Starting phenix.real_space_refine on Thu Jul 2 02:26:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8snc_40622/07_2026/8snc_40622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8snc_40622/07_2026/8snc_40622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8snc_40622/07_2026/8snc_40622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8snc_40622/07_2026/8snc_40622.map" model { file = "/net/cci-nas-00/data/ceres_data/8snc_40622/07_2026/8snc_40622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8snc_40622/07_2026/8snc_40622.cif" } resolution = 3.2 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= 0.049 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 Mn 2 7.51 5 S 35 5.16 5 C 3834 2.51 5 N 968 2.21 5 O 1088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5927 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4029 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 13, 'TRANS': 480} Chain breaks: 2 Chain: "B" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "C" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 895 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain breaks: 1 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1, 'water': 1} Chain breaks: 2 Time building chain proxies: 1.38, per 1000 atoms: 0.23 Number of scatterers: 5927 At special positions: 0 Unit cell: (74.7, 78.02, 142.76, 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) Mn 2 24.99 S 35 16.00 O 1088 8.00 N 968 7.00 C 3834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 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: 0.52 Conformation dependent library (CDL) restraints added in 217.6 milliseconds 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1358 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 6 sheets defined 46.2% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 50 through 74 removed outlier: 3.685A pdb=" N LEU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 124 through 138 removed outlier: 3.932A pdb=" N LYS A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.508A pdb=" N THR A 159 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.741A pdb=" N SER A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 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 255 through 262 removed outlier: 3.726A pdb=" N GLN A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TRP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 removed outlier: 5.110A 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 301 through 312 Processing helix chain 'A' and resid 331 through 356 removed outlier: 4.846A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 391 removed outlier: 3.685A pdb=" N ALA A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 420 Processing helix chain 'A' and resid 421 through 428 Processing helix chain 'A' and resid 429 through 437 removed outlier: 3.942A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 452 Processing helix chain 'A' and resid 470 through 476 Processing helix chain 'A' and resid 477 through 497 Processing helix chain 'A' and resid 504 through 535 Processing helix chain 'A' and resid 539 through 552 Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143 removed outlier: 7.374A pdb=" N VAL A 119 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE A 88 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ASP A 121 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLY A 90 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 198 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 89 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU A 272 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL A 317 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 227 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR A 319 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLY A 229 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N PHE A 321 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N CYS A 231 " --> pdb=" O PHE A 321 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N VAL A 323 " --> pdb=" O CYS A 231 " (cutoff:3.500A) removed outlier: 9.849A pdb=" N ILE A 233 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.431A 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: 6.285A 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 3 through 7 removed outlier: 3.789A pdb=" N VAL B 20 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 78 " --> pdb=" O CYS B 22 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR B 68 " --> pdb=" O GLN B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 59 removed outlier: 5.660A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.538A pdb=" N ALA C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR C 68 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 58 through 59 removed outlier: 6.562A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 0.70 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: 924 1.31 - 1.44: 1817 1.44 - 1.56: 3281 1.56 - 1.69: 0 1.69 - 1.82: 53 Bond restraints: 6075 Sorted by residual: bond pdb=" C7 NAG D 1 " pdb=" N2 NAG D 1 " ideal model delta sigma weight residual 1.346 1.458 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.506 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" CAX Y01 A 601 " pdb=" OAH Y01 A 601 " ideal model delta sigma weight residual 1.248 1.341 -0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C1 BDP D 2 " pdb=" O5 BDP D 2 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C5 BDP D 2 " pdb=" O5 BDP D 2 " ideal model delta sigma weight residual 1.407 1.482 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 6070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 8174 2.48 - 4.96: 65 4.96 - 7.44: 11 7.44 - 9.92: 1 9.92 - 12.40: 2 Bond angle restraints: 8253 Sorted by residual: angle pdb=" CB MET B 82 " pdb=" CG MET B 82 " pdb=" SD MET B 82 " ideal model delta sigma weight residual 112.70 125.10 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CAM Y01 A 601 " pdb=" CAY Y01 A 601 " pdb=" OAW Y01 A 601 " ideal model delta sigma weight residual 111.19 121.11 -9.92 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CBB Y01 A 601 " pdb=" CBE Y01 A 601 " pdb=" CBI Y01 A 601 " ideal model delta sigma weight residual 119.27 111.12 8.15 3.00e+00 1.11e-01 7.39e+00 angle pdb=" CA ASN A 78 " pdb=" CB ASN A 78 " pdb=" CG ASN A 78 " ideal model delta sigma weight residual 112.60 115.06 -2.46 1.00e+00 1.00e+00 6.07e+00 angle pdb=" CAJ Y01 A 601 " pdb=" CAO Y01 A 601 " pdb=" CBB Y01 A 601 " ideal model delta sigma weight residual 115.08 108.31 6.77 3.00e+00 1.11e-01 5.09e+00 ... (remaining 8248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 3043 16.94 - 33.88: 413 33.88 - 50.82: 109 50.82 - 67.76: 28 67.76 - 84.71: 7 Dihedral angle restraints: 3600 sinusoidal: 1471 harmonic: 2129 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 93.00 52.75 40.25 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CA VAL B 12 " pdb=" C VAL B 12 " pdb=" N GLN B 13 " pdb=" CA GLN B 13 " ideal model delta harmonic sigma weight residual -180.00 -158.89 -21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA PHE A 476 " pdb=" C PHE A 476 " pdb=" N LEU A 477 " pdb=" CA LEU A 477 " ideal model delta harmonic sigma weight residual 180.00 161.34 18.66 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 3597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 867 0.096 - 0.191: 38 0.191 - 0.287: 1 0.287 - 0.383: 1 0.383 - 0.478: 1 Chirality restraints: 908 Sorted by residual: chirality pdb=" CBG Y01 A 601 " pdb=" CAQ Y01 A 601 " pdb=" CBD Y01 A 601 " pdb=" CBI Y01 A 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.81 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CBH Y01 A 601 " pdb=" CAT Y01 A 601 " pdb=" CAZ Y01 A 601 " pdb=" CBF Y01 A 601 " both_signs ideal model delta sigma weight residual False -2.85 -2.53 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CBE Y01 A 601 " pdb=" CAP Y01 A 601 " pdb=" CBB Y01 A 601 " pdb=" CBI Y01 A 601 " both_signs ideal model delta sigma weight residual False 2.57 2.83 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 905 not shown) Planarity restraints: 1017 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 40 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO C 41 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 270 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO A 271 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 116 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C LEU A 116 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU A 116 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE A 117 " 0.008 2.00e-02 2.50e+03 ... (remaining 1014 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 172 2.70 - 3.25: 5759 3.25 - 3.80: 9587 3.80 - 4.35: 11902 4.35 - 4.90: 20905 Nonbonded interactions: 48325 Sorted by model distance: nonbonded pdb=" OE2 GLU A 93 " pdb="MN MN A 602 " model vdw 2.156 3.060 nonbonded pdb=" O ASN A 235 " pdb=" OG SER A 241 " model vdw 2.165 3.040 nonbonded pdb=" OD1 ASP A 203 " pdb="MN MN A 603 " model vdw 2.215 3.060 nonbonded pdb=" OD2 ASP A 203 " pdb="MN MN A 602 " model vdw 2.262 3.060 nonbonded pdb=" O TYR B 32 " pdb=" NH2 ARG B 71 " model vdw 2.265 3.120 ... (remaining 48320 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.080 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 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 : 0.005 0.112 6077 Z= 0.230 Angle : 0.597 12.403 8258 Z= 0.296 Chirality : 0.047 0.478 908 Planarity : 0.003 0.052 1017 Dihedral : 16.852 84.706 2239 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.16 % Allowed : 24.48 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.30), residues: 716 helix: 1.26 (0.29), residues: 297 sheet: 0.21 (0.44), residues: 140 loop : -1.85 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 66 TYR 0.011 0.001 TYR A 414 PHE 0.009 0.001 PHE B 47 TRP 0.014 0.001 TRP A 246 HIS 0.005 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.23 ( 6075) covalent geometry : angle 0.59614 / 0.30 ( 8253) SS BOND : bond 0.00010 / 0.01 ( 1) SS BOND : angle 0.11703 / 0.07 ( 2) hydrogen bonds : bond 0.14436 / 10.17 ( 304) hydrogen bonds : angle 6.16027 / 4.31 ( 852) link_BETA1-3 : bond 0.00333 / 0.18 ( 1) link_BETA1-3 : angle 1.43960 / 0.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.252 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 0.0548 time to fit residues: 3.6160 Evaluate side-chains 42 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.0170 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.174500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127229 restraints weight = 6465.259| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.04 r_work: 0.3252 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6077 Z= 0.120 Angle : 0.475 5.823 8258 Z= 0.256 Chirality : 0.041 0.161 908 Planarity : 0.003 0.048 1017 Dihedral : 5.732 44.776 928 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.92 % Allowed : 22.24 % Favored : 75.84 % 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 are not related in a simple way. whole: 0.07 (0.31), residues: 716 helix: 1.36 (0.28), residues: 305 sheet: 0.36 (0.43), residues: 145 loop : -1.74 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 71 TYR 0.011 0.001 TYR A 414 PHE 0.007 0.001 PHE A 476 TRP 0.013 0.001 TRP A 246 HIS 0.001 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 6075) covalent geometry : angle 0.47261 / 0.26 ( 8253) SS BOND : bond 0.00236 / 0.12 ( 1) SS BOND : angle 0.59374 / 0.35 ( 2) hydrogen bonds : bond 0.04229 / 2.73 ( 304) hydrogen bonds : angle 4.76993 / 3.37 ( 852) link_BETA1-3 : bond 0.00526 / 0.28 ( 1) link_BETA1-3 : angle 2.54067 / 1.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.132 Fit side-chains REVERT: A 472 TRP cc_start: 0.7913 (t60) cc_final: 0.7681 (t60) REVERT: C 67 PHE cc_start: 0.6496 (m-10) cc_final: 0.6156 (m-10) outliers start: 12 outliers final: 5 residues processed: 57 average time/residue: 0.0504 time to fit residues: 4.2133 Evaluate side-chains 48 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.167330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.119005 restraints weight = 6499.382| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.10 r_work: 0.3179 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 6077 Z= 0.242 Angle : 0.557 7.477 8258 Z= 0.298 Chirality : 0.045 0.150 908 Planarity : 0.004 0.047 1017 Dihedral : 5.861 48.793 928 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.20 % Allowed : 21.92 % Favored : 74.88 % 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 are not related in a simple way. whole: -0.31 (0.30), residues: 716 helix: 0.89 (0.28), residues: 305 sheet: 0.05 (0.44), residues: 151 loop : -1.67 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 71 TYR 0.015 0.001 TYR A 216 PHE 0.014 0.001 PHE A 369 TRP 0.014 0.001 TRP A 246 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.24 ( 6075) covalent geometry : angle 0.55609 / 0.30 ( 8253) SS BOND : bond 0.00434 / 0.23 ( 1) SS BOND : angle 0.39433 / 0.23 ( 2) hydrogen bonds : bond 0.04710 / 3.03 ( 304) hydrogen bonds : angle 4.72035 / 3.34 ( 852) link_BETA1-3 : bond 0.00383 / 0.20 ( 1) link_BETA1-3 : angle 2.13764 / 1.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.139 Fit side-chains REVERT: C 67 PHE cc_start: 0.6625 (m-10) cc_final: 0.6228 (m-10) outliers start: 20 outliers final: 13 residues processed: 69 average time/residue: 0.0598 time to fit residues: 5.8717 Evaluate side-chains 62 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.171395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123507 restraints weight = 6449.126| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.10 r_work: 0.3235 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6077 Z= 0.121 Angle : 0.466 8.234 8258 Z= 0.249 Chirality : 0.041 0.150 908 Planarity : 0.003 0.045 1017 Dihedral : 5.292 44.924 928 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.72 % Allowed : 22.72 % Favored : 74.56 % 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 are not related in a simple way. whole: 0.05 (0.31), residues: 716 helix: 1.30 (0.29), residues: 303 sheet: 0.42 (0.44), residues: 145 loop : -1.69 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 71 TYR 0.011 0.001 TYR A 414 PHE 0.008 0.001 PHE A 476 TRP 0.014 0.001 TRP A 246 HIS 0.005 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 6075) covalent geometry : angle 0.46450 / 0.25 ( 8253) SS BOND : bond 0.00034 / 0.02 ( 1) SS BOND : angle 0.11205 / 0.06 ( 2) hydrogen bonds : bond 0.03919 / 2.51 ( 304) hydrogen bonds : angle 4.41755 / 3.13 ( 852) link_BETA1-3 : bond 0.00530 / 0.28 ( 1) link_BETA1-3 : angle 2.12869 / 1.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.123 Fit side-chains REVERT: C 67 PHE cc_start: 0.6565 (m-10) cc_final: 0.6239 (m-10) outliers start: 17 outliers final: 9 residues processed: 60 average time/residue: 0.0454 time to fit residues: 3.9455 Evaluate side-chains 52 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 0.9980 chunk 67 optimal weight: 0.1980 chunk 34 optimal weight: 0.0570 chunk 3 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.170591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122462 restraints weight = 6491.631| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.08 r_work: 0.3278 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6077 Z= 0.102 Angle : 0.436 5.367 8258 Z= 0.234 Chirality : 0.040 0.138 908 Planarity : 0.003 0.044 1017 Dihedral : 5.049 45.267 928 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.72 % Allowed : 22.72 % Favored : 74.56 % 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 are not related in a simple way. whole: 0.31 (0.31), residues: 716 helix: 1.50 (0.29), residues: 308 sheet: 0.24 (0.44), residues: 151 loop : -1.43 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 66 TYR 0.010 0.001 TYR A 414 PHE 0.015 0.001 PHE B 67 TRP 0.012 0.001 TRP A 246 HIS 0.005 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 6075) covalent geometry : angle 0.43463 / 0.23 ( 8253) SS BOND : bond 0.00065 / 0.03 ( 1) SS BOND : angle 0.25990 / 0.15 ( 2) hydrogen bonds : bond 0.03646 / 2.33 ( 304) hydrogen bonds : angle 4.24931 / 3.01 ( 852) link_BETA1-3 : bond 0.00443 / 0.23 ( 1) link_BETA1-3 : angle 2.00439 / 1.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.159 Fit side-chains REVERT: C 67 PHE cc_start: 0.6430 (m-10) cc_final: 0.6146 (m-10) outliers start: 17 outliers final: 10 residues processed: 58 average time/residue: 0.0419 time to fit residues: 3.8166 Evaluate side-chains 53 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 0.0570 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 195 HIS ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.170177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.121984 restraints weight = 6423.982| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.07 r_work: 0.3267 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6077 Z= 0.114 Angle : 0.443 5.376 8258 Z= 0.238 Chirality : 0.041 0.134 908 Planarity : 0.003 0.044 1017 Dihedral : 4.991 45.599 928 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.08 % Allowed : 23.84 % Favored : 74.08 % 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 are not related in a simple way. whole: 0.33 (0.31), residues: 716 helix: 1.55 (0.29), residues: 308 sheet: 0.20 (0.44), residues: 151 loop : -1.41 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 66 TYR 0.011 0.001 TYR A 414 PHE 0.010 0.001 PHE A 476 TRP 0.012 0.001 TRP A 246 HIS 0.004 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 6075) covalent geometry : angle 0.44190 / 0.24 ( 8253) SS BOND : bond 0.00014 / 0.01 ( 1) SS BOND : angle 0.04620 / 0.03 ( 2) hydrogen bonds : bond 0.03662 / 2.34 ( 304) hydrogen bonds : angle 4.20812 / 2.98 ( 852) link_BETA1-3 : bond 0.00504 / 0.27 ( 1) link_BETA1-3 : angle 1.93335 / 1.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.177 Fit side-chains REVERT: C 67 PHE cc_start: 0.6463 (m-10) cc_final: 0.6190 (m-10) outliers start: 13 outliers final: 12 residues processed: 54 average time/residue: 0.0485 time to fit residues: 4.0126 Evaluate side-chains 54 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 38 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 22 optimal weight: 0.0050 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 0.0770 chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 195 HIS ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.170913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122901 restraints weight = 6416.075| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.05 r_work: 0.3280 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6077 Z= 0.106 Angle : 0.434 5.638 8258 Z= 0.234 Chirality : 0.040 0.132 908 Planarity : 0.003 0.044 1017 Dihedral : 4.925 45.148 928 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.56 % Allowed : 22.88 % Favored : 74.56 % 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 are not related in a simple way. whole: 0.39 (0.31), residues: 716 helix: 1.63 (0.29), residues: 308 sheet: 0.20 (0.44), residues: 151 loop : -1.40 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 66 TYR 0.011 0.001 TYR A 414 PHE 0.008 0.001 PHE A 476 TRP 0.012 0.001 TRP A 246 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 6075) covalent geometry : angle 0.43281 / 0.23 ( 8253) SS BOND : bond 0.00012 / 0.01 ( 1) SS BOND : angle 0.16411 / 0.09 ( 2) hydrogen bonds : bond 0.03587 / 2.29 ( 304) hydrogen bonds : angle 4.15823 / 2.95 ( 852) link_BETA1-3 : bond 0.00519 / 0.27 ( 1) link_BETA1-3 : angle 1.91092 / 1.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.213 Fit side-chains REVERT: C 67 PHE cc_start: 0.6453 (m-10) cc_final: 0.6193 (m-10) outliers start: 16 outliers final: 11 residues processed: 57 average time/residue: 0.0547 time to fit residues: 4.5455 Evaluate side-chains 55 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 69 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 195 HIS ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.170531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.122429 restraints weight = 6385.195| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.06 r_work: 0.3270 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6077 Z= 0.115 Angle : 0.442 6.353 8258 Z= 0.236 Chirality : 0.041 0.130 908 Planarity : 0.003 0.044 1017 Dihedral : 4.929 45.369 928 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.72 % Allowed : 22.24 % Favored : 75.04 % 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 are not related in a simple way. whole: 0.39 (0.31), residues: 716 helix: 1.58 (0.29), residues: 309 sheet: 0.22 (0.44), residues: 151 loop : -1.38 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 66 TYR 0.011 0.001 TYR A 414 PHE 0.008 0.001 PHE A 476 TRP 0.012 0.001 TRP A 246 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 6075) covalent geometry : angle 0.44078 / 0.24 ( 8253) SS BOND : bond 0.00016 / 0.01 ( 1) SS BOND : angle 0.19237 / 0.10 ( 2) hydrogen bonds : bond 0.03602 / 2.30 ( 304) hydrogen bonds : angle 4.14519 / 2.94 ( 852) link_BETA1-3 : bond 0.00509 / 0.27 ( 1) link_BETA1-3 : angle 1.88865 / 1.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.205 Fit side-chains REVERT: A 80 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7820 (p0) REVERT: C 67 PHE cc_start: 0.6466 (m-10) cc_final: 0.6211 (m-10) outliers start: 17 outliers final: 13 residues processed: 58 average time/residue: 0.0473 time to fit residues: 4.2318 Evaluate side-chains 57 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 46 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.170485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122406 restraints weight = 6397.041| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.05 r_work: 0.3271 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6077 Z= 0.115 Angle : 0.444 7.123 8258 Z= 0.237 Chirality : 0.041 0.130 908 Planarity : 0.003 0.044 1017 Dihedral : 4.926 45.315 928 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.40 % Allowed : 22.56 % Favored : 75.04 % 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 are not related in a simple way. whole: 0.41 (0.31), residues: 716 helix: 1.60 (0.29), residues: 309 sheet: 0.22 (0.44), residues: 151 loop : -1.36 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 66 TYR 0.011 0.001 TYR A 414 PHE 0.008 0.001 PHE A 476 TRP 0.012 0.001 TRP A 246 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 6075) covalent geometry : angle 0.44246 / 0.24 ( 8253) SS BOND : bond 0.00011 / 0.01 ( 1) SS BOND : angle 0.21092 / 0.11 ( 2) hydrogen bonds : bond 0.03603 / 2.29 ( 304) hydrogen bonds : angle 4.14465 / 2.94 ( 852) link_BETA1-3 : bond 0.00531 / 0.28 ( 1) link_BETA1-3 : angle 1.87089 / 1.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.123 Fit side-chains REVERT: A 140 ASP cc_start: 0.7868 (p0) cc_final: 0.7654 (p0) REVERT: C 67 PHE cc_start: 0.6418 (m-10) cc_final: 0.6161 (m-10) outliers start: 15 outliers final: 13 residues processed: 56 average time/residue: 0.0375 time to fit residues: 3.2491 Evaluate side-chains 58 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.174572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122743 restraints weight = 6535.686| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.41 r_work: 0.3401 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6077 Z= 0.108 Angle : 0.441 7.826 8258 Z= 0.235 Chirality : 0.040 0.130 908 Planarity : 0.003 0.044 1017 Dihedral : 4.893 45.020 928 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.40 % Allowed : 22.40 % Favored : 75.20 % 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 are not related in a simple way. whole: 0.45 (0.31), residues: 716 helix: 1.64 (0.29), residues: 309 sheet: 0.08 (0.43), residues: 158 loop : -1.26 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 66 TYR 0.011 0.001 TYR A 414 PHE 0.007 0.001 PHE A 476 TRP 0.012 0.001 TRP A 246 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 6075) covalent geometry : angle 0.43956 / 0.23 ( 8253) SS BOND : bond 0.00003 / 0.00 ( 1) SS BOND : angle 0.15959 / 0.09 ( 2) hydrogen bonds : bond 0.03559 / 2.27 ( 304) hydrogen bonds : angle 4.12459 / 2.93 ( 852) link_BETA1-3 : bond 0.00482 / 0.25 ( 1) link_BETA1-3 : angle 1.85633 / 1.04 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.197 Fit side-chains REVERT: A 140 ASP cc_start: 0.8018 (p0) cc_final: 0.7806 (p0) REVERT: C 67 PHE cc_start: 0.6335 (m-10) cc_final: 0.6082 (m-10) outliers start: 15 outliers final: 12 residues processed: 55 average time/residue: 0.0475 time to fit residues: 4.0719 Evaluate side-chains 57 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 10 optimal weight: 0.0770 chunk 28 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.0060 chunk 29 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 overall best weight: 0.5354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.175144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123345 restraints weight = 6506.964| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.39 r_work: 0.3391 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6077 Z= 0.102 Angle : 0.436 7.820 8258 Z= 0.233 Chirality : 0.040 0.131 908 Planarity : 0.003 0.044 1017 Dihedral : 4.855 44.781 928 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.08 % Allowed : 22.72 % Favored : 75.20 % 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 are not related in a simple way. whole: 0.53 (0.31), residues: 716 helix: 1.72 (0.29), residues: 308 sheet: 0.18 (0.43), residues: 156 loop : -1.25 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 66 TYR 0.011 0.001 TYR A 414 PHE 0.007 0.001 PHE A 476 TRP 0.012 0.001 TRP A 246 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 6075) covalent geometry : angle 0.43503 / 0.23 ( 8253) SS BOND : bond 0.00020 / 0.01 ( 1) SS BOND : angle 0.13009 / 0.07 ( 2) hydrogen bonds : bond 0.03507 / 2.23 ( 304) hydrogen bonds : angle 4.09894 / 2.91 ( 852) link_BETA1-3 : bond 0.00521 / 0.27 ( 1) link_BETA1-3 : angle 1.83556 / 1.03 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1599.21 seconds wall clock time: 28 minutes 5.81 seconds (1685.81 seconds total)