Starting phenix.real_space_refine on Wed Feb 12 03:47:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sne_40624/02_2025/8sne_40624.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sne_40624/02_2025/8sne_40624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sne_40624/02_2025/8sne_40624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sne_40624/02_2025/8sne_40624.map" model { file = "/net/cci-nas-00/data/ceres_data/8sne_40624/02_2025/8sne_40624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sne_40624/02_2025/8sne_40624.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1384 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 3 5.49 5 S 33 5.16 5 C 3883 2.51 5 N 988 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6025 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3979 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 13, 'TRANS': 474} Chain breaks: 2 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 950 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "C" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 956 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'BDP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {' MN': 2, '3PE': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.37, per 1000 atoms: 0.73 Number of scatterers: 6025 At special positions: 0 Unit cell: (65.88, 75.6, 165.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 33 16.00 P 3 15.00 O 1116 8.00 N 988 7.00 C 3883 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " 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 BETA1-3 " NAG D 1 " - " BDP D 2 " Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 769.1 milliseconds 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1364 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 45.7% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 39 through 73 removed outlier: 3.983A pdb=" N PHE A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.923A pdb=" N ALA A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.835A pdb=" N THR A 159 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 238 through 254 Processing helix chain 'A' and resid 254 through 262 removed outlier: 4.148A pdb=" N TRP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 4.874A pdb=" N ASP A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 331 through 354 removed outlier: 4.821A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N TYR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 362 removed outlier: 6.886A pdb=" N PHE A 362 " --> pdb=" O LYS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 392 removed outlier: 4.280A pdb=" N LEU A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 420 removed outlier: 3.694A pdb=" N ALA A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 428 removed outlier: 3.811A pdb=" N PHE A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 438 removed outlier: 3.975A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 450 removed outlier: 3.568A pdb=" N PHE A 450 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 497 Processing helix chain 'A' and resid 504 through 534 Processing helix chain 'A' and resid 539 through 552 Processing helix chain 'C' and resid 72 through 75 removed outlier: 3.686A pdb=" N ARG C 75 " --> pdb=" O ASP C 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 75' Processing helix chain 'C' and resid 86 through 90 removed outlier: 4.145A pdb=" N THR C 90 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143 removed outlier: 7.132A pdb=" N VAL A 84 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ILE A 117 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL A 86 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL A 119 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE A 88 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASP A 121 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N GLY A 90 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 89 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU A 272 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL A 317 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL A 227 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR A 319 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLY A 229 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE A 321 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 9.606A pdb=" N CYS A 231 " --> pdb=" O PHE A 321 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N VAL A 323 " --> pdb=" O CYS A 231 " (cutoff:3.500A) removed outlier: 9.670A pdb=" N ILE A 233 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N TRP A 325 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501 removed outlier: 6.183A pdb=" N PHE A 500 " --> pdb=" O GLY B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 8 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.734A pdb=" N SER B 123 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.734A pdb=" N SER B 123 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.577A pdb=" N ASP C 33 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ASN C 32 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA C 52 " --> pdb=" O ASN C 32 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N MET C 34 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ARG C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'C' and resid 20 through 23 332 hydrogen bonds defined for protein. 915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 936 1.31 - 1.43: 1779 1.43 - 1.56: 3395 1.56 - 1.68: 8 1.68 - 1.81: 51 Bond restraints: 6169 Sorted by residual: bond pdb=" C2' UDP A 601 " pdb=" C1' UDP A 601 " ideal model delta sigma weight residual 1.530 1.327 0.203 1.40e-02 5.10e+03 2.11e+02 bond pdb=" O4' UDP A 601 " pdb=" C1' UDP A 601 " ideal model delta sigma weight residual 1.415 1.600 -0.185 1.40e-02 5.10e+03 1.75e+02 bond pdb=" C4' UDP A 601 " pdb=" C3' UDP A 601 " ideal model delta sigma weight residual 1.526 1.365 0.161 1.30e-02 5.92e+03 1.54e+02 bond pdb=" C5 UDP A 601 " pdb=" C6 UDP A 601 " ideal model delta sigma weight residual 1.343 1.490 -0.147 1.60e-02 3.91e+03 8.49e+01 bond pdb=" C3' UDP A 601 " pdb=" C2' UDP A 601 " ideal model delta sigma weight residual 1.530 1.627 -0.097 1.30e-02 5.92e+03 5.62e+01 ... (remaining 6164 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 8241 2.88 - 5.76: 116 5.76 - 8.65: 14 8.65 - 11.53: 1 11.53 - 14.41: 1 Bond angle restraints: 8373 Sorted by residual: angle pdb=" C2 UDP A 601 " pdb=" N3 UDP A 601 " pdb=" C4 UDP A 601 " ideal model delta sigma weight residual 126.93 120.16 6.77 1.00e+00 1.00e+00 4.59e+01 angle pdb=" O2B UDP A 601 " pdb=" PB UDP A 601 " pdb=" O3A UDP A 601 " ideal model delta sigma weight residual 102.95 109.34 -6.39 1.00e+00 1.00e+00 4.09e+01 angle pdb=" O1B UDP A 601 " pdb=" PB UDP A 601 " pdb=" O3A UDP A 601 " ideal model delta sigma weight residual 102.95 109.32 -6.37 1.00e+00 1.00e+00 4.05e+01 angle pdb=" O5' UDP A 601 " pdb=" PA UDP A 601 " pdb=" O3A UDP A 601 " ideal model delta sigma weight residual 104.35 110.17 -5.82 1.00e+00 1.00e+00 3.39e+01 angle pdb=" N1 UDP A 601 " pdb=" C2 UDP A 601 " pdb=" N3 UDP A 601 " ideal model delta sigma weight residual 114.79 120.08 -5.29 1.00e+00 1.00e+00 2.80e+01 ... (remaining 8368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 3153 17.64 - 35.28: 395 35.28 - 52.92: 113 52.92 - 70.55: 38 70.55 - 88.19: 6 Dihedral angle restraints: 3705 sinusoidal: 1564 harmonic: 2141 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual -86.00 -20.16 -65.84 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CA GLN A 172 " pdb=" C GLN A 172 " pdb=" N PRO A 173 " pdb=" CA PRO A 173 " ideal model delta harmonic sigma weight residual 180.00 159.96 20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CG ARG A 508 " pdb=" CD ARG A 508 " pdb=" NE ARG A 508 " pdb=" CZ ARG A 508 " ideal model delta sinusoidal sigma weight residual -90.00 -132.61 42.61 2 1.50e+01 4.44e-03 9.78e+00 ... (remaining 3702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 868 0.093 - 0.186: 48 0.186 - 0.278: 4 0.278 - 0.371: 1 0.371 - 0.464: 1 Chirality restraints: 922 Sorted by residual: chirality pdb=" CBG Y01 A 602 " pdb=" CAQ Y01 A 602 " pdb=" CBD Y01 A 602 " pdb=" CBI Y01 A 602 " both_signs ideal model delta sigma weight residual False -2.33 -2.80 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CBH Y01 A 602 " pdb=" CAT Y01 A 602 " pdb=" CAZ Y01 A 602 " pdb=" CBF Y01 A 602 " both_signs ideal model delta sigma weight residual False -2.85 -2.55 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CBE Y01 A 602 " pdb=" CAP Y01 A 602 " pdb=" CBB Y01 A 602 " pdb=" CBI Y01 A 602 " both_signs ideal model delta sigma weight residual False 2.57 2.82 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 919 not shown) Planarity restraints: 1027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 86 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO B 87 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 270 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.04e+00 pdb=" N PRO A 271 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 13 " 0.019 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO C 14 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " 0.016 5.00e-02 4.00e+02 ... (remaining 1024 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 101 2.67 - 3.22: 5397 3.22 - 3.78: 9296 3.78 - 4.34: 12678 4.34 - 4.90: 21775 Nonbonded interactions: 49247 Sorted by model distance: nonbonded pdb=" OE1 GLN A 172 " pdb=" OG1 THR A 183 " model vdw 2.108 3.040 nonbonded pdb=" O2B UDP A 601 " pdb="MN MN A 605 " model vdw 2.174 2.320 nonbonded pdb=" OE2 GLU A 93 " pdb="MN MN A 604 " model vdw 2.215 2.320 nonbonded pdb=" O4 BDP D 2 " pdb=" O3B UDP A 601 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR A 46 " pdb=" OAG Y01 A 602 " model vdw 2.299 3.040 ... (remaining 49242 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.790 Find NCS groups from input model: 0.060 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:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.008 0.203 6169 Z= 0.506 Angle : 0.741 14.409 8373 Z= 0.380 Chirality : 0.049 0.464 922 Planarity : 0.004 0.055 1027 Dihedral : 17.690 88.192 2335 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.69 % Favored : 95.17 % Rotamer: Outliers : 0.63 % Allowed : 24.09 % Favored : 75.28 % 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: 0.12 (0.32), residues: 725 helix: 1.32 (0.30), residues: 312 sheet: 0.22 (0.44), residues: 146 loop : -1.50 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.001 0.001 HIS A 360 PHE 0.014 0.001 PHE A 450 TYR 0.016 0.001 TYR A 414 ARG 0.004 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8746 (ppp) cc_final: 0.8200 (ppp) REVERT: C 38 ARG cc_start: 0.8088 (ttp-170) cc_final: 0.7798 (ttm170) outliers start: 4 outliers final: 1 residues processed: 86 average time/residue: 1.1582 time to fit residues: 104.7341 Evaluate side-chains 80 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.177748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.135403 restraints weight = 6555.534| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.93 r_work: 0.3142 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.0651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6169 Z= 0.199 Angle : 0.507 7.729 8373 Z= 0.266 Chirality : 0.042 0.162 922 Planarity : 0.004 0.053 1027 Dihedral : 9.299 82.245 1017 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.00 % Favored : 95.86 % Rotamer: Outliers : 3.80 % Allowed : 23.30 % Favored : 72.90 % 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: 0.38 (0.32), residues: 725 helix: 1.60 (0.30), residues: 315 sheet: 0.37 (0.44), residues: 142 loop : -1.49 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.001 0.000 HIS A 174 PHE 0.013 0.001 PHE A 450 TYR 0.016 0.001 TYR A 414 ARG 0.007 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7358 (mpt180) REVERT: C 38 ARG cc_start: 0.7882 (ttp-170) cc_final: 0.7620 (ttm170) outliers start: 24 outliers final: 10 residues processed: 95 average time/residue: 1.1283 time to fit residues: 113.6538 Evaluate side-chains 86 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 82 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.177381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.135027 restraints weight = 6619.899| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.93 r_work: 0.3120 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6169 Z= 0.235 Angle : 0.519 9.128 8373 Z= 0.273 Chirality : 0.042 0.159 922 Planarity : 0.004 0.053 1027 Dihedral : 8.904 85.671 1017 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.28 % Favored : 95.59 % Rotamer: Outliers : 4.75 % Allowed : 23.30 % Favored : 71.95 % 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: 0.34 (0.31), residues: 725 helix: 1.57 (0.30), residues: 315 sheet: 0.31 (0.44), residues: 142 loop : -1.49 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.002 0.000 HIS A 360 PHE 0.013 0.001 PHE A 450 TYR 0.016 0.001 TYR A 414 ARG 0.008 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.715 Fit side-chains REVERT: A 43 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7260 (mp) REVERT: A 175 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7369 (mpt180) REVERT: C 23 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.6798 (tp40) REVERT: C 38 ARG cc_start: 0.7788 (ttp-170) cc_final: 0.7506 (ttm170) outliers start: 30 outliers final: 13 residues processed: 100 average time/residue: 1.1442 time to fit residues: 120.5289 Evaluate side-chains 88 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 82 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 65 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.0470 chunk 55 optimal weight: 0.0050 chunk 57 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 overall best weight: 0.3492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 GLN B 1 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.182026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141315 restraints weight = 6554.694| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.85 r_work: 0.3265 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6169 Z= 0.135 Angle : 0.478 8.620 8373 Z= 0.250 Chirality : 0.041 0.144 922 Planarity : 0.004 0.052 1027 Dihedral : 8.452 89.792 1016 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.00 % Favored : 95.86 % Rotamer: Outliers : 4.91 % Allowed : 22.82 % Favored : 72.27 % 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: 0.56 (0.32), residues: 725 helix: 1.81 (0.30), residues: 315 sheet: 0.15 (0.43), residues: 155 loop : -1.33 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 246 HIS 0.002 0.000 HIS A 174 PHE 0.010 0.001 PHE A 450 TYR 0.014 0.001 TYR A 414 ARG 0.009 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 0.609 Fit side-chains REVERT: A 43 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7324 (mp) REVERT: C 38 ARG cc_start: 0.7843 (ttp-170) cc_final: 0.7561 (ttm170) REVERT: C 71 ARG cc_start: 0.7702 (mmm-85) cc_final: 0.7347 (mmm-85) REVERT: C 75 ARG cc_start: 0.6387 (ttp-110) cc_final: 0.5921 (pmm150) REVERT: C 104 ARG cc_start: 0.7518 (mtm110) cc_final: 0.6809 (mmm160) outliers start: 31 outliers final: 5 residues processed: 100 average time/residue: 1.1488 time to fit residues: 120.7076 Evaluate side-chains 80 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 64 optimal weight: 0.0970 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.178680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.136499 restraints weight = 6644.531| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.92 r_work: 0.3153 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6169 Z= 0.174 Angle : 0.491 10.131 8373 Z= 0.254 Chirality : 0.041 0.144 922 Planarity : 0.004 0.052 1027 Dihedral : 8.325 89.347 1016 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.28 % Favored : 95.59 % Rotamer: Outliers : 4.60 % Allowed : 23.61 % Favored : 71.79 % 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: 0.56 (0.32), residues: 725 helix: 1.81 (0.30), residues: 315 sheet: 0.17 (0.42), residues: 155 loop : -1.34 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 246 HIS 0.001 0.000 HIS A 174 PHE 0.010 0.001 PHE A 450 TYR 0.015 0.001 TYR A 414 ARG 0.009 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.608 Fit side-chains REVERT: A 43 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7252 (mp) REVERT: A 139 ASN cc_start: 0.7607 (t0) cc_final: 0.7368 (m-40) REVERT: A 284 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.6344 (ttpt) REVERT: C 38 ARG cc_start: 0.7736 (ttp-170) cc_final: 0.7054 (ttm170) outliers start: 29 outliers final: 10 residues processed: 91 average time/residue: 0.8641 time to fit residues: 84.3619 Evaluate side-chains 81 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain C residue 23 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.176320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.134185 restraints weight = 6543.044| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.91 r_work: 0.3111 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6169 Z= 0.299 Angle : 0.568 13.416 8373 Z= 0.290 Chirality : 0.044 0.149 922 Planarity : 0.004 0.052 1027 Dihedral : 8.498 89.595 1016 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.28 % Favored : 95.59 % Rotamer: Outliers : 4.91 % Allowed : 23.77 % Favored : 71.32 % 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: 0.35 (0.32), residues: 725 helix: 1.60 (0.30), residues: 314 sheet: 0.22 (0.43), residues: 153 loop : -1.49 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.002 0.000 HIS A 360 PHE 0.012 0.002 PHE A 450 TYR 0.015 0.002 TYR A 414 ARG 0.009 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7156 (mp) REVERT: A 139 ASN cc_start: 0.7800 (t0) cc_final: 0.7435 (m-40) REVERT: A 284 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6366 (ttpt) REVERT: C 71 ARG cc_start: 0.7673 (mmm-85) cc_final: 0.7132 (tpt90) REVERT: C 104 ARG cc_start: 0.7669 (mtm110) cc_final: 0.6893 (mmm160) outliers start: 31 outliers final: 12 residues processed: 97 average time/residue: 1.0244 time to fit residues: 105.0979 Evaluate side-chains 88 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 105 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 41 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 0.0870 chunk 68 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.178840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.136496 restraints weight = 6578.482| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.94 r_work: 0.3174 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6169 Z= 0.169 Angle : 0.515 13.045 8373 Z= 0.263 Chirality : 0.041 0.146 922 Planarity : 0.004 0.052 1027 Dihedral : 8.158 87.971 1016 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.83 % Favored : 95.03 % Rotamer: Outliers : 3.96 % Allowed : 25.52 % Favored : 70.52 % 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: 0.51 (0.32), residues: 725 helix: 1.76 (0.30), residues: 315 sheet: 0.22 (0.42), residues: 152 loop : -1.39 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 246 HIS 0.001 0.000 HIS A 360 PHE 0.010 0.001 PHE C 67 TYR 0.015 0.001 TYR A 414 ARG 0.009 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7190 (mp) REVERT: A 49 PHE cc_start: 0.7870 (t80) cc_final: 0.7403 (t80) REVERT: A 139 ASN cc_start: 0.7620 (t0) cc_final: 0.7303 (m-40) REVERT: A 284 LYS cc_start: 0.6942 (OUTLIER) cc_final: 0.6299 (ttpt) REVERT: C 71 ARG cc_start: 0.7658 (mmm-85) cc_final: 0.7005 (tpp80) REVERT: C 104 ARG cc_start: 0.7590 (mtm110) cc_final: 0.6841 (mmm160) outliers start: 25 outliers final: 9 residues processed: 93 average time/residue: 1.1151 time to fit residues: 109.4163 Evaluate side-chains 86 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain C residue 58 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN C 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.174007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131901 restraints weight = 6520.303| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.89 r_work: 0.3136 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6169 Z= 0.216 Angle : 0.534 12.901 8373 Z= 0.273 Chirality : 0.042 0.147 922 Planarity : 0.004 0.052 1027 Dihedral : 8.024 88.249 1016 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.28 % Favored : 95.59 % Rotamer: Outliers : 3.49 % Allowed : 26.31 % Favored : 70.21 % 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: 0.45 (0.31), residues: 725 helix: 1.67 (0.30), residues: 315 sheet: 0.22 (0.42), residues: 151 loop : -1.39 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.001 0.000 HIS A 360 PHE 0.011 0.001 PHE C 67 TYR 0.016 0.001 TYR A 414 ARG 0.008 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7098 (mp) REVERT: A 139 ASN cc_start: 0.7739 (t0) cc_final: 0.7414 (m-40) REVERT: A 284 LYS cc_start: 0.6952 (OUTLIER) cc_final: 0.6353 (ttpt) REVERT: C 23 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6387 (tp-100) REVERT: C 71 ARG cc_start: 0.7664 (mmm-85) cc_final: 0.7036 (tpp80) REVERT: C 104 ARG cc_start: 0.7611 (mtm110) cc_final: 0.6854 (mmm160) outliers start: 22 outliers final: 14 residues processed: 92 average time/residue: 1.0987 time to fit residues: 106.5784 Evaluate side-chains 91 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 58 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.0370 chunk 35 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.3656 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.180277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.138791 restraints weight = 6587.767| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.88 r_work: 0.3214 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6169 Z= 0.137 Angle : 0.504 12.738 8373 Z= 0.257 Chirality : 0.041 0.145 922 Planarity : 0.004 0.051 1027 Dihedral : 7.645 85.695 1016 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.55 % Favored : 95.31 % Rotamer: Outliers : 3.17 % Allowed : 26.15 % Favored : 70.68 % 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: 0.66 (0.32), residues: 725 helix: 1.88 (0.30), residues: 315 sheet: 0.15 (0.41), residues: 156 loop : -1.22 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 246 HIS 0.001 0.000 HIS A 174 PHE 0.009 0.001 PHE C 67 TYR 0.014 0.001 TYR A 414 ARG 0.009 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.565 Fit side-chains REVERT: A 43 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7199 (mp) REVERT: A 139 ASN cc_start: 0.7492 (t0) cc_final: 0.7184 (m-40) REVERT: A 284 LYS cc_start: 0.6939 (OUTLIER) cc_final: 0.6301 (ttpt) REVERT: A 349 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8138 (mm-30) REVERT: B 37 PHE cc_start: 0.8230 (m-80) cc_final: 0.7923 (m-80) REVERT: C 71 ARG cc_start: 0.7618 (mmm-85) cc_final: 0.6972 (tpp80) REVERT: C 75 ARG cc_start: 0.6370 (ttp-110) cc_final: 0.6010 (pmm150) REVERT: C 104 ARG cc_start: 0.7504 (mtm110) cc_final: 0.6804 (mmm160) outliers start: 20 outliers final: 11 residues processed: 93 average time/residue: 1.1433 time to fit residues: 112.0977 Evaluate side-chains 90 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain C residue 34 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 0.0070 chunk 17 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.178477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.136069 restraints weight = 6663.991| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.93 r_work: 0.3137 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6169 Z= 0.191 Angle : 0.523 12.698 8373 Z= 0.266 Chirality : 0.042 0.142 922 Planarity : 0.004 0.051 1027 Dihedral : 7.635 85.881 1016 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.41 % Favored : 95.45 % Rotamer: Outliers : 2.38 % Allowed : 27.26 % Favored : 70.36 % 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: 0.61 (0.32), residues: 725 helix: 1.79 (0.30), residues: 315 sheet: 0.25 (0.41), residues: 152 loop : -1.24 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.001 0.000 HIS A 360 PHE 0.009 0.001 PHE A 450 TYR 0.016 0.001 TYR A 414 ARG 0.010 0.000 ARG A 334 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.7059 (mp) REVERT: A 139 ASN cc_start: 0.7701 (t0) cc_final: 0.7391 (m-40) REVERT: A 284 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6318 (ttpt) REVERT: A 349 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8137 (mm-30) REVERT: C 71 ARG cc_start: 0.7624 (mmm-85) cc_final: 0.6988 (tpp80) REVERT: C 104 ARG cc_start: 0.7523 (mtm110) cc_final: 0.6806 (mmm160) outliers start: 15 outliers final: 11 residues processed: 86 average time/residue: 1.1765 time to fit residues: 106.7512 Evaluate side-chains 89 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain C residue 34 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 45 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.177812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.135171 restraints weight = 6753.603| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.94 r_work: 0.3124 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6169 Z= 0.209 Angle : 0.539 12.757 8373 Z= 0.275 Chirality : 0.042 0.142 922 Planarity : 0.004 0.050 1027 Dihedral : 7.635 85.203 1016 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.69 % Favored : 95.17 % Rotamer: Outliers : 3.01 % Allowed : 27.26 % Favored : 69.73 % 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: 0.53 (0.32), residues: 725 helix: 1.74 (0.30), residues: 314 sheet: 0.13 (0.41), residues: 154 loop : -1.25 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.001 0.000 HIS A 360 PHE 0.011 0.001 PHE C 67 TYR 0.016 0.001 TYR A 414 ARG 0.010 0.000 ARG A 334 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4388.46 seconds wall clock time: 78 minutes 12.64 seconds (4692.64 seconds total)