptt180) REVERT: L 112 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7888 (ptpt) REVERT: L 160 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7267 (mm-40) outliers start: 13 outliers final: 6 residues processed: 46 average time/residue: 0.5399 time to fit residues: 25.9504 Evaluate side-chains 45 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain H residue 83 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.152482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.118170 restraints weight = 4845.313| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.25 r_work: 0.3172 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4720 Z= 0.173 Angle : 0.600 6.303 6484 Z= 0.310 Chirality : 0.045 0.155 753 Planarity : 0.005 0.044 837 Dihedral : 4.925 31.976 786 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.41 % Allowed : 12.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.33), residues: 647 helix: -1.66 (0.97), residues: 22 sheet: 0.08 (0.29), residues: 306 loop : -0.02 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 79 TYR 0.026 0.002 TYR L 54 PHE 0.014 0.002 PHE N 48 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS L 98 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 4708) covalent geometry : angle 0.59265 ( 6456) SS BOND : bond 0.00308 ( 8) SS BOND : angle 1.41111 ( 16) hydrogen bonds : bond 0.03015 ( 196) hydrogen bonds : angle 5.79226 ( 552) link_BETA1-4 : bond 0.00336 ( 2) link_BETA1-4 : angle 2.13236 ( 6) link_NAG-ASN : bond 0.00128 ( 2) link_NAG-ASN : angle 0.89580 ( 6) *********************** 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 47 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 346 ASN cc_start: 0.7521 (m-40) cc_final: 0.7248 (m-40) REVERT: A 357 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6472 (ptt180) REVERT: L 112 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7820 (ptpt) REVERT: L 160 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7332 (mm-40) outliers start: 12 outliers final: 7 residues processed: 42 average time/residue: 0.5267 time to fit residues: 23.1568 Evaluate side-chains 42 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 26 optimal weight: 0.0040 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 0.0270 chunk 60 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 0.0470 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.3948 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.154833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.120356 restraints weight = 4825.004| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.26 r_work: 0.3196 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4720 Z= 0.115 Angle : 0.552 5.216 6484 Z= 0.287 Chirality : 0.044 0.192 753 Planarity : 0.004 0.042 837 Dihedral : 4.674 31.828 786 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.34), residues: 647 helix: -1.37 (1.05), residues: 22 sheet: 0.13 (0.29), residues: 306 loop : 0.04 (0.38), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 79 TYR 0.025 0.002 TYR L 54 PHE 0.009 0.001 PHE L 214 TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS L 98 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 4708) covalent geometry : angle 0.54711 ( 6456) SS BOND : bond 0.00251 ( 8) SS BOND : angle 1.10719 ( 16) hydrogen bonds : bond 0.02731 ( 196) hydrogen bonds : angle 5.56377 ( 552) link_BETA1-4 : bond 0.00325 ( 2) link_BETA1-4 : angle 1.84295 ( 6) link_NAG-ASN : bond 0.00128 ( 2) link_NAG-ASN : angle 0.91262 ( 6) *********************** 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 49 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 346 ASN cc_start: 0.7515 (m-40) cc_final: 0.7251 (m-40) outliers start: 13 outliers final: 7 residues processed: 46 average time/residue: 0.4652 time to fit residues: 22.4500 Evaluate side-chains 40 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 CYS 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 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.150293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.115457 restraints weight = 4879.176| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.30 r_work: 0.3135 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 4720 Z= 0.232 Angle : 0.638 6.611 6484 Z= 0.330 Chirality : 0.047 0.163 753 Planarity : 0.005 0.048 837 Dihedral : 4.939 31.886 786 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.41 % Allowed : 14.20 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.34), residues: 647 helix: -1.43 (1.04), residues: 22 sheet: 0.05 (0.28), residues: 316 loop : -0.08 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 79 TYR 0.028 0.002 TYR L 54 PHE 0.017 0.002 PHE N 48 TRP 0.011 0.002 TRP H 47 HIS 0.004 0.001 HIS L 98 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 4708) covalent geometry : angle 0.63210 ( 6456) SS BOND : bond 0.00376 ( 8) SS BOND : angle 1.46707 ( 16) hydrogen bonds : bond 0.03191 ( 196) hydrogen bonds : angle 5.86510 ( 552) link_BETA1-4 : bond 0.00335 ( 2) link_BETA1-4 : angle 1.75972 ( 6) link_NAG-ASN : bond 0.00111 ( 2) link_NAG-ASN : angle 0.85424 ( 6) *********************** 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 44 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6599 (ptt180) REVERT: L 112 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8007 (ptpt) outliers start: 12 outliers final: 6 residues processed: 40 average time/residue: 0.5904 time to fit residues: 24.6664 Evaluate side-chains 38 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 12 optimal weight: 0.0570 chunk 3 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.152389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.117974 restraints weight = 4849.047| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.25 r_work: 0.3170 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4720 Z= 0.147 Angle : 0.577 6.101 6484 Z= 0.299 Chirality : 0.045 0.157 753 Planarity : 0.004 0.042 837 Dihedral : 4.757 31.794 786 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.78 % Favored : 97.06 % Rotamer: Outliers : 3.69 % Allowed : 14.20 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.34), residues: 647 helix: -1.53 (1.03), residues: 23 sheet: 0.06 (0.29), residues: 317 loop : -0.08 (0.39), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 79 TYR 0.026 0.002 TYR L 54 PHE 0.010 0.001 PHE N 48 TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS L 98 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 4708) covalent geometry : angle 0.57228 ( 6456) SS BOND : bond 0.00288 ( 8) SS BOND : angle 1.18155 ( 16) hydrogen bonds : bond 0.02886 ( 196) hydrogen bonds : angle 5.69068 ( 552) link_BETA1-4 : bond 0.00311 ( 2) link_BETA1-4 : angle 1.60691 ( 6) link_NAG-ASN : bond 0.00137 ( 2) link_NAG-ASN : angle 0.89219 ( 6) *********************** 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 48 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 346 ASN cc_start: 0.7593 (m-40) cc_final: 0.7330 (m-40) REVERT: L 112 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7848 (ptpt) outliers start: 13 outliers final: 6 residues processed: 44 average time/residue: 0.5022 time to fit residues: 23.1888 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 : 0.176 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 61 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 1 optimal weight: 0.2980 chunk 45 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.153894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.119066 restraints weight = 4804.061| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.30 r_work: 0.3182 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4720 Z= 0.117 Angle : 0.548 5.332 6484 Z= 0.284 Chirality : 0.044 0.154 753 Planarity : 0.004 0.042 837 Dihedral : 4.580 31.404 786 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.63 % Favored : 97.22 % Rotamer: Outliers : 2.84 % Allowed : 15.34 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.34), residues: 647 helix: -1.40 (1.05), residues: 23 sheet: 0.13 (0.29), residues: 317 loop : -0.02 (0.39), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 79 TYR 0.025 0.002 TYR L 54 PHE 0.009 0.001 PHE L 214 TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS L 98 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4708) covalent geometry : angle 0.54405 ( 6456) SS BOND : bond 0.00259 ( 8) SS BOND : angle 1.06974 ( 16) hydrogen bonds : bond 0.02708 ( 196) hydrogen bonds : angle 5.51395 ( 552) link_BETA1-4 : bond 0.00356 ( 2) link_BETA1-4 : angle 1.51117 ( 6) link_NAG-ASN : bond 0.00113 ( 2) link_NAG-ASN : angle 0.86898 ( 6) *********************** 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 44 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 346 ASN cc_start: 0.7569 (m-40) cc_final: 0.7309 (m-40) REVERT: L 112 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7841 (ptpt) outliers start: 10 outliers final: 6 residues processed: 40 average time/residue: 0.4112 time to fit residues: 17.3913 Evaluate side-chains 39 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 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 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.152452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.117677 restraints weight = 4865.454| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.30 r_work: 0.3162 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4720 Z= 0.161 Angle : 0.577 5.688 6484 Z= 0.299 Chirality : 0.045 0.159 753 Planarity : 0.005 0.043 837 Dihedral : 4.637 31.550 786 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.63 % Favored : 97.22 % Rotamer: Outliers : 1.99 % Allowed : 16.19 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.34), residues: 647 helix: -1.42 (1.04), residues: 23 sheet: 0.07 (0.29), residues: 318 loop : -0.04 (0.39), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 79 TYR 0.026 0.002 TYR L 54 PHE 0.012 0.001 PHE L 144 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS L 98 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 4708) covalent geometry : angle 0.57295 ( 6456) SS BOND : bond 0.00308 ( 8) SS BOND : angle 1.21551 ( 16) hydrogen bonds : bond 0.02866 ( 196) hydrogen bonds : angle 5.58415 ( 552) link_BETA1-4 : bond 0.00349 ( 2) link_BETA1-4 : angle 1.48314 ( 6) link_NAG-ASN : bond 0.00117 ( 2) link_NAG-ASN : angle 0.86348 ( 6) ********************** 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 40 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 346 ASN cc_start: 0.7579 (m-40) cc_final: 0.7318 (m-40) REVERT: L 112 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7809 (ptpt) outliers start: 7 outliers final: 6 residues processed: 38 average time/residue: 0.4236 time to fit residues: 17.0564 Evaluate side-chains 39 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 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 3 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 0.0370 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 overall best weight: 0.8664 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.151393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.116698 restraints weight = 4874.827| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.29 r_work: 0.3151 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 4720 Z= 0.183 Angle : 0.599 6.010 6484 Z= 0.311 Chirality : 0.045 0.161 753 Planarity : 0.005 0.043 837 Dihedral : 4.701 31.729 786 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.94 % Favored : 96.91 % Rotamer: Outliers : 2.56 % Allowed : 15.62 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.34), residues: 647 helix: -1.30 (1.08), residues: 22 sheet: 0.10 (0.29), residues: 311 loop : -0.19 (0.38), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 79 TYR 0.026 0.002 TYR L 54 PHE 0.013 0.002 PHE N 48 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS L 98 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 4708) covalent geometry : angle 0.59450 ( 6456) SS BOND : bond 0.00334 ( 8) SS BOND : angle 1.26948 ( 16) hydrogen bonds : bond 0.02955 ( 196) hydrogen bonds : angle 5.66755 ( 552) link_BETA1-4 : bond 0.00349 ( 2) link_BETA1-4 : angle 1.45910 ( 6) link_NAG-ASN : bond 0.00104 ( 2) link_NAG-ASN : angle 0.84671 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1709.67 seconds wall clock time: 29 minutes 49.97 seconds (1789.97 seconds total)