Starting phenix.real_space_refine on Fri Oct 10 13:17:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8snc_40622/10_2025/8snc_40622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8snc_40622/10_2025/8snc_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_40622/10_2025/8snc_40622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8snc_40622/10_2025/8snc_40622.map" model { file = "/net/cci-nas-00/data/ceres_data/8snc_40622/10_2025/8snc_40622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8snc_40622/10_2025/8snc_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/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, 38 Unusual residues: {' MN': 2, 'Y01': 1} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Time building chain proxies: 1.35, 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: 0.53 Conformation dependent library (CDL) restraints added in 319.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.25 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: 0.92 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 2.320 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 2.320 nonbonded pdb=" OD2 ASP A 203 " pdb="MN MN A 602 " model vdw 2.262 2.320 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: 1.190 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.920 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 aren 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 covalent geometry : bond 0.00470 ( 6075) covalent geometry : angle 0.59614 ( 8253) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.11703 ( 2) hydrogen bonds : bond 0.14436 ( 304) hydrogen bonds : angle 6.16027 ( 852) link_BETA1-3 : bond 0.00333 ( 1) link_BETA1-3 : angle 1.43960 ( 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 : 0.147 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 0.0655 time to fit residues: 4.2161 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 : 0.196 ------------------------------------------------------------------------------- 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: 0.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3925 r_free = 0.3925 target = 0.174635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127336 restraints weight = 6467.066| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.04 r_work: 0.3251 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6077 Z= 0.117 Angle : 0.472 5.913 8258 Z= 0.254 Chirality : 0.041 0.149 908 Planarity : 0.003 0.048 1017 Dihedral : 5.746 44.790 928 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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 aren not related in a simple way. whole: 0.06 (0.31), residues: 716 helix: 1.35 (0.28), residues: 305 sheet: 0.38 (0.44), 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 0.002 0.001 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6075) covalent geometry : angle 0.46976 ( 8253) SS BOND : bond 0.00219 ( 1) SS BOND : angle 0.58658 ( 2) hydrogen bonds : bond 0.04291 ( 304) hydrogen bonds : angle 4.77880 ( 852) link_BETA1-3 : bond 0.00541 ( 1) link_BETA1-3 : angle 2.50754 ( 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 : 0.219 Fit side-chains REVERT: A 472 TRP cc_start: 0.7908 (t60) cc_final: 0.7676 (t60) REVERT: C 67 PHE cc_start: 0.6467 (m-10) cc_final: 0.6064 (m-10) outliers start: 12 outliers final: 5 residues processed: 57 average time/residue: 0.0617 time to fit residues: 5.0783 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 : 0.204 ------------------------------------------------------------------------------- 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: 6.9990 chunk 55 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3831 r_free = 0.3831 target = 0.163395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.113124 restraints weight = 6602.914| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.22 r_work: 0.3130 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 6077 Z= 0.330 Angle : 0.623 6.738 8258 Z= 0.334 Chirality : 0.048 0.162 908 Planarity : 0.004 0.049 1017 Dihedral : 6.276 51.082 928 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.84 % Allowed : 21.60 % 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 aren not related in a simple way. whole: -0.58 (0.30), residues: 716 helix: 0.59 (0.28), residues: 305 sheet: -0.02 (0.44), residues: 151 loop : -1.73 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 83 TYR 0.017 0.002 TYR A 216 PHE 0.017 0.002 PHE A 369 TRP 0.015 0.001 TRP A 246 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00794 ( 6075) covalent geometry : angle 0.62128 ( 8253) SS BOND : bond 0.00554 ( 1) SS BOND : angle 0.44724 ( 2) hydrogen bonds : bond 0.05124 ( 304) hydrogen bonds : angle 4.87688 ( 852) link_BETA1-3 : bond 0.00746 ( 1) link_BETA1-3 : angle 2.17991 ( 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 74 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 50 time to evaluate : 0.216 Fit side-chains REVERT: A 44 SER cc_start: 0.7331 (t) cc_final: 0.6591 (p) REVERT: A 237 ASP cc_start: 0.8175 (p0) cc_final: 0.7879 (p0) REVERT: C 67 PHE cc_start: 0.6680 (m-10) cc_final: 0.6334 (m-10) outliers start: 24 outliers final: 15 residues processed: 73 average time/residue: 0.0523 time to fit residues: 5.5722 Evaluate side-chains 64 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 162 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 512 VAL 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: 2.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3909 r_free = 0.3909 target = 0.170589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121698 restraints weight = 6530.485| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.15 r_work: 0.3215 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.0986 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= 0.137 Angle : 0.488 8.141 8258 Z= 0.261 Chirality : 0.042 0.150 908 Planarity : 0.003 0.045 1017 Dihedral : 5.523 45.615 928 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.88 % Allowed : 22.56 % 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 aren not related in a simple way. whole: -0.21 (0.31), residues: 716 helix: 1.07 (0.28), residues: 303 sheet: 0.02 (0.44), residues: 147 loop : -1.65 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 71 TYR 0.012 0.001 TYR A 414 PHE 0.009 0.001 PHE A 476 TRP 0.015 0.001 TRP A 246 HIS 0.005 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6075) covalent geometry : angle 0.48636 ( 8253) SS BOND : bond 0.00173 ( 1) SS BOND : angle 0.22366 ( 2) hydrogen bonds : bond 0.04108 ( 304) hydrogen bonds : angle 4.51813 ( 852) link_BETA1-3 : bond 0.00615 ( 1) link_BETA1-3 : angle 2.16588 ( 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 64 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.221 Fit side-chains REVERT: C 67 PHE cc_start: 0.6650 (m-10) cc_final: 0.6315 (m-10) outliers start: 18 outliers final: 9 residues processed: 62 average time/residue: 0.0579 time to fit residues: 5.2885 Evaluate side-chains 55 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 0.0570 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3928 r_free = 0.3928 target = 0.172273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123207 restraints weight = 6569.386| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.19 r_work: 0.3241 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 0.028 6077 Z= 0.116 Angle : 0.463 8.354 8258 Z= 0.247 Chirality : 0.041 0.139 908 Planarity : 0.003 0.044 1017 Dihedral : 5.227 46.173 928 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.40 % Allowed : 22.72 % 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 aren not related in a simple way. whole: 0.10 (0.31), residues: 716 helix: 1.32 (0.28), residues: 308 sheet: 0.10 (0.44), residues: 151 loop : -1.50 (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 0.017 0.001 PHE B 67 TRP 0.013 0.001 TRP A 246 HIS 0.002 0.001 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6075) covalent geometry : angle 0.46183 ( 8253) SS BOND : bond 0.00027 ( 1) SS BOND : angle 0.16283 ( 2) hydrogen bonds : bond 0.03813 ( 304) hydrogen bonds : angle 4.33361 ( 852) link_BETA1-3 : bond 0.00479 ( 1) link_BETA1-3 : angle 2.03635 ( 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 62 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.148 Fit side-chains REVERT: C 67 PHE cc_start: 0.6669 (m-10) cc_final: 0.6375 (m-10) outliers start: 15 outliers final: 10 residues processed: 59 average time/residue: 0.0578 time to fit residues: 4.8619 Evaluate side-chains 56 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 380 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 33 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 7.9990 chunk 12 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.0020 overall best weight: 0.3086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3930 r_free = 0.3930 target = 0.172699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.125148 restraints weight = 6414.464| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.04 r_work: 0.3316 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6077 Z= 0.092 Angle : 0.427 5.350 8258 Z= 0.231 Chirality : 0.040 0.134 908 Planarity : 0.003 0.044 1017 Dihedral : 4.870 44.572 928 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.56 % Allowed : 23.20 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.31), residues: 716 helix: 1.67 (0.29), residues: 308 sheet: 0.54 (0.45), residues: 145 loop : -1.46 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 66 TYR 0.009 0.001 TYR A 414 PHE 0.006 0.001 PHE A 476 TRP 0.011 0.001 TRP A 246 HIS 0.002 0.000 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00183 ( 6075) covalent geometry : angle 0.42517 ( 8253) SS BOND : bond 0.00252 ( 1) SS BOND : angle 0.32301 ( 2) hydrogen bonds : bond 0.03402 ( 304) hydrogen bonds : angle 4.15063 ( 852) link_BETA1-3 : bond 0.00530 ( 1) link_BETA1-3 : angle 1.99644 ( 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 59 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.175 Fit side-chains REVERT: A 346 TRP cc_start: 0.7365 (t60) cc_final: 0.6269 (t60) REVERT: C 67 PHE cc_start: 0.6392 (m-10) cc_final: 0.6136 (m-10) outliers start: 16 outliers final: 9 residues processed: 58 average time/residue: 0.0509 time to fit residues: 4.5378 Evaluate side-chains 51 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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 119 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 120 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 38 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 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 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 = 0.3918 r_free = 0.3918 target = 0.171396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.123475 restraints weight = 6427.609| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.07 r_work: 0.3290 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1402 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= 0.104 Angle : 0.435 5.573 8258 Z= 0.234 Chirality : 0.040 0.133 908 Planarity : 0.003 0.044 1017 Dihedral : 4.854 45.531 928 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % 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 aren not related in a simple way. whole: 0.47 (0.31), residues: 716 helix: 1.69 (0.29), residues: 308 sheet: 0.26 (0.44), residues: 151 loop : -1.37 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 66 TYR 0.010 0.001 TYR A 414 PHE 0.006 0.001 PHE A 476 TRP 0.012 0.001 TRP A 246 HIS 0.005 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 6075) covalent geometry : angle 0.43410 ( 8253) SS BOND : bond 0.00036 ( 1) SS BOND : angle 0.35365 ( 2) hydrogen bonds : bond 0.03503 ( 304) hydrogen bonds : angle 4.12377 ( 852) link_BETA1-3 : bond 0.00380 ( 1) link_BETA1-3 : angle 1.88975 ( 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 55 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.226 Fit side-chains REVERT: C 67 PHE cc_start: 0.6449 (m-10) cc_final: 0.6207 (m-10) outliers start: 13 outliers final: 11 residues processed: 53 average time/residue: 0.0513 time to fit residues: 4.1911 Evaluate side-chains 53 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 80 ASN Chi-restraints excluded: chain A residue 119 VAL 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 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: 0.7980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3915 r_free = 0.3915 target = 0.170983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122178 restraints weight = 6400.664| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.14 r_work: 0.3267 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1418 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 : 0.446 6.370 8258 Z= 0.238 Chirality : 0.041 0.130 908 Planarity : 0.003 0.044 1017 Dihedral : 4.882 45.609 928 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.56 % Allowed : 23.04 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.31), residues: 716 helix: 1.65 (0.29), residues: 308 sheet: 0.27 (0.44), residues: 151 loop : -1.35 (0.37), residues: 257 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 0.010 0.001 PHE A 476 TRP 0.011 0.001 TRP A 246 HIS 0.005 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 6075) covalent geometry : angle 0.44432 ( 8253) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.41823 ( 2) hydrogen bonds : bond 0.03556 ( 304) hydrogen bonds : angle 4.12832 ( 852) link_BETA1-3 : bond 0.00473 ( 1) link_BETA1-3 : angle 1.86746 ( 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 63 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.202 Fit side-chains REVERT: A 144 LYS cc_start: 0.8827 (ttmt) cc_final: 0.8298 (mttp) REVERT: C 67 PHE cc_start: 0.6502 (m-10) cc_final: 0.6260 (m-10) outliers start: 16 outliers final: 13 residues processed: 59 average time/residue: 0.0569 time to fit residues: 4.9278 Evaluate side-chains 60 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 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 A residue 381 VAL 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 121 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4084 r_free = 0.4084 target = 0.173614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121951 restraints weight = 6550.330| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.40 r_work: 0.3368 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1411 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= 0.124 Angle : 0.451 7.156 8258 Z= 0.241 Chirality : 0.041 0.130 908 Planarity : 0.003 0.044 1017 Dihedral : 4.930 45.732 928 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.24 % Allowed : 23.04 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.31), residues: 716 helix: 1.61 (0.29), residues: 308 sheet: 0.33 (0.44), residues: 149 loop : -1.34 (0.37), residues: 259 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 0.009 0.001 PHE A 476 TRP 0.011 0.001 TRP A 246 HIS 0.005 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6075) covalent geometry : angle 0.45017 ( 8253) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.46056 ( 2) hydrogen bonds : bond 0.03617 ( 304) hydrogen bonds : angle 4.13612 ( 852) link_BETA1-3 : bond 0.00465 ( 1) link_BETA1-3 : angle 1.85564 ( 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 63 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.142 Fit side-chains REVERT: A 140 ASP cc_start: 0.8019 (p0) cc_final: 0.7785 (p0) REVERT: A 438 MET cc_start: 0.8258 (tpp) cc_final: 0.7968 (tpp) REVERT: C 67 PHE cc_start: 0.6342 (m-10) cc_final: 0.5827 (m-10) REVERT: C 82 MET cc_start: 0.5817 (mmt) cc_final: 0.5400 (mmt) outliers start: 14 outliers final: 12 residues processed: 60 average time/residue: 0.0580 time to fit residues: 5.2342 Evaluate side-chains 60 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 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 A residue 381 VAL Chi-restraints excluded: chain B residue 20 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4077 r_free = 0.4077 target = 0.172710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122415 restraints weight = 6531.707| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.31 r_work: 0.3388 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1455 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 : 0.449 7.812 8258 Z= 0.239 Chirality : 0.041 0.130 908 Planarity : 0.003 0.044 1017 Dihedral : 4.923 45.328 928 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.24 % Allowed : 22.88 % 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 aren not related in a simple way. whole: 0.48 (0.31), residues: 716 helix: 1.64 (0.29), residues: 308 sheet: 0.33 (0.44), residues: 150 loop : -1.31 (0.37), residues: 258 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 0.005 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6075) covalent geometry : angle 0.44808 ( 8253) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.47572 ( 2) hydrogen bonds : bond 0.03580 ( 304) hydrogen bonds : angle 4.12624 ( 852) link_BETA1-3 : bond 0.00466 ( 1) link_BETA1-3 : angle 1.84267 ( 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 60 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.218 Fit side-chains REVERT: A 438 MET cc_start: 0.8219 (tpp) cc_final: 0.7897 (tpp) REVERT: C 67 PHE cc_start: 0.6376 (m-10) cc_final: 0.5858 (m-10) REVERT: C 82 MET cc_start: 0.5801 (mmt) cc_final: 0.5384 (mmt) outliers start: 14 outliers final: 13 residues processed: 57 average time/residue: 0.0543 time to fit residues: 4.7672 Evaluate side-chains 59 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 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 A residue 381 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 14 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4090 r_free = 0.4090 target = 0.174275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122625 restraints weight = 6536.272| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.40 r_work: 0.3380 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1474 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= 0.109 Angle : 0.444 7.794 8258 Z= 0.237 Chirality : 0.040 0.130 908 Planarity : 0.003 0.044 1017 Dihedral : 4.902 45.134 928 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.56 % Allowed : 22.72 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.31), residues: 716 helix: 1.67 (0.29), residues: 308 sheet: 0.39 (0.44), residues: 149 loop : -1.32 (0.37), residues: 259 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 0.004 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6075) covalent geometry : angle 0.44320 ( 8253) SS BOND : bond 0.00040 ( 1) SS BOND : angle 0.46607 ( 2) hydrogen bonds : bond 0.03545 ( 304) hydrogen bonds : angle 4.10715 ( 852) link_BETA1-3 : bond 0.00523 ( 1) link_BETA1-3 : angle 1.82688 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1698.87 seconds wall clock time: 29 minutes 51.29 seconds (1791.29 seconds total)