Starting phenix.real_space_refine on Sun May 11 16:43:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k77_36935/05_2025/8k77_36935.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k77_36935/05_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_36935/05_2025/8k77_36935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k77_36935/05_2025/8k77_36935.map" model { file = "/net/cci-nas-00/data/ceres_data/8k77_36935/05_2025/8k77_36935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k77_36935/05_2025/8k77_36935.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.40, per 1000 atoms: 0.66 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: 2.53 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.80 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: 2.43 Time building geometry restraints manager: 2.82 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.480 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.570 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (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 TRP 0.010 0.001 TRP A 467 HIS 0.003 0.001 HIS A 494 PHE 0.019 0.001 PHE A 342 TYR 0.016 0.001 TYR A 306 ARG 0.014 0.001 ARG B 903 Details of bonding type rmsd link_NAG-ASN : bond 0.00659 ( 3) link_NAG-ASN : angle 4.86935 ( 9) link_BETA1-4 : bond 0.00740 ( 1) link_BETA1-4 : angle 1.04347 ( 3) hydrogen bonds : bond 0.09896 ( 367) hydrogen bonds : angle 5.23426 ( 1071) link_BETA1-6 : bond 0.00317 ( 1) link_BETA1-6 : angle 1.22969 ( 3) covalent geometry : bond 0.00787 ( 8386) covalent geometry : angle 0.98710 (11339) *********************** 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 : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2389 time to fit residues: 33.2320 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 : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.4980 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 0.0470 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 0.0570 chunk 91 optimal weight: 5.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS A 434 ASN A 504 GLN A 568 ASN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 ASN B 988 GLN B1003 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.206212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.162281 restraints weight = 8994.027| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.33 r_work: 0.3655 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 8391 Z= 0.111 Angle : 0.485 8.120 11354 Z= 0.259 Chirality : 0.043 0.418 1245 Planarity : 0.003 0.062 1428 Dihedral : 5.591 52.919 1226 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.93 % Allowed : 17.29 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.27), residues: 1006 helix: 2.43 (0.26), residues: 412 sheet: 0.21 (0.33), residues: 243 loop : -0.69 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 467 HIS 0.005 0.001 HIS A 494 PHE 0.010 0.001 PHE A 459 TYR 0.011 0.001 TYR A 306 ARG 0.002 0.000 ARG A 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 3) link_NAG-ASN : angle 3.94874 ( 9) link_BETA1-4 : bond 0.00475 ( 1) link_BETA1-4 : angle 0.44939 ( 3) hydrogen bonds : bond 0.04047 ( 367) hydrogen bonds : angle 4.21379 ( 1071) link_BETA1-6 : bond 0.00562 ( 1) link_BETA1-6 : angle 0.98585 ( 3) covalent geometry : bond 0.00241 ( 8386) covalent geometry : angle 0.47250 (11339) *********************** 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 123 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 442 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7669 (mt-10) REVERT: A 535 TYR cc_start: 0.8307 (t80) cc_final: 0.7954 (t80) REVERT: B 903 ARG cc_start: 0.7436 (mmm160) cc_final: 0.7080 (mmm160) REVERT: B 1058 ASP cc_start: 0.7413 (m-30) cc_final: 0.7099 (m-30) outliers start: 17 outliers final: 8 residues processed: 118 average time/residue: 0.2162 time to fit residues: 34.6884 Evaluate side-chains 113 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 988 GLN 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 64 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 88 optimal weight: 0.0270 chunk 24 optimal weight: 0.8980 chunk 58 optimal weight: 0.0670 chunk 29 optimal weight: 0.8980 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN B1022 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.204015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.160109 restraints weight = 9019.941| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.21 r_work: 0.3645 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8391 Z= 0.110 Angle : 0.470 7.234 11354 Z= 0.250 Chirality : 0.042 0.337 1245 Planarity : 0.003 0.042 1428 Dihedral : 5.314 55.765 1226 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.05 % Allowed : 17.18 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.27), residues: 1006 helix: 2.49 (0.26), residues: 411 sheet: 0.23 (0.33), residues: 237 loop : -0.71 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 467 HIS 0.005 0.001 HIS A 494 PHE 0.009 0.001 PHE A 499 TYR 0.012 0.001 TYR A 306 ARG 0.002 0.000 ARG B1175 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 3) link_NAG-ASN : angle 3.57391 ( 9) link_BETA1-4 : bond 0.00677 ( 1) link_BETA1-4 : angle 0.60227 ( 3) hydrogen bonds : bond 0.03917 ( 367) hydrogen bonds : angle 4.11550 ( 1071) link_BETA1-6 : bond 0.00537 ( 1) link_BETA1-6 : angle 0.99991 ( 3) covalent geometry : bond 0.00243 ( 8386) covalent geometry : angle 0.45871 (11339) *********************** 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 126 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.6315 (mtt) cc_final: 0.5073 (ttm) REVERT: A 442 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7665 (mt-10) REVERT: A 742 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7064 (tm-30) REVERT: B 903 ARG cc_start: 0.7495 (mmm160) cc_final: 0.7291 (mmm160) REVERT: B 988 GLN cc_start: 0.7352 (tt0) cc_final: 0.7036 (tt0) REVERT: B 1058 ASP cc_start: 0.7446 (m-30) cc_final: 0.7104 (m-30) REVERT: B 1085 LYS cc_start: 0.7594 (tppp) cc_final: 0.7169 (tppt) outliers start: 18 outliers final: 12 residues processed: 123 average time/residue: 0.2314 time to fit residues: 38.3039 Evaluate side-chains 112 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 954 SER Chi-restraints excluded: chain B residue 977 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 2 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 0.0040 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN B1003 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.203446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.158914 restraints weight = 9099.822| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.34 r_work: 0.3622 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8391 Z= 0.120 Angle : 0.471 6.742 11354 Z= 0.252 Chirality : 0.043 0.314 1245 Planarity : 0.003 0.035 1428 Dihedral : 5.027 47.338 1226 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.19 % Allowed : 16.72 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.27), residues: 1006 helix: 2.47 (0.26), residues: 412 sheet: 0.22 (0.33), residues: 236 loop : -0.68 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 467 HIS 0.004 0.001 HIS A 494 PHE 0.011 0.001 PHE A 459 TYR 0.014 0.001 TYR A 306 ARG 0.004 0.000 ARG B1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 3) link_NAG-ASN : angle 3.35944 ( 9) link_BETA1-4 : bond 0.00460 ( 1) link_BETA1-4 : angle 0.50019 ( 3) hydrogen bonds : bond 0.04007 ( 367) hydrogen bonds : angle 4.09063 ( 1071) link_BETA1-6 : bond 0.00568 ( 1) link_BETA1-6 : angle 1.08604 ( 3) covalent geometry : bond 0.00273 ( 8386) covalent geometry : angle 0.46119 (11339) *********************** 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 133 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.6392 (mtt) cc_final: 0.5120 (ttm) REVERT: A 442 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7731 (mt-10) REVERT: A 523 SER cc_start: 0.8757 (m) cc_final: 0.8329 (p) REVERT: A 742 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7251 (tm-30) REVERT: B 1058 ASP cc_start: 0.7401 (m-30) cc_final: 0.7033 (m-30) REVERT: B 1085 LYS cc_start: 0.7596 (tppp) cc_final: 0.7191 (tppt) outliers start: 28 outliers final: 17 residues processed: 124 average time/residue: 0.2251 time to fit residues: 37.4471 Evaluate side-chains 121 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 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 976 VAL Chi-restraints excluded: chain B residue 977 SER 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 91 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN B1003 GLN B1233 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.200204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.155335 restraints weight = 9029.393| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.34 r_work: 0.3562 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8391 Z= 0.149 Angle : 0.492 6.303 11354 Z= 0.262 Chirality : 0.043 0.305 1245 Planarity : 0.003 0.030 1428 Dihedral : 5.005 47.107 1226 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.19 % Allowed : 16.95 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.27), residues: 1006 helix: 2.48 (0.26), residues: 410 sheet: 0.20 (0.33), residues: 236 loop : -0.68 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 467 HIS 0.004 0.001 HIS A 494 PHE 0.012 0.001 PHE A 459 TYR 0.017 0.001 TYR A 306 ARG 0.003 0.000 ARG B 903 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 3) link_NAG-ASN : angle 3.25474 ( 9) link_BETA1-4 : bond 0.00618 ( 1) link_BETA1-4 : angle 0.50117 ( 3) hydrogen bonds : bond 0.04408 ( 367) hydrogen bonds : angle 4.17182 ( 1071) link_BETA1-6 : bond 0.00430 ( 1) link_BETA1-6 : angle 1.07695 ( 3) covalent geometry : bond 0.00351 ( 8386) covalent geometry : angle 0.48351 (11339) *********************** 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 137 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6434 (mtt) cc_final: 0.5125 (ttm) REVERT: A 442 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7771 (mt-10) REVERT: A 523 SER cc_start: 0.8773 (m) cc_final: 0.8365 (p) REVERT: B 903 ARG cc_start: 0.7740 (mmm160) cc_final: 0.7519 (mmm160) REVERT: B 1058 ASP cc_start: 0.7400 (m-30) cc_final: 0.7048 (m-30) REVERT: B 1085 LYS cc_start: 0.7555 (tppp) cc_final: 0.7128 (tppt) REVERT: B 1094 SER cc_start: 0.8125 (p) cc_final: 0.7750 (t) outliers start: 28 outliers final: 20 residues processed: 132 average time/residue: 0.2129 time to fit residues: 38.5684 Evaluate side-chains 123 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 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 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 1003 GLN 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 80 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 0.0970 chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN B 988 GLN B1003 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.197080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.152974 restraints weight = 9019.551| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.31 r_work: 0.3490 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8391 Z= 0.181 Angle : 0.523 6.962 11354 Z= 0.280 Chirality : 0.044 0.305 1245 Planarity : 0.003 0.033 1428 Dihedral : 5.217 46.491 1226 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.30 % Allowed : 17.52 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.27), residues: 1006 helix: 2.29 (0.26), residues: 410 sheet: 0.13 (0.34), residues: 216 loop : -0.69 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.005 0.001 HIS A 494 PHE 0.017 0.001 PHE A 499 TYR 0.019 0.002 TYR A 306 ARG 0.003 0.000 ARG B1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 3) link_NAG-ASN : angle 3.22283 ( 9) link_BETA1-4 : bond 0.00682 ( 1) link_BETA1-4 : angle 0.70012 ( 3) hydrogen bonds : bond 0.04808 ( 367) hydrogen bonds : angle 4.32453 ( 1071) link_BETA1-6 : bond 0.00336 ( 1) link_BETA1-6 : angle 1.11361 ( 3) covalent geometry : bond 0.00434 ( 8386) covalent geometry : angle 0.51510 (11339) *********************** 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 136 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6491 (mtt) cc_final: 0.4984 (ttm) REVERT: A 442 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7823 (mt-10) REVERT: A 523 SER cc_start: 0.8746 (m) cc_final: 0.8346 (p) REVERT: A 596 MET cc_start: 0.6411 (tpp) cc_final: 0.6199 (mmm) REVERT: A 693 CYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8090 (t) REVERT: B 1058 ASP cc_start: 0.7507 (m-30) cc_final: 0.7163 (m-30) REVERT: B 1085 LYS cc_start: 0.7474 (tppp) cc_final: 0.7039 (tppt) outliers start: 29 outliers final: 22 residues processed: 128 average time/residue: 0.2406 time to fit residues: 41.3736 Evaluate side-chains 129 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 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 588 THR Chi-restraints excluded: chain A residue 622 ILE 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 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 1003 GLN 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 10 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 77 optimal weight: 0.0870 chunk 90 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.200669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.155829 restraints weight = 8955.908| |-----------------------------------------------------------------------------| r_work (start): 0.3783 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: 0.7736 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8391 Z= 0.109 Angle : 0.473 7.479 11354 Z= 0.253 Chirality : 0.042 0.292 1245 Planarity : 0.003 0.031 1428 Dihedral : 4.791 46.274 1226 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.62 % Allowed : 18.66 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.27), residues: 1006 helix: 2.41 (0.26), residues: 411 sheet: 0.25 (0.34), residues: 211 loop : -0.71 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 467 HIS 0.005 0.001 HIS A 494 PHE 0.013 0.001 PHE A 499 TYR 0.012 0.001 TYR A 306 ARG 0.006 0.000 ARG A 163 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 3) link_NAG-ASN : angle 3.07423 ( 9) link_BETA1-4 : bond 0.00786 ( 1) link_BETA1-4 : angle 0.70471 ( 3) hydrogen bonds : bond 0.03969 ( 367) hydrogen bonds : angle 4.15046 ( 1071) link_BETA1-6 : bond 0.00525 ( 1) link_BETA1-6 : angle 1.09481 ( 3) covalent geometry : bond 0.00239 ( 8386) covalent geometry : angle 0.46492 (11339) *********************** 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 131 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 375 LYS cc_start: 0.6853 (tmtt) cc_final: 0.6051 (ttmm) REVERT: A 442 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7819 (mt-10) REVERT: A 523 SER cc_start: 0.8731 (m) cc_final: 0.8279 (p) REVERT: A 693 CYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8079 (t) REVERT: B 903 ARG cc_start: 0.7786 (mmm160) cc_final: 0.7581 (mmm160) REVERT: B 1058 ASP cc_start: 0.7465 (m-30) cc_final: 0.7117 (m-30) REVERT: B 1064 ARG cc_start: 0.7027 (mtt180) cc_final: 0.6381 (ttt180) REVERT: B 1085 LYS cc_start: 0.7597 (tppp) cc_final: 0.7309 (tppt) outliers start: 23 outliers final: 16 residues processed: 123 average time/residue: 0.2145 time to fit residues: 36.3640 Evaluate side-chains 121 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 464 LEU 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 944 SER Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 977 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.198332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.154233 restraints weight = 9097.303| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.33 r_work: 0.3509 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8391 Z= 0.137 Angle : 0.495 6.890 11354 Z= 0.263 Chirality : 0.043 0.291 1245 Planarity : 0.003 0.030 1428 Dihedral : 4.807 44.529 1226 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.50 % Allowed : 19.11 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.27), residues: 1006 helix: 2.40 (0.26), residues: 412 sheet: 0.19 (0.34), residues: 211 loop : -0.75 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 333 HIS 0.005 0.001 HIS A 494 PHE 0.013 0.001 PHE A 499 TYR 0.015 0.001 TYR A 306 ARG 0.003 0.000 ARG A 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 3) link_NAG-ASN : angle 3.01244 ( 9) link_BETA1-4 : bond 0.00703 ( 1) link_BETA1-4 : angle 0.53049 ( 3) hydrogen bonds : bond 0.04272 ( 367) hydrogen bonds : angle 4.18895 ( 1071) link_BETA1-6 : bond 0.00492 ( 1) link_BETA1-6 : angle 1.14658 ( 3) covalent geometry : bond 0.00319 ( 8386) covalent geometry : angle 0.48715 (11339) *********************** 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 138 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6417 (mtt) cc_final: 0.6202 (mtt) REVERT: A 375 LYS cc_start: 0.6887 (tmtt) cc_final: 0.6069 (ttmm) REVERT: A 442 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7833 (mt-10) REVERT: A 449 MET cc_start: 0.6733 (mtp) cc_final: 0.6493 (mtp) REVERT: A 523 SER cc_start: 0.8772 (m) cc_final: 0.8317 (p) REVERT: A 693 CYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8091 (t) REVERT: B 903 ARG cc_start: 0.7788 (mmm160) cc_final: 0.7532 (mmm160) REVERT: B 1058 ASP cc_start: 0.7441 (m-30) cc_final: 0.7080 (m-30) REVERT: B 1064 ARG cc_start: 0.7014 (mtt180) cc_final: 0.6447 (ttt180) REVERT: B 1077 LYS cc_start: 0.6748 (OUTLIER) cc_final: 0.6531 (mttp) REVERT: B 1085 LYS cc_start: 0.7604 (tppp) cc_final: 0.7316 (tppt) outliers start: 22 outliers final: 18 residues processed: 132 average time/residue: 0.2381 time to fit residues: 41.7361 Evaluate side-chains 133 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 622 ILE 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 944 SER Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 977 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 19 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 99 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 51 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.196972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151487 restraints weight = 9097.061| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.32 r_work: 0.3570 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8391 Z= 0.132 Angle : 0.489 6.875 11354 Z= 0.261 Chirality : 0.043 0.280 1245 Planarity : 0.003 0.030 1428 Dihedral : 4.744 43.771 1226 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.07 % Allowed : 19.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.27), residues: 1006 helix: 2.38 (0.26), residues: 412 sheet: 0.20 (0.35), residues: 208 loop : -0.71 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 467 HIS 0.005 0.001 HIS A 494 PHE 0.012 0.001 PHE A 459 TYR 0.014 0.001 TYR A 306 ARG 0.002 0.000 ARG A 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 3) link_NAG-ASN : angle 2.92482 ( 9) link_BETA1-4 : bond 0.00613 ( 1) link_BETA1-4 : angle 0.47600 ( 3) hydrogen bonds : bond 0.04186 ( 367) hydrogen bonds : angle 4.17880 ( 1071) link_BETA1-6 : bond 0.00394 ( 1) link_BETA1-6 : angle 1.11737 ( 3) covalent geometry : bond 0.00307 ( 8386) covalent geometry : angle 0.48152 (11339) *********************** 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 138 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6352 (mtt) cc_final: 0.6132 (mtt) REVERT: A 375 LYS cc_start: 0.6837 (tmtt) cc_final: 0.6065 (ttpp) REVERT: A 442 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7834 (mt-10) REVERT: A 523 SER cc_start: 0.8742 (m) cc_final: 0.8312 (p) REVERT: A 693 CYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8081 (t) REVERT: B 903 ARG cc_start: 0.7806 (mmm160) cc_final: 0.7573 (mmm160) REVERT: B 1058 ASP cc_start: 0.7447 (m-30) cc_final: 0.7087 (m-30) REVERT: B 1064 ARG cc_start: 0.7010 (mtt180) cc_final: 0.6472 (ttt180) REVERT: B 1077 LYS cc_start: 0.6813 (OUTLIER) cc_final: 0.6591 (mttp) REVERT: B 1085 LYS cc_start: 0.7609 (tppp) cc_final: 0.7320 (tppt) REVERT: B 1188 ASN cc_start: 0.7586 (m110) cc_final: 0.7328 (t0) REVERT: B 1210 GLU cc_start: 0.7564 (mp0) cc_final: 0.7361 (mp0) outliers start: 27 outliers final: 22 residues processed: 131 average time/residue: 0.2518 time to fit residues: 43.3455 Evaluate side-chains 134 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 622 ILE 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 A residue 693 CYS 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 1077 LYS Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1164 LYS Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1226 LYS Chi-restraints excluded: chain B residue 1254 LEU 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 78 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.197403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.152583 restraints weight = 8918.344| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.26 r_work: 0.3578 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8391 Z= 0.123 Angle : 0.483 6.681 11354 Z= 0.258 Chirality : 0.042 0.273 1245 Planarity : 0.003 0.030 1428 Dihedral : 4.649 43.314 1226 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.84 % Allowed : 19.45 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.27), residues: 1006 helix: 2.37 (0.26), residues: 412 sheet: 0.19 (0.35), residues: 208 loop : -0.72 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.005 0.001 HIS A 494 PHE 0.012 0.001 PHE A 499 TYR 0.014 0.001 TYR A 306 ARG 0.002 0.000 ARG A 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 3) link_NAG-ASN : angle 2.79800 ( 9) link_BETA1-4 : bond 0.00566 ( 1) link_BETA1-4 : angle 0.44193 ( 3) hydrogen bonds : bond 0.04044 ( 367) hydrogen bonds : angle 4.13839 ( 1071) link_BETA1-6 : bond 0.00465 ( 1) link_BETA1-6 : angle 1.15978 ( 3) covalent geometry : bond 0.00283 ( 8386) covalent geometry : angle 0.47663 (11339) ********************** 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 136 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6341 (mtt) cc_final: 0.6127 (mtt) REVERT: A 375 LYS cc_start: 0.6858 (tmtt) cc_final: 0.6087 (ttmm) REVERT: A 442 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7848 (mt-10) REVERT: A 523 SER cc_start: 0.8752 (m) cc_final: 0.8334 (p) REVERT: A 693 CYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8086 (t) REVERT: A 742 GLN cc_start: 0.7776 (tm-30) cc_final: 0.6790 (tm-30) REVERT: B 903 ARG cc_start: 0.7815 (mmm160) cc_final: 0.7599 (mmm160) REVERT: B 1058 ASP cc_start: 0.7438 (m-30) cc_final: 0.7080 (m-30) REVERT: B 1077 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6518 (mttp) REVERT: B 1188 ASN cc_start: 0.7595 (m110) cc_final: 0.7321 (t0) REVERT: B 1210 GLU cc_start: 0.7539 (mp0) cc_final: 0.7329 (mp0) outliers start: 25 outliers final: 23 residues processed: 128 average time/residue: 0.2383 time to fit residues: 40.6239 Evaluate side-chains 133 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 622 ILE 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 A residue 693 CYS 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 1077 LYS Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1164 LYS Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1226 LYS Chi-restraints excluded: chain B residue 1254 LEU 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 71 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 7 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.200079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.155528 restraints weight = 9072.531| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.35 r_work: 0.3587 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8391 Z= 0.116 Angle : 0.476 6.730 11354 Z= 0.255 Chirality : 0.042 0.269 1245 Planarity : 0.003 0.030 1428 Dihedral : 4.578 42.725 1226 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.73 % Allowed : 19.45 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.27), residues: 1006 helix: 2.39 (0.26), residues: 410 sheet: 0.20 (0.35), residues: 208 loop : -0.72 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 467 HIS 0.005 0.001 HIS A 494 PHE 0.013 0.001 PHE A 499 TYR 0.013 0.001 TYR A 306 ARG 0.003 0.000 ARG B1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 3) link_NAG-ASN : angle 2.78559 ( 9) link_BETA1-4 : bond 0.00572 ( 1) link_BETA1-4 : angle 0.61481 ( 3) hydrogen bonds : bond 0.03948 ( 367) hydrogen bonds : angle 4.11424 ( 1071) link_BETA1-6 : bond 0.00553 ( 1) link_BETA1-6 : angle 1.06160 ( 3) covalent geometry : bond 0.00264 ( 8386) covalent geometry : angle 0.46983 (11339) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4281.29 seconds wall clock time: 74 minutes 54.43 seconds (4494.43 seconds total)