Starting phenix.real_space_refine on Wed Sep 17 22:33:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fqv_50670/09_2025/9fqv_50670_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fqv_50670/09_2025/9fqv_50670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fqv_50670/09_2025/9fqv_50670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fqv_50670/09_2025/9fqv_50670.map" model { file = "/net/cci-nas-00/data/ceres_data/9fqv_50670/09_2025/9fqv_50670_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fqv_50670/09_2025/9fqv_50670_trim.cif" } resolution = 2.95 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= -0.000 sd= 0.048 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 3934 2.51 5 N 953 2.21 5 O 1102 1.98 5 H 5800 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11831 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 8296 Classifications: {'peptide': 546} Link IDs: {'PTRANS': 22, 'TRANS': 523} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3327 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: 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: "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: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.00, per 1000 atoms: 0.17 Number of scatterers: 11831 At special positions: 0 Unit cell: (112.2, 76.725, 95.7, 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 1102 8.00 N 953 7.00 C 3934 6.00 H 5800 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=2.03 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 " 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: 0.99 Conformation dependent library (CDL) restraints added in 328.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 64.5% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 33 through 46 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.617A pdb=" N ALA A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 90 Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 107 through 140 Processing helix chain 'A' and resid 142 through 152 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 260 removed outlier: 4.272A pdb=" N TYR A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 259 " --> pdb=" O CYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 269 removed outlier: 4.615A pdb=" N GLY A 269 " --> pdb=" O ILE A 265 " (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: 3.995A pdb=" N ALA A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 361 removed outlier: 4.325A pdb=" N ARG A 353 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 3.976A 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 424 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 Processing helix chain 'A' and resid 558 through 574 removed outlier: 3.711A pdb=" N LEU A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 596 Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'B' and resid 78 through 84 removed outlier: 3.553A 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 134 through 147 Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.632A pdb=" N SER B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 168 No H-bonds generated for 'chain 'B' and resid 167 through 168' Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 204 through 214 removed outlier: 3.958A pdb=" N GLN B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 211 " --> pdb=" O GLN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 Processing sheet with id=AA1, first strand: chain 'B' and resid 58 through 67 removed outlier: 3.698A pdb=" N GLY B 151 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 197 through 201 375 hydrogen bonds defined for protein. 1080 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: 2.48 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5787 1.03 - 1.23: 22 1.23 - 1.42: 2556 1.42 - 1.62: 3567 1.62 - 1.81: 59 Bond restraints: 11991 Sorted by residual: bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.561 -0.042 2.00e-02 2.50e+03 4.47e+00 bond pdb=" C2 BMA D 3 " pdb=" C3 BMA D 3 " ideal model delta sigma weight residual 1.544 1.512 0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sigma weight residual 1.410 1.441 -0.031 2.00e-02 2.50e+03 2.47e+00 bond pdb=" C1 MAN D 4 " pdb=" C2 MAN D 4 " ideal model delta sigma weight residual 1.526 1.555 -0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 11986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 21201 1.47 - 2.94: 356 2.94 - 4.41: 40 4.41 - 5.88: 9 5.88 - 7.34: 3 Bond angle restraints: 21609 Sorted by residual: angle pdb=" N CYS B 175 " pdb=" CA CYS B 175 " pdb=" C CYS B 175 " ideal model delta sigma weight residual 107.20 111.49 -4.29 1.70e+00 3.46e-01 6.38e+00 angle pdb=" C3 BMA D 3 " pdb=" C2 BMA D 3 " pdb=" O2 BMA D 3 " ideal model delta sigma weight residual 112.95 105.61 7.34 3.00e+00 1.11e-01 5.99e+00 angle pdb=" N VAL A 556 " pdb=" CA VAL A 556 " pdb=" C VAL A 556 " ideal model delta sigma weight residual 108.88 113.88 -5.00 2.16e+00 2.14e-01 5.36e+00 angle pdb=" C3 MAN D 4 " pdb=" C2 MAN D 4 " pdb=" O2 MAN D 4 " ideal model delta sigma weight residual 111.77 105.69 6.08 3.00e+00 1.11e-01 4.11e+00 angle pdb=" CA VAL A 556 " pdb=" C VAL A 556 " pdb=" N PRO A 557 " ideal model delta sigma weight residual 118.88 122.00 -3.12 1.54e+00 4.22e-01 4.11e+00 ... (remaining 21604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.48: 5576 20.48 - 40.96: 233 40.96 - 61.44: 117 61.44 - 81.92: 11 81.92 - 102.40: 5 Dihedral angle restraints: 5942 sinusoidal: 3284 harmonic: 2658 Sorted by residual: dihedral pdb=" CB CYS B 155 " pdb=" SG CYS B 155 " pdb=" SG CYS B 175 " pdb=" CB CYS B 175 " ideal model delta sinusoidal sigma weight residual 93.00 54.19 38.81 1 1.00e+01 1.00e-02 2.12e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual -71.29 -173.69 102.40 1 3.00e+01 1.11e-03 1.30e+01 dihedral pdb=" C3 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 47.62 -52.45 100.07 1 3.00e+01 1.11e-03 1.25e+01 ... (remaining 5939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 874 0.057 - 0.114: 121 0.114 - 0.171: 11 0.171 - 0.228: 1 0.228 - 0.285: 1 Chirality restraints: 1008 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 -2.56 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C2 BMA D 3 " pdb=" C1 BMA D 3 " pdb=" C3 BMA D 3 " pdb=" O2 BMA D 3 " both_signs ideal model delta sigma weight residual False 2.47 2.69 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 46 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 1005 not shown) Planarity restraints: 1756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 155 " 0.051 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO B 156 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 156 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 156 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 130 " -0.244 9.50e-02 1.11e+02 8.16e-02 7.19e+00 pdb=" NE ARG A 130 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 130 " 0.005 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 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 130 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG A 130 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 556 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 557 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 557 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 557 " -0.028 5.00e-02 4.00e+02 ... (remaining 1753 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 174 2.08 - 2.71: 19309 2.71 - 3.34: 36434 3.34 - 3.97: 45218 3.97 - 4.60: 72226 Nonbonded interactions: 173361 Sorted by model distance: nonbonded pdb="HH21 ARG A 130 " pdb=" O ALA A 393 " model vdw 1.454 2.450 nonbonded pdb="HH22 ARG A 130 " pdb=" O PHE A 396 " model vdw 1.534 2.450 nonbonded pdb="HD22 ASN A 216 " pdb=" O LEU A 303 " model vdw 1.605 2.450 nonbonded pdb="HH22 ARG B 160 " pdb=" O GLY B 168 " model vdw 1.651 2.450 nonbonded pdb=" O ASP B 195 " pdb=" HG1 THR B 226 " model vdw 1.665 2.450 ... (remaining 173356 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'I' } 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: 0.880 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: 0.040 Extract box with map and model: 0.120 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 11.390 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 0.042 6206 Z= 0.138 Angle : 0.548 10.830 8503 Z= 0.259 Chirality : 0.039 0.285 1008 Planarity : 0.005 0.106 1028 Dihedral : 12.898 102.404 2385 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: 1.64 (0.31), residues: 761 helix: 1.85 (0.26), residues: 429 sheet: -0.42 (0.76), residues: 50 loop : 0.30 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 250 TYR 0.020 0.001 TYR A 102 PHE 0.011 0.001 PHE A 394 TRP 0.020 0.001 TRP A 540 HIS 0.002 0.000 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6191) covalent geometry : angle 0.52920 ( 8464) SS BOND : bond 0.00268 ( 6) SS BOND : angle 0.81152 ( 12) hydrogen bonds : bond 0.15225 ( 375) hydrogen bonds : angle 6.24886 ( 1080) link_ALPHA1-3 : bond 0.00590 ( 1) link_ALPHA1-3 : angle 1.38289 ( 3) link_BETA1-4 : bond 0.01324 ( 4) link_BETA1-4 : angle 3.68763 ( 12) link_BETA1-6 : bond 0.00453 ( 1) link_BETA1-6 : angle 1.32112 ( 3) link_NAG-ASN : bond 0.00239 ( 3) link_NAG-ASN : angle 0.78600 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 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 467 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 98 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 138 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7608 (mp0) REVERT: A 372 ASN cc_start: 0.7099 (t0) cc_final: 0.6733 (t0) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.8949 time to fit residues: 93.2392 Evaluate side-chains 75 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.1980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.148578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111787 restraints weight = 19127.389| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.14 r_work: 0.3100 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6206 Z= 0.144 Angle : 0.541 6.401 8503 Z= 0.274 Chirality : 0.038 0.169 1008 Planarity : 0.004 0.063 1028 Dihedral : 8.732 61.236 1139 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.80 % Allowed : 7.05 % Favored : 92.15 % 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: 2.05 (0.31), residues: 761 helix: 2.17 (0.25), residues: 436 sheet: -0.51 (0.73), residues: 52 loop : 0.53 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 185 TYR 0.013 0.001 TYR A 102 PHE 0.014 0.001 PHE A 87 TRP 0.008 0.001 TRP A 540 HIS 0.002 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6191) covalent geometry : angle 0.52983 ( 8464) SS BOND : bond 0.00471 ( 6) SS BOND : angle 1.00563 ( 12) hydrogen bonds : bond 0.04543 ( 375) hydrogen bonds : angle 4.63520 ( 1080) link_ALPHA1-3 : bond 0.00968 ( 1) link_ALPHA1-3 : angle 2.86961 ( 3) link_BETA1-4 : bond 0.01027 ( 4) link_BETA1-4 : angle 2.35101 ( 12) link_BETA1-6 : bond 0.00285 ( 1) link_BETA1-6 : angle 1.31520 ( 3) link_NAG-ASN : bond 0.00355 ( 3) link_NAG-ASN : angle 0.73799 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 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 467 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 81 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7730 (mp0) REVERT: A 372 ASN cc_start: 0.7221 (t0) cc_final: 0.6936 (t0) REVERT: A 548 LYS cc_start: 0.8426 (tppt) cc_final: 0.8216 (tptp) outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 0.8480 time to fit residues: 69.9125 Evaluate side-chains 77 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 178 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.143778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.106695 restraints weight = 19640.935| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.17 r_work: 0.2983 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6206 Z= 0.179 Angle : 0.545 6.130 8503 Z= 0.275 Chirality : 0.038 0.151 1008 Planarity : 0.004 0.053 1028 Dihedral : 7.136 55.147 1139 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.64 % Allowed : 7.69 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.81 (0.31), residues: 761 helix: 2.06 (0.25), residues: 432 sheet: -0.31 (0.73), residues: 52 loop : 0.23 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 160 TYR 0.018 0.002 TYR A 102 PHE 0.014 0.001 PHE A 291 TRP 0.011 0.001 TRP A 132 HIS 0.002 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 6191) covalent geometry : angle 0.53470 ( 8464) SS BOND : bond 0.00364 ( 6) SS BOND : angle 1.17112 ( 12) hydrogen bonds : bond 0.04499 ( 375) hydrogen bonds : angle 4.47742 ( 1080) link_ALPHA1-3 : bond 0.01157 ( 1) link_ALPHA1-3 : angle 2.19690 ( 3) link_BETA1-4 : bond 0.00876 ( 4) link_BETA1-4 : angle 2.27574 ( 12) link_BETA1-6 : bond 0.00319 ( 1) link_BETA1-6 : angle 1.05546 ( 3) link_NAG-ASN : bond 0.00404 ( 3) link_NAG-ASN : angle 1.16804 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 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 467 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 80 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 138 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7610 (mp0) REVERT: A 372 ASN cc_start: 0.7300 (t0) cc_final: 0.6929 (t0) REVERT: A 548 LYS cc_start: 0.8454 (tppt) cc_final: 0.8202 (tptp) outliers start: 4 outliers final: 3 residues processed: 77 average time/residue: 0.8546 time to fit residues: 70.2524 Evaluate side-chains 74 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 314 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.145643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.108546 restraints weight = 19358.536| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.16 r_work: 0.3015 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6206 Z= 0.111 Angle : 0.495 5.755 8503 Z= 0.248 Chirality : 0.036 0.127 1008 Planarity : 0.004 0.044 1028 Dihedral : 6.355 58.192 1139 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.64 % Allowed : 8.17 % Favored : 91.19 % 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: 1.96 (0.31), residues: 761 helix: 2.17 (0.25), residues: 440 sheet: -0.28 (0.73), residues: 52 loop : 0.25 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 185 TYR 0.011 0.001 TYR B 187 PHE 0.009 0.001 PHE A 291 TRP 0.008 0.001 TRP B 188 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 6191) covalent geometry : angle 0.48604 ( 8464) SS BOND : bond 0.00280 ( 6) SS BOND : angle 0.88243 ( 12) hydrogen bonds : bond 0.03889 ( 375) hydrogen bonds : angle 4.28960 ( 1080) link_ALPHA1-3 : bond 0.00848 ( 1) link_ALPHA1-3 : angle 2.27695 ( 3) link_BETA1-4 : bond 0.00780 ( 4) link_BETA1-4 : angle 2.07177 ( 12) link_BETA1-6 : bond 0.00338 ( 1) link_BETA1-6 : angle 1.19190 ( 3) link_NAG-ASN : bond 0.00226 ( 3) link_NAG-ASN : angle 0.68240 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 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 467 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 78 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7861 (mp) REVERT: A 138 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7569 (mp0) REVERT: A 372 ASN cc_start: 0.7311 (t0) cc_final: 0.6964 (t0) REVERT: A 548 LYS cc_start: 0.8448 (tppt) cc_final: 0.8224 (tptp) outliers start: 4 outliers final: 2 residues processed: 74 average time/residue: 0.8558 time to fit residues: 67.5790 Evaluate side-chains 73 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 305 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 16 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.143997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.107494 restraints weight = 19489.109| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.10 r_work: 0.3040 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6206 Z= 0.143 Angle : 0.506 5.973 8503 Z= 0.255 Chirality : 0.037 0.130 1008 Planarity : 0.004 0.046 1028 Dihedral : 5.684 53.950 1139 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.96 % Allowed : 8.49 % Favored : 90.54 % 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: 1.95 (0.31), residues: 761 helix: 2.17 (0.25), residues: 440 sheet: -0.25 (0.74), residues: 54 loop : 0.22 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.014 0.001 TYR A 84 PHE 0.011 0.001 PHE A 367 TRP 0.010 0.001 TRP A 132 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6191) covalent geometry : angle 0.49658 ( 8464) SS BOND : bond 0.00328 ( 6) SS BOND : angle 1.04889 ( 12) hydrogen bonds : bond 0.03973 ( 375) hydrogen bonds : angle 4.24540 ( 1080) link_ALPHA1-3 : bond 0.00875 ( 1) link_ALPHA1-3 : angle 1.87294 ( 3) link_BETA1-4 : bond 0.00834 ( 4) link_BETA1-4 : angle 2.14829 ( 12) link_BETA1-6 : bond 0.00335 ( 1) link_BETA1-6 : angle 1.15249 ( 3) link_NAG-ASN : bond 0.00280 ( 3) link_NAG-ASN : angle 0.94479 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 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 467 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 77 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7931 (mp) REVERT: A 138 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7600 (mp0) REVERT: A 188 MET cc_start: 0.7660 (tpp) cc_final: 0.7363 (ttm) REVERT: A 327 GLU cc_start: 0.7969 (mp0) cc_final: 0.7543 (mp0) REVERT: A 372 ASN cc_start: 0.7310 (t0) cc_final: 0.6977 (t0) REVERT: A 533 MET cc_start: 0.7167 (mtt) cc_final: 0.6927 (mtt) REVERT: A 548 LYS cc_start: 0.8488 (tppt) cc_final: 0.8268 (tptp) REVERT: B 93 GLU cc_start: 0.8219 (pm20) cc_final: 0.7987 (pm20) outliers start: 6 outliers final: 3 residues processed: 74 average time/residue: 0.8750 time to fit residues: 69.1484 Evaluate side-chains 75 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.143570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.106906 restraints weight = 19482.734| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.10 r_work: 0.3032 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6206 Z= 0.137 Angle : 0.501 5.949 8503 Z= 0.253 Chirality : 0.036 0.131 1008 Planarity : 0.004 0.045 1028 Dihedral : 5.546 52.920 1139 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.80 % Allowed : 8.97 % Favored : 90.22 % 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: 1.96 (0.31), residues: 761 helix: 2.21 (0.25), residues: 440 sheet: -0.27 (0.74), residues: 54 loop : 0.16 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 185 TYR 0.015 0.001 TYR A 84 PHE 0.011 0.001 PHE A 291 TRP 0.012 0.001 TRP A 132 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6191) covalent geometry : angle 0.49200 ( 8464) SS BOND : bond 0.00327 ( 6) SS BOND : angle 0.99499 ( 12) hydrogen bonds : bond 0.03903 ( 375) hydrogen bonds : angle 4.20133 ( 1080) link_ALPHA1-3 : bond 0.00804 ( 1) link_ALPHA1-3 : angle 1.78523 ( 3) link_BETA1-4 : bond 0.00784 ( 4) link_BETA1-4 : angle 2.05776 ( 12) link_BETA1-6 : bond 0.00320 ( 1) link_BETA1-6 : angle 1.18115 ( 3) link_NAG-ASN : bond 0.00259 ( 3) link_NAG-ASN : angle 0.88807 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 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 467 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 78 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7591 (mp0) REVERT: A 188 MET cc_start: 0.7654 (tpp) cc_final: 0.7381 (ttm) REVERT: A 372 ASN cc_start: 0.7323 (t0) cc_final: 0.7001 (t0) REVERT: A 548 LYS cc_start: 0.8448 (tppt) cc_final: 0.8223 (tptp) REVERT: B 93 GLU cc_start: 0.8213 (pm20) cc_final: 0.7997 (pm20) REVERT: B 129 THR cc_start: 0.8943 (m) cc_final: 0.8694 (m) outliers start: 5 outliers final: 2 residues processed: 74 average time/residue: 0.9208 time to fit residues: 72.8170 Evaluate side-chains 71 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 overall best weight: 0.8764 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.144102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.106970 restraints weight = 19344.909| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.14 r_work: 0.3036 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6206 Z= 0.123 Angle : 0.496 5.915 8503 Z= 0.250 Chirality : 0.036 0.131 1008 Planarity : 0.004 0.045 1028 Dihedral : 5.344 52.865 1139 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.80 % Allowed : 9.62 % Favored : 89.58 % 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: 2.03 (0.31), residues: 761 helix: 2.29 (0.25), residues: 440 sheet: -0.28 (0.74), residues: 54 loop : 0.17 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 185 TYR 0.016 0.001 TYR A 84 PHE 0.010 0.001 PHE A 291 TRP 0.013 0.001 TRP A 132 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6191) covalent geometry : angle 0.48786 ( 8464) SS BOND : bond 0.00322 ( 6) SS BOND : angle 0.92814 ( 12) hydrogen bonds : bond 0.03791 ( 375) hydrogen bonds : angle 4.13718 ( 1080) link_ALPHA1-3 : bond 0.00743 ( 1) link_ALPHA1-3 : angle 1.65411 ( 3) link_BETA1-4 : bond 0.00828 ( 4) link_BETA1-4 : angle 2.01861 ( 12) link_BETA1-6 : bond 0.00336 ( 1) link_BETA1-6 : angle 1.17718 ( 3) link_NAG-ASN : bond 0.00197 ( 3) link_NAG-ASN : angle 0.82297 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 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 467 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 77 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 138 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7624 (mp0) REVERT: A 188 MET cc_start: 0.7707 (tpp) cc_final: 0.7447 (ttm) REVERT: A 314 SER cc_start: 0.7986 (OUTLIER) cc_final: 0.7707 (p) REVERT: A 327 GLU cc_start: 0.8055 (mp0) cc_final: 0.7583 (mp0) REVERT: A 372 ASN cc_start: 0.7341 (t0) cc_final: 0.7042 (t0) REVERT: A 548 LYS cc_start: 0.8444 (tppt) cc_final: 0.8222 (tptp) REVERT: B 129 THR cc_start: 0.8969 (m) cc_final: 0.8727 (m) outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 0.8455 time to fit residues: 69.1678 Evaluate side-chains 75 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 36 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 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 = 0.3554 r_free = 0.3554 target = 0.144029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.107248 restraints weight = 19355.300| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.10 r_work: 0.2998 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6206 Z= 0.120 Angle : 0.494 5.860 8503 Z= 0.249 Chirality : 0.036 0.133 1008 Planarity : 0.004 0.045 1028 Dihedral : 5.242 52.687 1139 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.80 % Allowed : 9.94 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.09 (0.31), residues: 761 helix: 2.33 (0.25), residues: 440 sheet: -0.24 (0.74), residues: 54 loop : 0.21 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 185 TYR 0.013 0.001 TYR A 84 PHE 0.010 0.001 PHE A 367 TRP 0.020 0.001 TRP A 132 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6191) covalent geometry : angle 0.48650 ( 8464) SS BOND : bond 0.00345 ( 6) SS BOND : angle 0.88735 ( 12) hydrogen bonds : bond 0.03732 ( 375) hydrogen bonds : angle 4.09281 ( 1080) link_ALPHA1-3 : bond 0.00711 ( 1) link_ALPHA1-3 : angle 1.62055 ( 3) link_BETA1-4 : bond 0.00833 ( 4) link_BETA1-4 : angle 1.99399 ( 12) link_BETA1-6 : bond 0.00343 ( 1) link_BETA1-6 : angle 1.17117 ( 3) link_NAG-ASN : bond 0.00198 ( 3) link_NAG-ASN : angle 0.80286 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 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 467 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 75 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 138 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7572 (mp0) REVERT: A 188 MET cc_start: 0.7639 (tpp) cc_final: 0.7361 (ttm) REVERT: A 314 SER cc_start: 0.7908 (OUTLIER) cc_final: 0.7592 (p) REVERT: A 327 GLU cc_start: 0.8101 (mp0) cc_final: 0.7549 (mp0) REVERT: A 372 ASN cc_start: 0.7347 (t0) cc_final: 0.6994 (t0) REVERT: A 548 LYS cc_start: 0.8486 (tppt) cc_final: 0.8256 (tptp) REVERT: B 129 THR cc_start: 0.8946 (m) cc_final: 0.8708 (m) outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 0.8574 time to fit residues: 66.9620 Evaluate side-chains 74 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 51 optimal weight: 0.3980 chunk 74 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.144434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.107846 restraints weight = 19241.945| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.09 r_work: 0.3010 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6206 Z= 0.112 Angle : 0.490 5.856 8503 Z= 0.246 Chirality : 0.036 0.132 1008 Planarity : 0.004 0.045 1028 Dihedral : 5.094 53.053 1139 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.64 % Allowed : 10.42 % Favored : 88.94 % 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: 2.18 (0.31), residues: 761 helix: 2.40 (0.25), residues: 440 sheet: -0.26 (0.74), residues: 54 loop : 0.26 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 185 TYR 0.014 0.001 TYR A 84 PHE 0.009 0.001 PHE A 367 TRP 0.021 0.001 TRP A 132 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 6191) covalent geometry : angle 0.48201 ( 8464) SS BOND : bond 0.00344 ( 6) SS BOND : angle 0.87859 ( 12) hydrogen bonds : bond 0.03633 ( 375) hydrogen bonds : angle 4.03158 ( 1080) link_ALPHA1-3 : bond 0.00688 ( 1) link_ALPHA1-3 : angle 1.55448 ( 3) link_BETA1-4 : bond 0.00827 ( 4) link_BETA1-4 : angle 1.94368 ( 12) link_BETA1-6 : bond 0.00340 ( 1) link_BETA1-6 : angle 1.17745 ( 3) link_NAG-ASN : bond 0.00160 ( 3) link_NAG-ASN : angle 0.74573 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 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 467 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 71 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.250 Fit side-chains REVERT: A 138 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7583 (mp0) REVERT: A 188 MET cc_start: 0.7624 (tpp) cc_final: 0.7360 (ttm) REVERT: A 314 SER cc_start: 0.7924 (OUTLIER) cc_final: 0.7618 (p) REVERT: A 327 GLU cc_start: 0.8129 (mp0) cc_final: 0.7557 (mp0) REVERT: A 372 ASN cc_start: 0.7355 (t0) cc_final: 0.7010 (t0) REVERT: A 533 MET cc_start: 0.7166 (mtt) cc_final: 0.6922 (mtt) REVERT: A 548 LYS cc_start: 0.8481 (tppt) cc_final: 0.8250 (tptp) outliers start: 4 outliers final: 4 residues processed: 70 average time/residue: 0.9138 time to fit residues: 68.2775 Evaluate side-chains 73 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.143776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.107016 restraints weight = 19472.944| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.10 r_work: 0.2996 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6206 Z= 0.136 Angle : 0.503 5.946 8503 Z= 0.254 Chirality : 0.036 0.133 1008 Planarity : 0.004 0.045 1028 Dihedral : 5.057 51.088 1139 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.80 % Allowed : 10.42 % Favored : 88.78 % 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: 2.18 (0.31), residues: 761 helix: 2.41 (0.25), residues: 434 sheet: -0.25 (0.75), residues: 54 loop : 0.29 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 185 TYR 0.015 0.001 TYR A 84 PHE 0.011 0.001 PHE A 367 TRP 0.021 0.001 TRP A 132 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6191) covalent geometry : angle 0.49530 ( 8464) SS BOND : bond 0.00289 ( 6) SS BOND : angle 0.80632 ( 12) hydrogen bonds : bond 0.03739 ( 375) hydrogen bonds : angle 4.05804 ( 1080) link_ALPHA1-3 : bond 0.00666 ( 1) link_ALPHA1-3 : angle 1.55388 ( 3) link_BETA1-4 : bond 0.00854 ( 4) link_BETA1-4 : angle 1.98007 ( 12) link_BETA1-6 : bond 0.00304 ( 1) link_BETA1-6 : angle 1.19103 ( 3) link_NAG-ASN : bond 0.00240 ( 3) link_NAG-ASN : angle 0.88817 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 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 467 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 74 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.332 Fit side-chains REVERT: A 138 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7585 (mp0) REVERT: A 188 MET cc_start: 0.7619 (tpp) cc_final: 0.7347 (ttm) REVERT: A 209 PHE cc_start: 0.6421 (m-10) cc_final: 0.6183 (m-10) REVERT: A 314 SER cc_start: 0.7922 (OUTLIER) cc_final: 0.7619 (p) REVERT: A 372 ASN cc_start: 0.7377 (t0) cc_final: 0.7023 (t0) REVERT: A 533 MET cc_start: 0.7168 (mtt) cc_final: 0.6925 (mtt) REVERT: A 548 LYS cc_start: 0.8492 (tppt) cc_final: 0.8258 (tptp) outliers start: 5 outliers final: 3 residues processed: 72 average time/residue: 0.8377 time to fit residues: 64.6495 Evaluate side-chains 73 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.141718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.105161 restraints weight = 19808.317| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.06 r_work: 0.2955 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6206 Z= 0.178 Angle : 0.543 6.202 8503 Z= 0.276 Chirality : 0.037 0.135 1008 Planarity : 0.004 0.046 1028 Dihedral : 5.166 46.701 1139 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.80 % Allowed : 10.74 % Favored : 88.46 % 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: 1.89 (0.31), residues: 761 helix: 2.23 (0.25), residues: 428 sheet: -0.19 (0.75), residues: 54 loop : 0.07 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 185 TYR 0.022 0.002 TYR A 84 PHE 0.013 0.002 PHE A 367 TRP 0.028 0.001 TRP A 132 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 6191) covalent geometry : angle 0.53452 ( 8464) SS BOND : bond 0.00525 ( 6) SS BOND : angle 1.14606 ( 12) hydrogen bonds : bond 0.04052 ( 375) hydrogen bonds : angle 4.19033 ( 1080) link_ALPHA1-3 : bond 0.00642 ( 1) link_ALPHA1-3 : angle 1.54605 ( 3) link_BETA1-4 : bond 0.00864 ( 4) link_BETA1-4 : angle 2.07976 ( 12) link_BETA1-6 : bond 0.00262 ( 1) link_BETA1-6 : angle 1.20446 ( 3) link_NAG-ASN : bond 0.00391 ( 3) link_NAG-ASN : angle 1.15429 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3914.40 seconds wall clock time: 66 minutes 58.25 seconds (4018.25 seconds total)