Starting phenix.real_space_refine on Fri Oct 10 17:51:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k77_36935/10_2025/8k77_36935.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k77_36935/10_2025/8k77_36935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k77_36935/10_2025/8k77_36935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k77_36935/10_2025/8k77_36935.map" model { file = "/net/cci-nas-00/data/ceres_data/8k77_36935/10_2025/8k77_36935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k77_36935/10_2025/8k77_36935.cif" } resolution = 3.11 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= 1.097 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: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 5294 2.51 5 N 1362 2.21 5 O 1489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s 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: 8192 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4674 Classifications: {'peptide': 592} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 576} Chain breaks: 1 Chain: "B" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3437 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 411} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'NAG': 2, 'VLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.97, per 1000 atoms: 0.24 Number of scatterers: 8192 At special positions: 0 Unit cell: (84.66, 83.83, 146.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1489 8.00 N 1362 7.00 C 5294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 BETA1-4 " NAG C 1 " - " NAG C 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 801 " - " ASN A 498 " " NAG A 802 " - " ASN A 548 " " NAG C 1 " - " ASN A 573 " Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 406.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1866 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 5 sheets defined 43.5% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 137 through 160 Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.700A pdb=" N ASP A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 197 Proline residue: A 191 - end of helix removed outlier: 4.108A pdb=" N LYS A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 4.435A pdb=" N VAL A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 220 " --> pdb=" O MET A 216 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 250 Processing helix chain 'A' and resid 255 through 271 removed outlier: 4.491A pdb=" N GLY A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.568A pdb=" N ILE A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 284 No H-bonds generated for 'chain 'A' and resid 283 through 284' Processing helix chain 'A' and resid 285 through 288 removed outlier: 3.711A pdb=" N LYS A 288 " --> pdb=" O ALA A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.826A pdb=" N MET A 301 " --> pdb=" O CYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.725A pdb=" N VAL A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.669A pdb=" N PHE A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 386 Processing helix chain 'A' and resid 419 through 439 Processing helix chain 'A' and resid 444 through 483 Proline residue: A 469 - end of helix Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 593 through 619 removed outlier: 3.729A pdb=" N VAL A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 609 " --> pdb=" O THR A 605 " (cutoff:3.500A) Proline residue: A 610 - end of helix removed outlier: 3.530A pdb=" N ILE A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 642 removed outlier: 3.836A pdb=" N MET A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 676 removed outlier: 3.791A pdb=" N ILE A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 707 Processing helix chain 'A' and resid 712 through 731 removed outlier: 4.000A pdb=" N ILE A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 933 removed outlier: 3.888A pdb=" N VAL B 933 " --> pdb=" O ASN B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 958 removed outlier: 3.639A pdb=" N LEU B 958 " --> pdb=" O LYS B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1092 Processing helix chain 'B' and resid 1265 through 1273 Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 492 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 485 through 492 current: chain 'A' and resid 514 through 527 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 514 through 527 current: chain 'B' and resid 1142 through 1144 Processing sheet with id=AA2, first strand: chain 'B' and resid 877 through 884 removed outlier: 3.720A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 887 through 890 current: chain 'B' and resid 914 through 917 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 914 through 917 current: chain 'B' and resid 1015 through 1021 removed outlier: 3.856A pdb=" N ASP B1037 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE B1031 " --> pdb=" O LEU B1035 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU B1035 " --> pdb=" O ILE B1031 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 897 through 900 removed outlier: 7.659A pdb=" N MET B1054 " --> pdb=" O CYS B 967 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS B 967 " --> pdb=" O MET B1054 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LYS B1056 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE B 965 " --> pdb=" O LYS B1056 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N THR B 963 " --> pdb=" O LEU B 978 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU B 978 " --> pdb=" O THR B 963 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP B 974 " --> pdb=" O CYS B 967 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1112 through 1115 Processing sheet with id=AA5, first strand: chain 'B' and resid 1122 through 1125 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1134 through 1137 current: chain 'B' and resid 1179 through 1186 removed outlier: 5.618A pdb=" N ILE B1182 " --> pdb=" O LEU B1193 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1189 through 1194 current: chain 'B' and resid 1232 through 1240 removed outlier: 27.341A pdb=" N ASN B1233 " --> pdb=" O LEU B1254 " (cutoff:3.500A) removed outlier: 23.656A pdb=" N LEU B1254 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 15.969A pdb=" N CYS B1235 " --> pdb=" O PHE B1252 " (cutoff:3.500A) removed outlier: 11.261A pdb=" N PHE B1252 " --> pdb=" O CYS B1235 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N MET B1237 " --> pdb=" O ILE B1250 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 2 1.18 - 1.34: 2535 1.34 - 1.49: 2386 1.49 - 1.65: 3387 1.65 - 1.81: 76 Bond restraints: 8386 Sorted by residual: bond pdb=" CG PRO A 343 " pdb=" CD PRO A 343 " ideal model delta sigma weight residual 1.503 1.158 0.345 3.40e-02 8.65e+02 1.03e+02 bond pdb=" CB PRO A 343 " pdb=" CG PRO A 343 " ideal model delta sigma weight residual 1.492 1.021 0.471 5.00e-02 4.00e+02 8.89e+01 bond pdb=" C6 VLX A 803 " pdb=" N1 VLX A 803 " ideal model delta sigma weight residual 1.351 1.500 -0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" C9 VLX A 803 " pdb=" N2 VLX A 803 " ideal model delta sigma weight residual 1.339 1.448 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" N PRO A 343 " pdb=" CA PRO A 343 " ideal model delta sigma weight residual 1.471 1.525 -0.054 1.32e-02 5.74e+03 1.67e+01 ... (remaining 8381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 11336 14.77 - 29.54: 2 29.54 - 44.31: 0 44.31 - 59.08: 0 59.08 - 73.85: 1 Bond angle restraints: 11339 Sorted by residual: angle pdb=" CB PRO A 343 " pdb=" CG PRO A 343 " pdb=" CD PRO A 343 " ideal model delta sigma weight residual 106.10 179.95 -73.85 3.20e+00 9.77e-02 5.33e+02 angle pdb=" N PRO A 343 " pdb=" CD PRO A 343 " pdb=" CG PRO A 343 " ideal model delta sigma weight residual 103.20 76.47 26.73 1.50e+00 4.44e-01 3.18e+02 angle pdb=" CA PRO A 343 " pdb=" CB PRO A 343 " pdb=" CG PRO A 343 " ideal model delta sigma weight residual 104.50 75.32 29.18 1.90e+00 2.77e-01 2.36e+02 angle pdb=" CA PRO A 343 " pdb=" N PRO A 343 " pdb=" CD PRO A 343 " ideal model delta sigma weight residual 112.00 101.62 10.38 1.40e+00 5.10e-01 5.50e+01 angle pdb=" N PRO A 343 " pdb=" CA PRO A 343 " pdb=" C PRO A 343 " ideal model delta sigma weight residual 113.84 120.10 -6.26 1.30e+00 5.92e-01 2.32e+01 ... (remaining 11334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 4257 16.65 - 33.31: 502 33.31 - 49.96: 161 49.96 - 66.62: 34 66.62 - 83.27: 15 Dihedral angle restraints: 4969 sinusoidal: 2046 harmonic: 2923 Sorted by residual: dihedral pdb=" CA ASP A 528 " pdb=" CB ASP A 528 " pdb=" CG ASP A 528 " pdb=" OD1 ASP A 528 " ideal model delta sinusoidal sigma weight residual -30.00 -84.32 54.32 1 2.00e+01 2.50e-03 1.00e+01 dihedral pdb=" CA ASP A 620 " pdb=" CB ASP A 620 " pdb=" CG ASP A 620 " pdb=" OD1 ASP A 620 " ideal model delta sinusoidal sigma weight residual -30.00 -84.03 54.03 1 2.00e+01 2.50e-03 9.90e+00 dihedral pdb=" CG ARG B 996 " pdb=" CD ARG B 996 " pdb=" NE ARG B 996 " pdb=" CZ ARG B 996 " ideal model delta sinusoidal sigma weight residual 90.00 132.49 -42.49 2 1.50e+01 4.44e-03 9.73e+00 ... (remaining 4966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1217 0.113 - 0.226: 26 0.226 - 0.338: 1 0.338 - 0.451: 0 0.451 - 0.564: 1 Chirality restraints: 1245 Sorted by residual: chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 498 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.94e+00 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 548 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.53e+00 ... (remaining 1242 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 440 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO A 441 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO A 441 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 441 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 342 " -0.071 5.00e-02 4.00e+02 9.80e-02 1.54e+01 pdb=" N PRO A 343 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 343 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 343 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 343 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C PRO A 343 " -0.044 2.00e-02 2.50e+03 pdb=" O PRO A 343 " 0.016 2.00e-02 2.50e+03 pdb=" N SER A 344 " 0.015 2.00e-02 2.50e+03 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 223 2.71 - 3.26: 8033 3.26 - 3.80: 13167 3.80 - 4.35: 16905 4.35 - 4.90: 28823 Nonbonded interactions: 67151 Sorted by model distance: nonbonded pdb=" O GLY B1129 " pdb=" OG SER B1207 " model vdw 2.160 3.040 nonbonded pdb=" OH TYR A 279 " pdb=" O PRO A 355 " model vdw 2.180 3.040 nonbonded pdb=" OH TYR B 934 " pdb=" O GLU B 939 " model vdw 2.206 3.040 nonbonded pdb=" NH2 ARG B 903 " pdb=" OH TYR B 905 " model vdw 2.234 3.120 nonbonded pdb=" OG1 THR B1195 " pdb=" O ILE B1205 " model vdw 2.263 3.040 ... (remaining 67146 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.660 Find NCS groups from input model: 0.030 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.471 8391 Z= 0.261 Angle : 0.996 73.852 11354 Z= 0.452 Chirality : 0.047 0.564 1245 Planarity : 0.005 0.106 1428 Dihedral : 16.518 83.272 3103 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 19.11 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.80 (0.27), residues: 1006 helix: 1.90 (0.26), residues: 407 sheet: 0.20 (0.33), residues: 243 loop : -0.79 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 903 TYR 0.016 0.001 TYR A 306 PHE 0.019 0.001 PHE A 342 TRP 0.010 0.001 TRP A 467 HIS 0.003 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00787 ( 8386) covalent geometry : angle 0.98710 (11339) hydrogen bonds : bond 0.09896 ( 367) hydrogen bonds : angle 5.23426 ( 1071) link_BETA1-4 : bond 0.00740 ( 1) link_BETA1-4 : angle 1.04347 ( 3) link_BETA1-6 : bond 0.00317 ( 1) link_BETA1-6 : angle 1.22969 ( 3) link_NAG-ASN : bond 0.00659 ( 3) link_NAG-ASN : angle 4.86935 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.0991 time to fit residues: 13.8058 Evaluate side-chains 105 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.0000 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 ASN ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 ASN B 960 ASN B 970 ASN B1003 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.205342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.160925 restraints weight = 9085.306| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.36 r_work: 0.3619 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8391 Z= 0.118 Angle : 0.491 7.934 11354 Z= 0.261 Chirality : 0.044 0.410 1245 Planarity : 0.003 0.059 1428 Dihedral : 5.626 56.419 1226 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.16 % Allowed : 16.72 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.27), residues: 1006 helix: 2.39 (0.26), residues: 412 sheet: 0.24 (0.33), residues: 237 loop : -0.73 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1175 TYR 0.012 0.001 TYR A 306 PHE 0.010 0.001 PHE A 499 TRP 0.010 0.001 TRP A 467 HIS 0.005 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8386) covalent geometry : angle 0.47780 (11339) hydrogen bonds : bond 0.04105 ( 367) hydrogen bonds : angle 4.21549 ( 1071) link_BETA1-4 : bond 0.00548 ( 1) link_BETA1-4 : angle 0.47009 ( 3) link_BETA1-6 : bond 0.00532 ( 1) link_BETA1-6 : angle 1.02288 ( 3) link_NAG-ASN : bond 0.00532 ( 3) link_NAG-ASN : angle 3.93904 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.6207 (mtt) cc_final: 0.5067 (ttm) REVERT: A 442 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7645 (mt-10) REVERT: A 535 TYR cc_start: 0.8337 (t80) cc_final: 0.8065 (t80) REVERT: B 1058 ASP cc_start: 0.7409 (m-30) cc_final: 0.7100 (m-30) outliers start: 19 outliers final: 8 residues processed: 124 average time/residue: 0.1017 time to fit residues: 17.0090 Evaluate side-chains 112 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1270 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 62 optimal weight: 0.0170 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN A 354 GLN A 504 GLN B1003 GLN B1022 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.203974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.159269 restraints weight = 9027.529| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.37 r_work: 0.3629 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8391 Z= 0.118 Angle : 0.483 7.180 11354 Z= 0.257 Chirality : 0.043 0.333 1245 Planarity : 0.003 0.041 1428 Dihedral : 5.363 52.208 1226 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.50 % Allowed : 17.06 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.27), residues: 1006 helix: 2.41 (0.26), residues: 412 sheet: 0.21 (0.33), residues: 237 loop : -0.74 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1175 TYR 0.013 0.001 TYR A 306 PHE 0.010 0.001 PHE A 499 TRP 0.009 0.001 TRP A 467 HIS 0.004 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8386) covalent geometry : angle 0.47221 (11339) hydrogen bonds : bond 0.04074 ( 367) hydrogen bonds : angle 4.15272 ( 1071) link_BETA1-4 : bond 0.00503 ( 1) link_BETA1-4 : angle 0.60001 ( 3) link_BETA1-6 : bond 0.00588 ( 1) link_BETA1-6 : angle 1.05518 ( 3) link_NAG-ASN : bond 0.00474 ( 3) link_NAG-ASN : angle 3.57609 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.6307 (mtt) cc_final: 0.5067 (ttm) REVERT: A 442 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 523 SER cc_start: 0.8723 (m) cc_final: 0.8304 (p) REVERT: A 742 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7073 (tm-30) REVERT: B 1058 ASP cc_start: 0.7416 (m-30) cc_final: 0.7067 (m-30) REVERT: B 1085 LYS cc_start: 0.7576 (tppp) cc_final: 0.7146 (tppt) outliers start: 22 outliers final: 13 residues processed: 123 average time/residue: 0.1082 time to fit residues: 17.7320 Evaluate side-chains 118 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1270 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 94 optimal weight: 0.0770 chunk 63 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 988 GLN B1003 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.200767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.156693 restraints weight = 9151.776| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.35 r_work: 0.3619 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8391 Z= 0.114 Angle : 0.462 6.656 11354 Z= 0.247 Chirality : 0.042 0.311 1245 Planarity : 0.003 0.034 1428 Dihedral : 5.009 47.389 1226 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.07 % Allowed : 17.18 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.27), residues: 1006 helix: 2.48 (0.26), residues: 411 sheet: 0.19 (0.33), residues: 237 loop : -0.72 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1064 TYR 0.013 0.001 TYR A 306 PHE 0.011 0.001 PHE A 599 TRP 0.010 0.001 TRP A 467 HIS 0.004 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8386) covalent geometry : angle 0.45179 (11339) hydrogen bonds : bond 0.03957 ( 367) hydrogen bonds : angle 4.08945 ( 1071) link_BETA1-4 : bond 0.00455 ( 1) link_BETA1-4 : angle 0.58099 ( 3) link_BETA1-6 : bond 0.00479 ( 1) link_BETA1-6 : angle 1.02016 ( 3) link_NAG-ASN : bond 0.00459 ( 3) link_NAG-ASN : angle 3.34525 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.6401 (mtt) cc_final: 0.5128 (ttm) REVERT: A 442 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7748 (mt-10) REVERT: A 523 SER cc_start: 0.8755 (m) cc_final: 0.8316 (p) REVERT: A 742 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7220 (tm-30) REVERT: B 1058 ASP cc_start: 0.7445 (m-30) cc_final: 0.7098 (m-30) REVERT: B 1085 LYS cc_start: 0.7585 (tppp) cc_final: 0.7182 (tppt) REVERT: B 1094 SER cc_start: 0.7985 (p) cc_final: 0.7602 (t) outliers start: 27 outliers final: 17 residues processed: 129 average time/residue: 0.1047 time to fit residues: 18.1541 Evaluate side-chains 120 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 988 GLN Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1270 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 88 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1003 GLN B1233 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.201269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.156543 restraints weight = 9055.365| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.35 r_work: 0.3578 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8391 Z= 0.135 Angle : 0.478 6.351 11354 Z= 0.255 Chirality : 0.043 0.303 1245 Planarity : 0.003 0.030 1428 Dihedral : 4.917 47.001 1226 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.41 % Allowed : 17.06 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.27), residues: 1006 helix: 2.46 (0.26), residues: 413 sheet: 0.18 (0.33), residues: 236 loop : -0.71 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1064 TYR 0.015 0.001 TYR A 306 PHE 0.011 0.001 PHE A 459 TRP 0.010 0.001 TRP A 467 HIS 0.004 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8386) covalent geometry : angle 0.46871 (11339) hydrogen bonds : bond 0.04185 ( 367) hydrogen bonds : angle 4.11865 ( 1071) link_BETA1-4 : bond 0.00654 ( 1) link_BETA1-4 : angle 0.58087 ( 3) link_BETA1-6 : bond 0.00467 ( 1) link_BETA1-6 : angle 1.06984 ( 3) link_NAG-ASN : bond 0.00434 ( 3) link_NAG-ASN : angle 3.24154 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6449 (mtt) cc_final: 0.5145 (ttm) REVERT: A 442 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7733 (mt-10) REVERT: A 471 MET cc_start: 0.7834 (tpp) cc_final: 0.7634 (tpt) REVERT: A 523 SER cc_start: 0.8776 (m) cc_final: 0.8339 (p) REVERT: A 742 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7411 (tm-30) REVERT: B 1058 ASP cc_start: 0.7389 (m-30) cc_final: 0.7040 (m-30) REVERT: B 1085 LYS cc_start: 0.7584 (tppp) cc_final: 0.7159 (tppt) REVERT: B 1094 SER cc_start: 0.8117 (p) cc_final: 0.7742 (t) outliers start: 30 outliers final: 21 residues processed: 131 average time/residue: 0.1068 time to fit residues: 18.6084 Evaluate side-chains 128 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1226 LYS Chi-restraints excluded: chain B residue 1270 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 4.9990 chunk 92 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 65 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.201469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.156405 restraints weight = 9018.197| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.27 r_work: 0.3579 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8391 Z= 0.123 Angle : 0.475 7.250 11354 Z= 0.254 Chirality : 0.042 0.300 1245 Planarity : 0.003 0.029 1428 Dihedral : 4.735 46.514 1226 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.84 % Allowed : 17.86 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.28), residues: 1006 helix: 2.46 (0.26), residues: 412 sheet: 0.18 (0.33), residues: 236 loop : -0.67 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1064 TYR 0.014 0.001 TYR A 306 PHE 0.015 0.001 PHE A 499 TRP 0.010 0.001 TRP A 467 HIS 0.004 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8386) covalent geometry : angle 0.46635 (11339) hydrogen bonds : bond 0.04045 ( 367) hydrogen bonds : angle 4.11764 ( 1071) link_BETA1-4 : bond 0.00662 ( 1) link_BETA1-4 : angle 0.69767 ( 3) link_BETA1-6 : bond 0.00506 ( 1) link_BETA1-6 : angle 1.11851 ( 3) link_NAG-ASN : bond 0.00479 ( 3) link_NAG-ASN : angle 3.09586 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6471 (mtt) cc_final: 0.5037 (ttm) REVERT: A 442 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7741 (mt-10) REVERT: A 523 SER cc_start: 0.8735 (m) cc_final: 0.8342 (p) REVERT: A 693 CYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8088 (t) REVERT: B 1058 ASP cc_start: 0.7461 (m-30) cc_final: 0.7123 (m-30) REVERT: B 1087 LEU cc_start: 0.6973 (tp) cc_final: 0.6715 (tp) REVERT: B 1094 SER cc_start: 0.8120 (p) cc_final: 0.7770 (t) outliers start: 25 outliers final: 21 residues processed: 125 average time/residue: 0.0965 time to fit residues: 16.5041 Evaluate side-chains 127 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 693 CYS Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1226 LYS Chi-restraints excluded: chain B residue 1270 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 13 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 14 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.200704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.155725 restraints weight = 9103.008| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.26 r_work: 0.3595 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8391 Z= 0.120 Angle : 0.470 6.515 11354 Z= 0.251 Chirality : 0.042 0.285 1245 Planarity : 0.003 0.030 1428 Dihedral : 4.600 45.274 1226 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.19 % Allowed : 17.97 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.27), residues: 1006 helix: 2.46 (0.26), residues: 412 sheet: 0.16 (0.34), residues: 231 loop : -0.69 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 163 TYR 0.014 0.001 TYR A 306 PHE 0.012 0.001 PHE A 499 TRP 0.010 0.001 TRP A 467 HIS 0.005 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8386) covalent geometry : angle 0.46228 (11339) hydrogen bonds : bond 0.04000 ( 367) hydrogen bonds : angle 4.10976 ( 1071) link_BETA1-4 : bond 0.00619 ( 1) link_BETA1-4 : angle 0.46559 ( 3) link_BETA1-6 : bond 0.00478 ( 1) link_BETA1-6 : angle 1.09823 ( 3) link_NAG-ASN : bond 0.00449 ( 3) link_NAG-ASN : angle 2.97447 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6387 (mtt) cc_final: 0.4917 (ttm) REVERT: A 442 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7811 (mt-10) REVERT: A 523 SER cc_start: 0.8735 (m) cc_final: 0.8341 (p) REVERT: B 1058 ASP cc_start: 0.7486 (m-30) cc_final: 0.7114 (m-30) REVERT: B 1077 LYS cc_start: 0.6746 (OUTLIER) cc_final: 0.6536 (mttp) outliers start: 28 outliers final: 23 residues processed: 127 average time/residue: 0.0929 time to fit residues: 16.2690 Evaluate side-chains 129 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1077 LYS Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1226 LYS Chi-restraints excluded: chain B residue 1270 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 97 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 74 optimal weight: 0.0770 chunk 82 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.202237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.157474 restraints weight = 9060.194| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.26 r_work: 0.3592 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8391 Z= 0.101 Angle : 0.465 6.655 11354 Z= 0.246 Chirality : 0.042 0.281 1245 Planarity : 0.003 0.030 1428 Dihedral : 4.449 44.535 1226 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.39 % Allowed : 19.11 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.27), residues: 1006 helix: 2.54 (0.26), residues: 410 sheet: 0.19 (0.34), residues: 230 loop : -0.71 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 491 TYR 0.011 0.001 TYR A 306 PHE 0.012 0.001 PHE A 499 TRP 0.010 0.001 TRP A 467 HIS 0.004 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8386) covalent geometry : angle 0.45802 (11339) hydrogen bonds : bond 0.03669 ( 367) hydrogen bonds : angle 4.03463 ( 1071) link_BETA1-4 : bond 0.00630 ( 1) link_BETA1-4 : angle 0.69085 ( 3) link_BETA1-6 : bond 0.00453 ( 1) link_BETA1-6 : angle 1.04189 ( 3) link_NAG-ASN : bond 0.00536 ( 3) link_NAG-ASN : angle 2.88894 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7800 (mt-10) REVERT: A 523 SER cc_start: 0.8724 (m) cc_final: 0.8277 (p) REVERT: B 903 ARG cc_start: 0.7787 (mmm160) cc_final: 0.7028 (mmm160) REVERT: B 1058 ASP cc_start: 0.7465 (m-30) cc_final: 0.7099 (m-30) REVERT: B 1064 ARG cc_start: 0.6922 (mtt180) cc_final: 0.6331 (ttt180) REVERT: B 1085 LYS cc_start: 0.7555 (tppp) cc_final: 0.7315 (tppt) outliers start: 21 outliers final: 19 residues processed: 124 average time/residue: 0.0915 time to fit residues: 15.7436 Evaluate side-chains 123 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1226 LYS Chi-restraints excluded: chain B residue 1270 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 80 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1003 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.200027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.155328 restraints weight = 9049.224| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.36 r_work: 0.3564 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8391 Z= 0.130 Angle : 0.492 7.295 11354 Z= 0.260 Chirality : 0.042 0.276 1245 Planarity : 0.003 0.029 1428 Dihedral : 4.561 43.643 1226 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.62 % Allowed : 19.11 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.27), residues: 1006 helix: 2.46 (0.26), residues: 411 sheet: 0.25 (0.35), residues: 208 loop : -0.71 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 491 TYR 0.015 0.001 TYR A 306 PHE 0.013 0.001 PHE A 499 TRP 0.009 0.001 TRP A 333 HIS 0.004 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8386) covalent geometry : angle 0.48544 (11339) hydrogen bonds : bond 0.04086 ( 367) hydrogen bonds : angle 4.09413 ( 1071) link_BETA1-4 : bond 0.00597 ( 1) link_BETA1-4 : angle 0.51904 ( 3) link_BETA1-6 : bond 0.00545 ( 1) link_BETA1-6 : angle 1.17263 ( 3) link_NAG-ASN : bond 0.00447 ( 3) link_NAG-ASN : angle 2.82923 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6356 (mtt) cc_final: 0.4846 (ttm) REVERT: A 375 LYS cc_start: 0.7141 (tmtt) cc_final: 0.6108 (ttmm) REVERT: A 523 SER cc_start: 0.8753 (m) cc_final: 0.8316 (p) REVERT: B 903 ARG cc_start: 0.7834 (mmm160) cc_final: 0.7625 (mmm160) REVERT: B 1058 ASP cc_start: 0.7450 (m-30) cc_final: 0.7082 (m-30) REVERT: B 1064 ARG cc_start: 0.6875 (mtt180) cc_final: 0.6176 (ttt180) REVERT: B 1077 LYS cc_start: 0.6745 (OUTLIER) cc_final: 0.6521 (mttp) REVERT: B 1245 ASN cc_start: 0.7788 (m-40) cc_final: 0.7159 (t0) outliers start: 23 outliers final: 20 residues processed: 117 average time/residue: 0.0872 time to fit residues: 14.2895 Evaluate side-chains 121 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1077 LYS Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1226 LYS Chi-restraints excluded: chain B residue 1270 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 93 optimal weight: 3.9990 chunk 90 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.200482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.156003 restraints weight = 8903.092| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.24 r_work: 0.3597 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8391 Z= 0.115 Angle : 0.480 7.498 11354 Z= 0.254 Chirality : 0.042 0.265 1245 Planarity : 0.003 0.029 1428 Dihedral : 4.432 43.066 1226 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.62 % Allowed : 19.23 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.27), residues: 1006 helix: 2.46 (0.26), residues: 411 sheet: 0.20 (0.34), residues: 227 loop : -0.73 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1064 TYR 0.013 0.001 TYR A 306 PHE 0.013 0.001 PHE A 499 TRP 0.010 0.001 TRP A 333 HIS 0.004 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8386) covalent geometry : angle 0.47421 (11339) hydrogen bonds : bond 0.03809 ( 367) hydrogen bonds : angle 4.03874 ( 1071) link_BETA1-4 : bond 0.00655 ( 1) link_BETA1-4 : angle 0.44578 ( 3) link_BETA1-6 : bond 0.00410 ( 1) link_BETA1-6 : angle 1.11660 ( 3) link_NAG-ASN : bond 0.00481 ( 3) link_NAG-ASN : angle 2.67637 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6327 (mtt) cc_final: 0.4687 (ttm) REVERT: A 375 LYS cc_start: 0.7166 (tmtt) cc_final: 0.6101 (ttmm) REVERT: A 523 SER cc_start: 0.8733 (m) cc_final: 0.8317 (p) REVERT: B 903 ARG cc_start: 0.7774 (mmm160) cc_final: 0.7530 (mmm160) REVERT: B 1058 ASP cc_start: 0.7462 (m-30) cc_final: 0.7097 (m-30) REVERT: B 1064 ARG cc_start: 0.6888 (mtt180) cc_final: 0.6322 (ttt180) REVERT: B 1077 LYS cc_start: 0.6757 (OUTLIER) cc_final: 0.6527 (mttp) REVERT: B 1085 LYS cc_start: 0.7585 (tppp) cc_final: 0.7342 (tppt) REVERT: B 1188 ASN cc_start: 0.7601 (m110) cc_final: 0.7328 (t0) outliers start: 23 outliers final: 21 residues processed: 117 average time/residue: 0.0900 time to fit residues: 14.7059 Evaluate side-chains 122 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain B residue 1077 LYS Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1226 LYS Chi-restraints excluded: chain B residue 1270 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 0.0970 chunk 92 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 0.0670 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1038 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.202269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.157384 restraints weight = 9032.751| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.26 r_work: 0.3611 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8391 Z= 0.103 Angle : 0.465 7.479 11354 Z= 0.248 Chirality : 0.042 0.265 1245 Planarity : 0.003 0.029 1428 Dihedral : 4.280 42.281 1226 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.28 % Allowed : 20.14 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.27), residues: 1006 helix: 2.51 (0.26), residues: 411 sheet: 0.25 (0.35), residues: 227 loop : -0.71 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 491 TYR 0.011 0.001 TYR A 598 PHE 0.012 0.001 PHE A 499 TRP 0.009 0.001 TRP A 333 HIS 0.004 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 8386) covalent geometry : angle 0.45913 (11339) hydrogen bonds : bond 0.03601 ( 367) hydrogen bonds : angle 3.99027 ( 1071) link_BETA1-4 : bond 0.00626 ( 1) link_BETA1-4 : angle 0.41496 ( 3) link_BETA1-6 : bond 0.00439 ( 1) link_BETA1-6 : angle 1.12626 ( 3) link_NAG-ASN : bond 0.00514 ( 3) link_NAG-ASN : angle 2.59376 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2150.25 seconds wall clock time: 37 minutes 43.42 seconds (2263.42 seconds total)