Starting phenix.real_space_refine on Wed Jul 30 01:21:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fqw_50671/07_2025/9fqw_50671_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fqw_50671/07_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_50671/07_2025/9fqw_50671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fqw_50671/07_2025/9fqw_50671.map" model { file = "/net/cci-nas-00/data/ceres_data/9fqw_50671/07_2025/9fqw_50671_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fqw_50671/07_2025/9fqw_50671_trim.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.044 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 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: 6.69, per 1000 atoms: 0.57 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: 3.57 Conformation dependent library (CDL) restraints added in 928.7 milliseconds 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: 0.97 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: 4.11 Time building geometry restraints manager: 4.22 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: 0.910 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: 0.200 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.260 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.890 ------------------------------------------------------------------------------- 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 : 4.65 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (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 TRP 0.026 0.001 TRP A 109 HIS 0.001 0.000 HIS B 66 PHE 0.012 0.001 PHE A 87 TYR 0.006 0.001 TYR B 187 ARG 0.008 0.001 ARG B 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 3) link_NAG-ASN : angle 0.75953 ( 9) link_BETA1-4 : bond 0.00908 ( 5) link_BETA1-4 : angle 2.86474 ( 15) link_ALPHA1-3 : bond 0.00645 ( 1) link_ALPHA1-3 : angle 1.53141 ( 3) hydrogen bonds : bond 0.13433 ( 372) hydrogen bonds : angle 5.98918 ( 1047) link_BETA1-6 : bond 0.00420 ( 1) link_BETA1-6 : angle 1.46825 ( 3) SS BOND : bond 0.00734 ( 6) SS BOND : angle 0.72662 ( 12) covalent geometry : bond 0.00285 ( 6191) covalent geometry : angle 0.57082 ( 8464) *********************** 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 : 0.902 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: 0.4938 time to fit residues: 62.5162 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 : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.140802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.106535 restraints weight = 19896.271| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.97 r_work: 0.2993 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0942 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= 0.136 Angle : 0.546 5.869 8506 Z= 0.274 Chirality : 0.038 0.171 1011 Planarity : 0.004 0.054 1026 Dihedral : 9.611 64.593 1157 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.32 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.31), residues: 759 helix: 2.40 (0.25), residues: 415 sheet: -0.32 (0.74), residues: 56 loop : 0.43 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 520 HIS 0.001 0.001 HIS B 89 PHE 0.020 0.001 PHE A 87 TYR 0.015 0.001 TYR A 257 ARG 0.008 0.001 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 3) link_NAG-ASN : angle 0.61379 ( 9) link_BETA1-4 : bond 0.00752 ( 5) link_BETA1-4 : angle 2.10521 ( 15) link_ALPHA1-3 : bond 0.00926 ( 1) link_ALPHA1-3 : angle 2.22188 ( 3) hydrogen bonds : bond 0.04258 ( 372) hydrogen bonds : angle 4.51391 ( 1047) link_BETA1-6 : bond 0.00077 ( 1) link_BETA1-6 : angle 1.41044 ( 3) SS BOND : bond 0.00300 ( 6) SS BOND : angle 1.08398 ( 12) covalent geometry : bond 0.00298 ( 6191) covalent geometry : angle 0.53548 ( 8464) *********************** 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 87 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: B 230 LYS cc_start: 0.7901 (mttp) cc_final: 0.7663 (mmtp) REVERT: B 231 GLN cc_start: 0.8753 (mp10) cc_final: 0.8518 (mp10) outliers start: 2 outliers final: 2 residues processed: 86 average time/residue: 0.3653 time to fit residues: 42.3494 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 : 0.828 ------------------------------------------------------------------------------- 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 45 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.139427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.104269 restraints weight = 20091.819| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.02 r_work: 0.2962 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6207 Z= 0.140 Angle : 0.516 5.942 8506 Z= 0.259 Chirality : 0.038 0.162 1011 Planarity : 0.004 0.067 1026 Dihedral : 7.467 58.813 1157 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.80 % Allowed : 4.49 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.32), residues: 759 helix: 2.55 (0.25), residues: 410 sheet: -0.31 (0.72), residues: 57 loop : 0.55 (0.40), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 188 HIS 0.002 0.001 HIS B 89 PHE 0.018 0.001 PHE A 87 TYR 0.013 0.001 TYR A 257 ARG 0.004 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 3) link_NAG-ASN : angle 0.54548 ( 9) link_BETA1-4 : bond 0.00558 ( 5) link_BETA1-4 : angle 1.97951 ( 15) link_ALPHA1-3 : bond 0.01117 ( 1) link_ALPHA1-3 : angle 1.41970 ( 3) hydrogen bonds : bond 0.04203 ( 372) hydrogen bonds : angle 4.32602 ( 1047) link_BETA1-6 : bond 0.00230 ( 1) link_BETA1-6 : angle 1.28980 ( 3) SS BOND : bond 0.00323 ( 6) SS BOND : angle 1.01978 ( 12) covalent geometry : bond 0.00315 ( 6191) covalent geometry : angle 0.50774 ( 8464) *********************** 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 94 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 598 ILE cc_start: 0.7811 (tp) cc_final: 0.7598 (pt) outliers start: 5 outliers final: 3 residues processed: 92 average time/residue: 0.3804 time to fit residues: 46.8854 Evaluate side-chains 90 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 149 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.137393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.102137 restraints weight = 20048.917| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.02 r_work: 0.3014 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6207 Z= 0.157 Angle : 0.515 5.966 8506 Z= 0.262 Chirality : 0.038 0.153 1011 Planarity : 0.005 0.079 1026 Dihedral : 6.231 59.334 1157 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.64 % Allowed : 5.30 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.31), residues: 759 helix: 2.54 (0.25), residues: 409 sheet: -0.41 (0.72), residues: 57 loop : 0.52 (0.40), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 188 HIS 0.003 0.001 HIS B 89 PHE 0.018 0.001 PHE A 87 TYR 0.014 0.001 TYR A 257 ARG 0.008 0.001 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 3) link_NAG-ASN : angle 0.59594 ( 9) link_BETA1-4 : bond 0.00493 ( 5) link_BETA1-4 : angle 1.72877 ( 15) link_ALPHA1-3 : bond 0.01168 ( 1) link_ALPHA1-3 : angle 0.98113 ( 3) hydrogen bonds : bond 0.04055 ( 372) hydrogen bonds : angle 4.23355 ( 1047) link_BETA1-6 : bond 0.00166 ( 1) link_BETA1-6 : angle 1.34692 ( 3) SS BOND : bond 0.00415 ( 6) SS BOND : angle 1.01838 ( 12) covalent geometry : bond 0.00360 ( 6191) covalent geometry : angle 0.50870 ( 8464) *********************** 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 90 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.952 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 89 average time/residue: 0.3646 time to fit residues: 46.1480 Evaluate side-chains 87 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 60 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3463 r_free = 0.3463 target = 0.135707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.100389 restraints weight = 20260.657| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.04 r_work: 0.2899 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6207 Z= 0.188 Angle : 0.533 6.021 8506 Z= 0.273 Chirality : 0.038 0.151 1011 Planarity : 0.005 0.085 1026 Dihedral : 5.840 57.794 1157 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.12 % Allowed : 5.62 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.31), residues: 759 helix: 2.46 (0.25), residues: 409 sheet: -0.41 (0.74), residues: 57 loop : 0.38 (0.39), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 188 HIS 0.003 0.001 HIS B 89 PHE 0.018 0.001 PHE A 87 TYR 0.016 0.001 TYR A 257 ARG 0.009 0.001 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 3) link_NAG-ASN : angle 0.75800 ( 9) link_BETA1-4 : bond 0.00428 ( 5) link_BETA1-4 : angle 1.52510 ( 15) link_ALPHA1-3 : bond 0.01245 ( 1) link_ALPHA1-3 : angle 1.09383 ( 3) hydrogen bonds : bond 0.04191 ( 372) hydrogen bonds : angle 4.25570 ( 1047) link_BETA1-6 : bond 0.00219 ( 1) link_BETA1-6 : angle 1.36689 ( 3) SS BOND : bond 0.00440 ( 6) SS BOND : angle 1.61642 ( 12) covalent geometry : bond 0.00441 ( 6191) covalent geometry : angle 0.52556 ( 8464) *********************** 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: 7 poor density : 86 time to evaluate : 1.693 Fit side-chains revert: symmetry clash REVERT: B 93 GLU cc_start: 0.7994 (pm20) cc_final: 0.7780 (pm20) outliers start: 7 outliers final: 5 residues processed: 91 average time/residue: 0.4396 time to fit residues: 56.4379 Evaluate side-chains 88 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 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 3 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.136308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.100861 restraints weight = 20299.664| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.04 r_work: 0.2977 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6207 Z= 0.155 Angle : 0.516 5.992 8506 Z= 0.266 Chirality : 0.037 0.149 1011 Planarity : 0.004 0.071 1026 Dihedral : 5.654 56.270 1157 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.64 % Allowed : 6.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.31), residues: 759 helix: 2.48 (0.25), residues: 410 sheet: -0.39 (0.74), residues: 57 loop : 0.34 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 188 HIS 0.004 0.001 HIS B 89 PHE 0.013 0.001 PHE A 87 TYR 0.014 0.001 TYR A 257 ARG 0.006 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00104 ( 3) link_NAG-ASN : angle 0.67186 ( 9) link_BETA1-4 : bond 0.00437 ( 5) link_BETA1-4 : angle 1.46344 ( 15) link_ALPHA1-3 : bond 0.01207 ( 1) link_ALPHA1-3 : angle 1.17658 ( 3) hydrogen bonds : bond 0.04021 ( 372) hydrogen bonds : angle 4.18875 ( 1047) link_BETA1-6 : bond 0.00170 ( 1) link_BETA1-6 : angle 1.30166 ( 3) SS BOND : bond 0.00370 ( 6) SS BOND : angle 1.18020 ( 12) covalent geometry : bond 0.00357 ( 6191) covalent geometry : angle 0.51020 ( 8464) *********************** 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 89 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: B 93 GLU cc_start: 0.7957 (pm20) cc_final: 0.7719 (pm20) outliers start: 4 outliers final: 4 residues processed: 89 average time/residue: 0.3588 time to fit residues: 45.0243 Evaluate side-chains 87 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 18 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.136329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.101014 restraints weight = 20375.489| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.04 r_work: 0.2980 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1816 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= 0.145 Angle : 0.506 5.995 8506 Z= 0.259 Chirality : 0.037 0.148 1011 Planarity : 0.005 0.083 1026 Dihedral : 5.488 54.902 1157 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.64 % Allowed : 6.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.31), residues: 759 helix: 2.48 (0.24), residues: 413 sheet: -0.41 (0.75), residues: 57 loop : 0.24 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 188 HIS 0.004 0.001 HIS B 89 PHE 0.015 0.001 PHE A 147 TYR 0.013 0.001 TYR A 257 ARG 0.008 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00081 ( 3) link_NAG-ASN : angle 0.64687 ( 9) link_BETA1-4 : bond 0.00442 ( 5) link_BETA1-4 : angle 1.43684 ( 15) link_ALPHA1-3 : bond 0.01139 ( 1) link_ALPHA1-3 : angle 1.17082 ( 3) hydrogen bonds : bond 0.03947 ( 372) hydrogen bonds : angle 4.14244 ( 1047) link_BETA1-6 : bond 0.00203 ( 1) link_BETA1-6 : angle 1.29850 ( 3) SS BOND : bond 0.00342 ( 6) SS BOND : angle 1.17403 ( 12) covalent geometry : bond 0.00333 ( 6191) covalent geometry : angle 0.49974 ( 8464) *********************** 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 88 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 1.809 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 88 average time/residue: 0.3399 time to fit residues: 41.2223 Evaluate side-chains 86 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 59 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.137558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.102461 restraints weight = 20197.421| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.03 r_work: 0.2979 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6207 Z= 0.117 Angle : 0.490 5.952 8506 Z= 0.250 Chirality : 0.036 0.149 1011 Planarity : 0.004 0.075 1026 Dihedral : 5.327 53.203 1157 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.48 % Allowed : 6.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.31), residues: 759 helix: 2.61 (0.25), residues: 413 sheet: -0.44 (0.75), residues: 57 loop : 0.26 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 188 HIS 0.004 0.001 HIS B 89 PHE 0.019 0.001 PHE A 147 TYR 0.012 0.001 TYR A 257 ARG 0.008 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00071 ( 3) link_NAG-ASN : angle 0.57329 ( 9) link_BETA1-4 : bond 0.00464 ( 5) link_BETA1-4 : angle 1.37947 ( 15) link_ALPHA1-3 : bond 0.01144 ( 1) link_ALPHA1-3 : angle 1.18223 ( 3) hydrogen bonds : bond 0.03809 ( 372) hydrogen bonds : angle 4.06851 ( 1047) link_BETA1-6 : bond 0.00249 ( 1) link_BETA1-6 : angle 1.25789 ( 3) SS BOND : bond 0.00299 ( 6) SS BOND : angle 1.04287 ( 12) covalent geometry : bond 0.00260 ( 6191) covalent geometry : angle 0.48453 ( 8464) *********************** 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 84 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 230 ASP cc_start: 0.8437 (t70) cc_final: 0.8105 (t70) REVERT: B 231 GLN cc_start: 0.8619 (mp10) cc_final: 0.8209 (mp10) outliers start: 3 outliers final: 3 residues processed: 84 average time/residue: 0.3373 time to fit residues: 39.4245 Evaluate side-chains 83 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.136311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.101320 restraints weight = 20224.613| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.03 r_work: 0.2978 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6207 Z= 0.154 Angle : 0.511 6.014 8506 Z= 0.262 Chirality : 0.037 0.150 1011 Planarity : 0.005 0.079 1026 Dihedral : 5.262 52.644 1157 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.48 % Allowed : 7.38 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.31), residues: 759 helix: 2.54 (0.24), residues: 413 sheet: -0.52 (0.76), residues: 57 loop : 0.20 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 188 HIS 0.003 0.001 HIS B 89 PHE 0.018 0.001 PHE A 147 TYR 0.015 0.001 TYR A 257 ARG 0.009 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00074 ( 3) link_NAG-ASN : angle 0.68239 ( 9) link_BETA1-4 : bond 0.00446 ( 5) link_BETA1-4 : angle 1.44683 ( 15) link_ALPHA1-3 : bond 0.01166 ( 1) link_ALPHA1-3 : angle 1.25967 ( 3) hydrogen bonds : bond 0.03930 ( 372) hydrogen bonds : angle 4.09448 ( 1047) link_BETA1-6 : bond 0.00191 ( 1) link_BETA1-6 : angle 1.31575 ( 3) SS BOND : bond 0.00356 ( 6) SS BOND : angle 1.13867 ( 12) covalent geometry : bond 0.00355 ( 6191) covalent geometry : angle 0.50542 ( 8464) *********************** 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 87 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: B 231 GLN cc_start: 0.8692 (mp10) cc_final: 0.8289 (mp10) outliers start: 3 outliers final: 3 residues processed: 87 average time/residue: 0.3787 time to fit residues: 46.5272 Evaluate side-chains 86 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 2.133 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.135907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.100130 restraints weight = 20257.007| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.13 r_work: 0.2904 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6207 Z= 0.138 Angle : 0.498 6.016 8506 Z= 0.255 Chirality : 0.037 0.146 1011 Planarity : 0.004 0.079 1026 Dihedral : 5.195 51.198 1157 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.64 % Allowed : 7.54 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.31), residues: 759 helix: 2.61 (0.25), residues: 413 sheet: -0.63 (0.75), residues: 57 loop : 0.18 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 188 HIS 0.004 0.001 HIS B 89 PHE 0.018 0.001 PHE A 147 TYR 0.012 0.001 TYR A 257 ARG 0.009 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 3) link_NAG-ASN : angle 0.57947 ( 9) link_BETA1-4 : bond 0.00465 ( 5) link_BETA1-4 : angle 1.37279 ( 15) link_ALPHA1-3 : bond 0.01078 ( 1) link_ALPHA1-3 : angle 1.22591 ( 3) hydrogen bonds : bond 0.03835 ( 372) hydrogen bonds : angle 4.05506 ( 1047) link_BETA1-6 : bond 0.00227 ( 1) link_BETA1-6 : angle 1.28096 ( 3) SS BOND : bond 0.00350 ( 6) SS BOND : angle 1.08695 ( 12) covalent geometry : bond 0.00315 ( 6191) covalent geometry : angle 0.49297 ( 8464) ********************** 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 88 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: B 231 GLN cc_start: 0.8577 (mp10) cc_final: 0.8157 (mp10) outliers start: 4 outliers final: 3 residues processed: 88 average time/residue: 0.3202 time to fit residues: 39.1648 Evaluate side-chains 87 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 48 optimal weight: 0.1980 chunk 55 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.136783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.100821 restraints weight = 20234.806| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.15 r_work: 0.2947 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1993 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= 0.110 Angle : 0.488 5.995 8506 Z= 0.248 Chirality : 0.036 0.148 1011 Planarity : 0.004 0.078 1026 Dihedral : 5.095 49.674 1157 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.32 % Allowed : 7.87 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.31), residues: 759 helix: 2.73 (0.25), residues: 413 sheet: -0.64 (0.76), residues: 57 loop : 0.19 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 188 HIS 0.004 0.001 HIS B 89 PHE 0.018 0.001 PHE A 147 TYR 0.011 0.001 TYR A 257 ARG 0.010 0.000 ARG B 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00065 ( 3) link_NAG-ASN : angle 0.56213 ( 9) link_BETA1-4 : bond 0.00487 ( 5) link_BETA1-4 : angle 1.34621 ( 15) link_ALPHA1-3 : bond 0.01062 ( 1) link_ALPHA1-3 : angle 1.21953 ( 3) hydrogen bonds : bond 0.03698 ( 372) hydrogen bonds : angle 3.97897 ( 1047) link_BETA1-6 : bond 0.00269 ( 1) link_BETA1-6 : angle 1.24495 ( 3) SS BOND : bond 0.00362 ( 6) SS BOND : angle 1.02760 ( 12) covalent geometry : bond 0.00241 ( 6191) covalent geometry : angle 0.48295 ( 8464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7102.86 seconds wall clock time: 124 minutes 50.39 seconds (7490.39 seconds total)