Starting phenix.real_space_refine on Sat Aug 23 11:46:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fqw_50671/08_2025/9fqw_50671_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fqw_50671/08_2025/9fqw_50671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fqw_50671/08_2025/9fqw_50671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fqw_50671/08_2025/9fqw_50671.map" model { file = "/net/cci-nas-00/data/ceres_data/9fqw_50671/08_2025/9fqw_50671_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fqw_50671/08_2025/9fqw_50671_trim.cif" } resolution = 3.01 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= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 42 5.16 5 C 3933 2.51 5 N 951 2.21 5 O 1105 1.98 5 H 5796 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11827 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 8282 Classifications: {'peptide': 544} Link IDs: {'PTRANS': 22, 'TRANS': 521} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3331 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 87 Unusual residues: {'Y01': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 2.46, per 1000 atoms: 0.21 Number of scatterers: 11827 At special positions: 0 Unit cell: (109.725, 80.025, 99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 O 1105 8.00 N 951 7.00 C 3933 6.00 H 5796 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 132 " distance=2.03 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 117 " distance=2.05 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 218 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " BETA1-6 " NAG D 1 " - " FUC D 5 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN A 223 " " NAG D 1 " - " ASN B 46 " " NAG I 1 " - " ASN B 202 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 385.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1402 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 2 sheets defined 65.0% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 33 through 46 Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.729A pdb=" N ALA A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 90 Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 106 through 140 removed outlier: 3.591A pdb=" N ALA A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 152 removed outlier: 3.565A pdb=" N GLU A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 181 Processing helix chain 'A' and resid 186 through 212 Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 257 through 261 removed outlier: 6.084A pdb=" N GLY A 261 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 268 removed outlier: 4.107A pdb=" N ALA A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 305 Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 314 through 323 Processing helix chain 'A' and resid 327 through 349 removed outlier: 4.110A pdb=" N ALA A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 361 removed outlier: 4.089A pdb=" N ARG A 353 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 355 " --> pdb=" O MET A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 378 through 396 Processing helix chain 'A' and resid 397 through 425 removed outlier: 4.126A pdb=" N TYR A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 482 through 509 Processing helix chain 'A' and resid 510 through 517 Processing helix chain 'A' and resid 518 through 542 removed outlier: 3.517A pdb=" N GLN A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 573 Processing helix chain 'A' and resid 575 through 596 Processing helix chain 'B' and resid 78 through 84 removed outlier: 3.555A pdb=" N LEU B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.840A pdb=" N CYS B 121 " --> pdb=" O SER B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 147 Processing helix chain 'B' and resid 161 through 168 removed outlier: 4.472A pdb=" N SER B 166 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 168 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 204 through 214 removed outlier: 4.164A pdb=" N GLN B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL B 211 " --> pdb=" O GLN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 233 through 237 removed outlier: 4.227A pdb=" N THR B 236 " --> pdb=" O THR B 233 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 58 through 67 Processing sheet with id=AA2, first strand: chain 'B' and resid 197 through 201 372 hydrogen bonds defined for protein. 1047 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: 2.97 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 5783 1.04 - 1.23: 110 1.23 - 1.43: 2474 1.43 - 1.63: 3561 1.63 - 1.82: 59 Bond restraints: 11987 Sorted by residual: bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.77e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 2.99e+00 bond pdb=" C2 BMA D 3 " pdb=" C3 BMA D 3 " ideal model delta sigma weight residual 1.544 1.513 0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C1 MAN D 4 " pdb=" C2 MAN D 4 " ideal model delta sigma weight residual 1.526 1.556 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C5 MAN D 4 " pdb=" O5 MAN D 4 " ideal model delta sigma weight residual 1.418 1.447 -0.029 2.00e-02 2.50e+03 2.11e+00 ... (remaining 11982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 20899 1.35 - 2.70: 605 2.70 - 4.05: 68 4.05 - 5.40: 19 5.40 - 6.74: 7 Bond angle restraints: 21598 Sorted by residual: angle pdb=" C3 BMA D 3 " pdb=" C2 BMA D 3 " pdb=" O2 BMA D 3 " ideal model delta sigma weight residual 112.95 106.21 6.74 3.00e+00 1.11e-01 5.05e+00 angle pdb=" SG CYS B 107 " pdb=" CB CYS B 107 " pdb=" HB2 CYS B 107 " ideal model delta sigma weight residual 108.00 101.70 6.30 3.00e+00 1.11e-01 4.42e+00 angle pdb=" N ORN A1003 " pdb=" CA ORN A1003 " pdb=" C ORN A1003 " ideal model delta sigma weight residual 111.00 105.12 5.88 2.80e+00 1.28e-01 4.41e+00 angle pdb=" N VAL A 67 " pdb=" CA VAL A 67 " pdb=" C VAL A 67 " ideal model delta sigma weight residual 110.62 108.50 2.12 1.02e+00 9.61e-01 4.30e+00 angle pdb=" C3 MAN D 4 " pdb=" C2 MAN D 4 " pdb=" O2 MAN D 4 " ideal model delta sigma weight residual 111.77 105.58 6.19 3.00e+00 1.11e-01 4.25e+00 ... (remaining 21593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 5552 21.67 - 43.34: 260 43.34 - 65.01: 115 65.01 - 86.68: 15 86.68 - 108.35: 10 Dihedral angle restraints: 5952 sinusoidal: 3300 harmonic: 2652 Sorted by residual: dihedral pdb=" CB CYS B 107 " pdb=" SG CYS B 107 " pdb=" SG CYS B 117 " pdb=" CB CYS B 117 " ideal model delta sinusoidal sigma weight residual 93.00 30.04 62.96 1 1.00e+01 1.00e-02 5.24e+01 dihedral pdb=" CA CYS B 107 " pdb=" C CYS B 107 " pdb=" N SER B 108 " pdb=" CA SER B 108 " ideal model delta harmonic sigma weight residual 180.00 150.86 29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" O4 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C5 BMA I 3 " pdb=" O5 BMA I 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.64 108.35 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 5949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 882 0.059 - 0.119: 116 0.119 - 0.178: 10 0.178 - 0.237: 1 0.237 - 0.297: 2 Chirality restraints: 1011 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ORN A1003 " pdb=" N ORN A1003 " pdb=" C ORN A1003 " pdb=" CB ORN A1003 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 1008 not shown) Planarity restraints: 1752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 130 " -0.193 9.50e-02 1.11e+02 6.45e-02 4.69e+00 pdb=" NE ARG A 130 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 130 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 130 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 130 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 130 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 130 " 0.003 2.00e-02 2.50e+03 pdb="HH21 ARG A 130 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG A 130 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 109 " -0.014 2.00e-02 2.50e+03 8.00e-03 2.56e+00 pdb=" CG TRP A 109 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A 109 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 109 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 109 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 109 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 109 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 109 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 109 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 109 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TRP A 109 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP A 109 " 0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP A 109 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 109 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 109 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP A 109 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 227 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C ASN B 227 " 0.027 2.00e-02 2.50e+03 pdb=" O ASN B 227 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA B 228 " -0.009 2.00e-02 2.50e+03 ... (remaining 1749 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 208 2.09 - 2.72: 19572 2.72 - 3.35: 36078 3.35 - 3.97: 44705 3.97 - 4.60: 71570 Nonbonded interactions: 172133 Sorted by model distance: nonbonded pdb="HH21 ARG A 130 " pdb=" O ALA A 393 " model vdw 1.468 2.450 nonbonded pdb="HH22 ARG A 130 " pdb=" O PHE A 396 " model vdw 1.519 2.450 nonbonded pdb="HD22 ASN A 216 " pdb=" O LEU A 303 " model vdw 1.574 2.450 nonbonded pdb=" OE1 GLU A 86 " pdb=" H VAL A 553 " model vdw 1.602 2.450 nonbonded pdb=" O TYR A 235 " pdb=" HH TYR A 307 " model vdw 1.613 2.450 ... (remaining 172128 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: 1.140 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: 0.070 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.420 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.003 0.039 6207 Z= 0.146 Angle : 0.584 9.015 8506 Z= 0.275 Chirality : 0.041 0.297 1011 Planarity : 0.005 0.085 1026 Dihedral : 14.915 108.347 2399 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.62 (0.31), residues: 759 helix: 1.87 (0.26), residues: 414 sheet: -0.22 (0.72), residues: 56 loop : 0.30 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 185 TYR 0.006 0.001 TYR B 187 PHE 0.012 0.001 PHE A 87 TRP 0.026 0.001 TRP A 109 HIS 0.001 0.000 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6191) covalent geometry : angle 0.57082 ( 8464) SS BOND : bond 0.00734 ( 6) SS BOND : angle 0.72662 ( 12) hydrogen bonds : bond 0.13433 ( 372) hydrogen bonds : angle 5.98918 ( 1047) link_ALPHA1-3 : bond 0.00645 ( 1) link_ALPHA1-3 : angle 1.53141 ( 3) link_BETA1-4 : bond 0.00908 ( 5) link_BETA1-4 : angle 2.86474 ( 15) link_BETA1-6 : bond 0.00420 ( 1) link_BETA1-6 : angle 1.46825 ( 3) link_NAG-ASN : bond 0.00183 ( 3) link_NAG-ASN : angle 0.75953 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 572 MET cc_start: 0.8688 (mmt) cc_final: 0.8467 (mmt) REVERT: B 94 TYR cc_start: 0.7732 (m-80) cc_final: 0.7378 (m-80) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2285 time to fit residues: 28.7117 Evaluate side-chains 82 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.140775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.106443 restraints weight = 19960.301| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.98 r_work: 0.3103 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6207 Z= 0.138 Angle : 0.544 5.875 8506 Z= 0.274 Chirality : 0.039 0.168 1011 Planarity : 0.004 0.055 1026 Dihedral : 9.647 65.016 1157 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.32 % Allowed : 3.53 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.19 (0.32), residues: 759 helix: 2.41 (0.25), residues: 414 sheet: -0.32 (0.74), residues: 56 loop : 0.50 (0.40), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 56 TYR 0.015 0.001 TYR A 257 PHE 0.020 0.001 PHE A 87 TRP 0.014 0.001 TRP A 520 HIS 0.001 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6191) covalent geometry : angle 0.53445 ( 8464) SS BOND : bond 0.00299 ( 6) SS BOND : angle 1.08360 ( 12) hydrogen bonds : bond 0.04299 ( 372) hydrogen bonds : angle 4.51842 ( 1047) link_ALPHA1-3 : bond 0.00865 ( 1) link_ALPHA1-3 : angle 2.02836 ( 3) link_BETA1-4 : bond 0.00660 ( 5) link_BETA1-4 : angle 2.13509 ( 15) link_BETA1-6 : bond 0.00035 ( 1) link_BETA1-6 : angle 1.41698 ( 3) link_NAG-ASN : bond 0.00271 ( 3) link_NAG-ASN : angle 0.60867 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 230 ASP cc_start: 0.8328 (t70) cc_final: 0.8075 (t70) REVERT: B 230 LYS cc_start: 0.8027 (mttp) cc_final: 0.7799 (mmtp) REVERT: B 231 GLN cc_start: 0.8811 (mp10) cc_final: 0.8589 (mp10) outliers start: 2 outliers final: 2 residues processed: 87 average time/residue: 0.1776 time to fit residues: 20.6598 Evaluate side-chains 85 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 149 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 56 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 17 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.140411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.105364 restraints weight = 20134.422| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.02 r_work: 0.3052 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6207 Z= 0.120 Angle : 0.504 5.923 8506 Z= 0.252 Chirality : 0.037 0.160 1011 Planarity : 0.004 0.064 1026 Dihedral : 7.433 59.346 1157 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.64 % Allowed : 4.49 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.26 (0.32), residues: 759 helix: 2.51 (0.25), residues: 416 sheet: -0.30 (0.73), residues: 57 loop : 0.44 (0.40), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 56 TYR 0.011 0.001 TYR A 257 PHE 0.017 0.001 PHE A 87 TRP 0.008 0.001 TRP B 188 HIS 0.002 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 6191) covalent geometry : angle 0.49586 ( 8464) SS BOND : bond 0.00288 ( 6) SS BOND : angle 0.94060 ( 12) hydrogen bonds : bond 0.04095 ( 372) hydrogen bonds : angle 4.29355 ( 1047) link_ALPHA1-3 : bond 0.01167 ( 1) link_ALPHA1-3 : angle 1.49710 ( 3) link_BETA1-4 : bond 0.00583 ( 5) link_BETA1-4 : angle 1.94514 ( 15) link_BETA1-6 : bond 0.00240 ( 1) link_BETA1-6 : angle 1.22126 ( 3) link_NAG-ASN : bond 0.00170 ( 3) link_NAG-ASN : angle 0.49333 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 230 ASP cc_start: 0.8333 (t70) cc_final: 0.8039 (t70) outliers start: 4 outliers final: 2 residues processed: 89 average time/residue: 0.1610 time to fit residues: 19.6002 Evaluate side-chains 87 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 478 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 0.0070 chunk 41 optimal weight: 3.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.139536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.104278 restraints weight = 20007.505| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.03 r_work: 0.3042 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6207 Z= 0.122 Angle : 0.492 5.920 8506 Z= 0.249 Chirality : 0.037 0.153 1011 Planarity : 0.004 0.074 1026 Dihedral : 6.268 58.655 1157 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.48 % Allowed : 5.14 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.31 (0.32), residues: 759 helix: 2.57 (0.25), residues: 416 sheet: -0.41 (0.73), residues: 57 loop : 0.46 (0.40), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 56 TYR 0.012 0.001 TYR A 257 PHE 0.016 0.001 PHE A 87 TRP 0.008 0.001 TRP B 188 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6191) covalent geometry : angle 0.48494 ( 8464) SS BOND : bond 0.00305 ( 6) SS BOND : angle 0.87895 ( 12) hydrogen bonds : bond 0.03890 ( 372) hydrogen bonds : angle 4.17113 ( 1047) link_ALPHA1-3 : bond 0.01150 ( 1) link_ALPHA1-3 : angle 1.10912 ( 3) link_BETA1-4 : bond 0.00518 ( 5) link_BETA1-4 : angle 1.75190 ( 15) link_BETA1-6 : bond 0.00238 ( 1) link_BETA1-6 : angle 1.26540 ( 3) link_NAG-ASN : bond 0.00161 ( 3) link_NAG-ASN : angle 0.48389 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 230 ASP cc_start: 0.8380 (t70) cc_final: 0.8074 (t70) REVERT: B 231 GLN cc_start: 0.8827 (mp10) cc_final: 0.8505 (mp10) outliers start: 3 outliers final: 3 residues processed: 89 average time/residue: 0.1406 time to fit residues: 17.7230 Evaluate side-chains 88 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 149 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 5 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.138761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.103365 restraints weight = 20178.222| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.05 r_work: 0.3005 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6207 Z= 0.128 Angle : 0.490 5.951 8506 Z= 0.249 Chirality : 0.036 0.147 1011 Planarity : 0.005 0.085 1026 Dihedral : 5.655 56.548 1157 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.80 % Allowed : 5.62 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.42 (0.31), residues: 759 helix: 2.70 (0.25), residues: 412 sheet: -0.43 (0.73), residues: 57 loop : 0.49 (0.39), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 56 TYR 0.012 0.001 TYR A 257 PHE 0.017 0.001 PHE A 87 TRP 0.008 0.001 TRP B 188 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6191) covalent geometry : angle 0.48315 ( 8464) SS BOND : bond 0.00334 ( 6) SS BOND : angle 1.38579 ( 12) hydrogen bonds : bond 0.03833 ( 372) hydrogen bonds : angle 4.08392 ( 1047) link_ALPHA1-3 : bond 0.01205 ( 1) link_ALPHA1-3 : angle 0.97591 ( 3) link_BETA1-4 : bond 0.00476 ( 5) link_BETA1-4 : angle 1.48703 ( 15) link_BETA1-6 : bond 0.00239 ( 1) link_BETA1-6 : angle 1.27126 ( 3) link_NAG-ASN : bond 0.00122 ( 3) link_NAG-ASN : angle 0.49411 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7809 (tp30) cc_final: 0.7552 (tp30) REVERT: A 230 ASP cc_start: 0.8408 (t70) cc_final: 0.8086 (t70) REVERT: B 93 GLU cc_start: 0.7972 (pm20) cc_final: 0.7720 (pm20) outliers start: 5 outliers final: 4 residues processed: 91 average time/residue: 0.1457 time to fit residues: 18.4214 Evaluate side-chains 90 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 149 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.142613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.108526 restraints weight = 20131.055| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.98 r_work: 0.3011 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6207 Z= 0.171 Angle : 0.512 5.981 8506 Z= 0.262 Chirality : 0.037 0.145 1011 Planarity : 0.005 0.079 1026 Dihedral : 5.608 56.529 1157 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.12 % Allowed : 5.46 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.34 (0.31), residues: 759 helix: 2.63 (0.25), residues: 412 sheet: -0.41 (0.73), residues: 57 loop : 0.45 (0.39), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 56 TYR 0.015 0.001 TYR A 257 PHE 0.015 0.001 PHE A 87 TRP 0.008 0.001 TRP B 188 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 6191) covalent geometry : angle 0.50571 ( 8464) SS BOND : bond 0.00363 ( 6) SS BOND : angle 1.10954 ( 12) hydrogen bonds : bond 0.03976 ( 372) hydrogen bonds : angle 4.11612 ( 1047) link_ALPHA1-3 : bond 0.01096 ( 1) link_ALPHA1-3 : angle 1.07532 ( 3) link_BETA1-4 : bond 0.00420 ( 5) link_BETA1-4 : angle 1.50384 ( 15) link_BETA1-6 : bond 0.00180 ( 1) link_BETA1-6 : angle 1.32591 ( 3) link_NAG-ASN : bond 0.00116 ( 3) link_NAG-ASN : angle 0.62766 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: B 93 GLU cc_start: 0.7911 (pm20) cc_final: 0.7590 (pm20) outliers start: 7 outliers final: 4 residues processed: 92 average time/residue: 0.1197 time to fit residues: 15.6513 Evaluate side-chains 89 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 149 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 50 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.139289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.105033 restraints weight = 20139.330| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.98 r_work: 0.2994 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6207 Z= 0.217 Angle : 0.557 6.055 8506 Z= 0.289 Chirality : 0.040 0.203 1011 Planarity : 0.005 0.077 1026 Dihedral : 5.657 56.719 1157 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.64 % Allowed : 6.42 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.31), residues: 759 helix: 2.39 (0.24), residues: 410 sheet: -0.41 (0.74), residues: 57 loop : 0.34 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 56 TYR 0.018 0.002 TYR A 257 PHE 0.016 0.002 PHE A 87 TRP 0.008 0.001 TRP B 188 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 6191) covalent geometry : angle 0.55026 ( 8464) SS BOND : bond 0.00441 ( 6) SS BOND : angle 1.24477 ( 12) hydrogen bonds : bond 0.04270 ( 372) hydrogen bonds : angle 4.26145 ( 1047) link_ALPHA1-3 : bond 0.01181 ( 1) link_ALPHA1-3 : angle 1.25452 ( 3) link_BETA1-4 : bond 0.00413 ( 5) link_BETA1-4 : angle 1.55637 ( 15) link_BETA1-6 : bond 0.00106 ( 1) link_BETA1-6 : angle 1.39229 ( 3) link_NAG-ASN : bond 0.00185 ( 3) link_NAG-ASN : angle 0.87173 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: B 93 GLU cc_start: 0.7925 (pm20) cc_final: 0.7649 (pm20) REVERT: B 118 SER cc_start: 0.8919 (t) cc_final: 0.8688 (p) outliers start: 4 outliers final: 4 residues processed: 92 average time/residue: 0.1281 time to fit residues: 16.3583 Evaluate side-chains 89 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 149 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 57 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.141404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.107482 restraints weight = 20010.593| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.97 r_work: 0.3029 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6207 Z= 0.115 Angle : 0.490 5.945 8506 Z= 0.251 Chirality : 0.036 0.152 1011 Planarity : 0.004 0.077 1026 Dihedral : 5.413 53.559 1157 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.32 % Allowed : 7.06 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.20 (0.31), residues: 759 helix: 2.58 (0.25), residues: 413 sheet: -0.47 (0.74), residues: 57 loop : 0.28 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 56 TYR 0.011 0.001 TYR A 257 PHE 0.011 0.001 PHE A 87 TRP 0.009 0.001 TRP B 188 HIS 0.004 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6191) covalent geometry : angle 0.48404 ( 8464) SS BOND : bond 0.00344 ( 6) SS BOND : angle 1.20781 ( 12) hydrogen bonds : bond 0.03835 ( 372) hydrogen bonds : angle 4.09731 ( 1047) link_ALPHA1-3 : bond 0.01138 ( 1) link_ALPHA1-3 : angle 1.16336 ( 3) link_BETA1-4 : bond 0.00468 ( 5) link_BETA1-4 : angle 1.34857 ( 15) link_BETA1-6 : bond 0.00255 ( 1) link_BETA1-6 : angle 1.25392 ( 3) link_NAG-ASN : bond 0.00089 ( 3) link_NAG-ASN : angle 0.53411 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: B 93 GLU cc_start: 0.7822 (pm20) cc_final: 0.7509 (pm20) REVERT: B 231 GLN cc_start: 0.8549 (mp10) cc_final: 0.8191 (mp10) outliers start: 2 outliers final: 2 residues processed: 85 average time/residue: 0.1134 time to fit residues: 13.5245 Evaluate side-chains 85 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 56 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.137900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.102794 restraints weight = 20002.939| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.03 r_work: 0.3015 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6207 Z= 0.121 Angle : 0.484 5.999 8506 Z= 0.247 Chirality : 0.036 0.148 1011 Planarity : 0.005 0.082 1026 Dihedral : 5.150 51.297 1157 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.32 % Allowed : 6.90 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.35 (0.31), residues: 759 helix: 2.71 (0.24), residues: 413 sheet: -0.44 (0.76), residues: 57 loop : 0.34 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 56 TYR 0.012 0.001 TYR A 257 PHE 0.013 0.001 PHE A 87 TRP 0.009 0.001 TRP B 188 HIS 0.004 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6191) covalent geometry : angle 0.47874 ( 8464) SS BOND : bond 0.00330 ( 6) SS BOND : angle 0.99348 ( 12) hydrogen bonds : bond 0.03740 ( 372) hydrogen bonds : angle 3.99712 ( 1047) link_ALPHA1-3 : bond 0.01109 ( 1) link_ALPHA1-3 : angle 1.24990 ( 3) link_BETA1-4 : bond 0.00466 ( 5) link_BETA1-4 : angle 1.39373 ( 15) link_BETA1-6 : bond 0.00237 ( 1) link_BETA1-6 : angle 1.28676 ( 3) link_NAG-ASN : bond 0.00041 ( 3) link_NAG-ASN : angle 0.57173 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8990 (t80) cc_final: 0.8738 (t80) REVERT: B 93 GLU cc_start: 0.7892 (pm20) cc_final: 0.7681 (pm20) REVERT: B 231 GLN cc_start: 0.8779 (mp10) cc_final: 0.8388 (mp10) outliers start: 2 outliers final: 2 residues processed: 90 average time/residue: 0.1195 time to fit residues: 15.2967 Evaluate side-chains 88 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 19 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 53 optimal weight: 0.0370 chunk 35 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.139306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.104022 restraints weight = 20213.140| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.06 r_work: 0.3008 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6207 Z= 0.100 Angle : 0.476 5.957 8506 Z= 0.242 Chirality : 0.036 0.151 1011 Planarity : 0.004 0.079 1026 Dihedral : 5.062 49.319 1157 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.32 % Allowed : 7.06 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.44 (0.32), residues: 759 helix: 2.82 (0.25), residues: 413 sheet: -0.56 (0.76), residues: 57 loop : 0.35 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 56 TYR 0.009 0.001 TYR A 257 PHE 0.010 0.001 PHE A 87 TRP 0.009 0.001 TRP B 188 HIS 0.004 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 6191) covalent geometry : angle 0.47089 ( 8464) SS BOND : bond 0.00310 ( 6) SS BOND : angle 0.94649 ( 12) hydrogen bonds : bond 0.03623 ( 372) hydrogen bonds : angle 3.93053 ( 1047) link_ALPHA1-3 : bond 0.01075 ( 1) link_ALPHA1-3 : angle 1.22556 ( 3) link_BETA1-4 : bond 0.00492 ( 5) link_BETA1-4 : angle 1.31632 ( 15) link_BETA1-6 : bond 0.00294 ( 1) link_BETA1-6 : angle 1.23010 ( 3) link_NAG-ASN : bond 0.00115 ( 3) link_NAG-ASN : angle 0.49653 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 159 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8949 (t80) cc_final: 0.8742 (t80) REVERT: B 93 GLU cc_start: 0.7866 (pm20) cc_final: 0.7640 (pm20) REVERT: B 231 GLN cc_start: 0.8759 (mp10) cc_final: 0.8372 (mp10) outliers start: 2 outliers final: 2 residues processed: 90 average time/residue: 0.1435 time to fit residues: 17.9832 Evaluate side-chains 87 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 55 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.138806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.103119 restraints weight = 20030.486| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.12 r_work: 0.2950 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6207 Z= 0.099 Angle : 0.467 5.968 8506 Z= 0.237 Chirality : 0.036 0.149 1011 Planarity : 0.004 0.079 1026 Dihedral : 4.872 47.591 1157 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.32 % Allowed : 7.22 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.53 (0.32), residues: 759 helix: 2.93 (0.25), residues: 413 sheet: -0.63 (0.76), residues: 57 loop : 0.37 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 56 TYR 0.009 0.001 TYR A 257 PHE 0.011 0.001 PHE A 87 TRP 0.009 0.001 TRP B 188 HIS 0.004 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 6191) covalent geometry : angle 0.46197 ( 8464) SS BOND : bond 0.00286 ( 6) SS BOND : angle 0.83811 ( 12) hydrogen bonds : bond 0.03538 ( 372) hydrogen bonds : angle 3.83843 ( 1047) link_ALPHA1-3 : bond 0.01014 ( 1) link_ALPHA1-3 : angle 1.23462 ( 3) link_BETA1-4 : bond 0.00497 ( 5) link_BETA1-4 : angle 1.32592 ( 15) link_BETA1-6 : bond 0.00286 ( 1) link_BETA1-6 : angle 1.24412 ( 3) link_NAG-ASN : bond 0.00100 ( 3) link_NAG-ASN : angle 0.52828 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3121.54 seconds wall clock time: 53 minutes 32.66 seconds (3212.66 seconds total)