Starting phenix.real_space_refine on Mon Nov 18 00:40:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opt_17087/11_2024/8opt_17087.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opt_17087/11_2024/8opt_17087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opt_17087/11_2024/8opt_17087.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opt_17087/11_2024/8opt_17087.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opt_17087/11_2024/8opt_17087.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opt_17087/11_2024/8opt_17087.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 54 5.49 5 S 36 5.16 5 C 4781 2.51 5 N 1338 2.21 5 O 1563 1.98 5 H 7197 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14971 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 12651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 12651 Classifications: {'peptide': 783} Link IDs: {'PTRANS': 43, 'TRANS': 739} Chain breaks: 7 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1740 Classifications: {'RNA': 54} Modifications used: {'3*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 26, 'rna3p_pyr': 18} Link IDs: {'rna2p': 10, 'rna3p': 43} Chain: "B" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 578 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 4, 'TRANS': 37} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7018 SG CYS A 965 30.740 58.816 80.274 1.00 76.39 S ATOM 7058 SG CYS A 968 32.244 56.154 82.639 1.00 79.01 S ATOM 7229 SG CYS A 978 28.562 56.027 81.831 1.00 71.28 S ATOM 14423 SG CYS B 139 45.794 36.750 28.084 1.00101.21 S ATOM 14468 SG CYS B 142 49.793 36.545 27.527 1.00103.47 S ATOM 14591 SG CYS B 152 48.043 36.623 31.187 1.00 98.61 S Time building chain proxies: 8.67, per 1000 atoms: 0.58 Number of scatterers: 14971 At special positions: 0 Unit cell: (81.084, 114.636, 142.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 36 16.00 P 54 15.00 O 1563 8.00 N 1338 7.00 C 4781 6.00 H 7197 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 447 " - pdb=" SG CYS A 621 " distance=2.04 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 Time building additional restraints: 4.60 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" ND1 HIS A 973 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 978 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 968 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 965 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 152 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 139 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 142 " Number of angles added : 3 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 6 sheets defined 44.2% alpha, 9.8% beta 6 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 7.92 Creating SS restraints... Processing helix chain 'A' and resid 210 through 227 Processing helix chain 'A' and resid 255 through 265 removed outlier: 3.673A pdb=" N LYS A 264 " --> pdb=" O HIS A 260 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 284 removed outlier: 3.752A pdb=" N LYS A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 307 Processing helix chain 'A' and resid 309 through 328 Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 416 through 430 Processing helix chain 'A' and resid 432 through 448 removed outlier: 3.814A pdb=" N LEU A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.713A pdb=" N LEU A 464 " --> pdb=" O TYR A 460 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 495 removed outlier: 3.890A pdb=" N GLY A 495 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 563 Processing helix chain 'A' and resid 611 through 630 Processing helix chain 'A' and resid 951 through 957 Processing helix chain 'A' and resid 994 through 1013 Processing helix chain 'A' and resid 1015 through 1037 removed outlier: 4.213A pdb=" N ASP A1036 " --> pdb=" O PHE A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1090 removed outlier: 3.591A pdb=" N LYS A1089 " --> pdb=" O ARG A1085 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS A1090 " --> pdb=" O VAL A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1141 removed outlier: 4.373A pdb=" N ASP A1141 " --> pdb=" O TYR A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1158 removed outlier: 4.028A pdb=" N LYS A1145 " --> pdb=" O ASP A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1183 Processing helix chain 'A' and resid 1219 through 1224 removed outlier: 3.731A pdb=" N TYR A1223 " --> pdb=" O GLU A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1247 Processing helix chain 'A' and resid 1266 through 1270 Processing helix chain 'A' and resid 1293 through 1311 Processing helix chain 'A' and resid 1324 through 1330 removed outlier: 3.780A pdb=" N PHE A1329 " --> pdb=" O LYS A1325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 229 through 230 Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 339 removed outlier: 4.555A pdb=" N ASN A 354 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL A 353 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N SER A 410 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE A 355 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG A 399 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ASP A 384 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 498 through 503 removed outlier: 5.455A pdb=" N LEU A 499 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLU A 510 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 596 through 597 removed outlier: 4.492A pdb=" N ASP A 597 " --> pdb=" O SER A 600 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1040 through 1045 removed outlier: 3.844A pdb=" N ASP A1060 " --> pdb=" O PHE A1045 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU A1059 " --> pdb=" O ASP A1119 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N SER A1121 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A1061 " --> pdb=" O SER A1121 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE A1110 " --> pdb=" O ASN A1095 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ASN A1095 " --> pdb=" O PHE A1110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1205 through 1206 removed outlier: 3.677A pdb=" N TRP A1209 " --> pdb=" O VAL A1206 " (cutoff:3.500A) 298 hydrogen bonds defined for protein. 861 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 6.01 Time building geometry restraints manager: 5.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7179 1.03 - 1.23: 55 1.23 - 1.43: 3475 1.43 - 1.62: 4502 1.62 - 1.82: 46 Bond restraints: 15257 Sorted by residual: bond pdb=" CB LYS A 270 " pdb=" CG LYS A 270 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 7.90e-01 bond pdb=" CA ARG A1184 " pdb=" CB ARG A1184 " ideal model delta sigma weight residual 1.533 1.519 0.014 1.66e-02 3.63e+03 7.17e-01 bond pdb=" CB GLU A 222 " pdb=" CG GLU A 222 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.93e-01 bond pdb=" C GLN A1183 " pdb=" N ARG A1184 " ideal model delta sigma weight residual 1.331 1.341 -0.010 1.24e-02 6.50e+03 6.77e-01 bond pdb=" CB GLU A1327 " pdb=" CG GLU A1327 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.76e-01 ... (remaining 15252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 27260 1.78 - 3.57: 326 3.57 - 5.35: 19 5.35 - 7.14: 1 7.14 - 8.92: 1 Bond angle restraints: 27607 Sorted by residual: angle pdb=" CB LYS A 270 " pdb=" CG LYS A 270 " pdb=" CD LYS A 270 " ideal model delta sigma weight residual 111.30 117.96 -6.66 2.30e+00 1.89e-01 8.39e+00 angle pdb=" CA LEU A 214 " pdb=" CB LEU A 214 " pdb=" CG LEU A 214 " ideal model delta sigma weight residual 116.30 125.22 -8.92 3.50e+00 8.16e-02 6.50e+00 angle pdb=" C4' C D 48 " pdb=" C3' C D 48 " pdb=" O3' C D 48 " ideal model delta sigma weight residual 109.40 112.76 -3.36 1.50e+00 4.44e-01 5.02e+00 angle pdb=" C VAL A1206 " pdb=" N ASP A1207 " pdb=" CA ASP A1207 " ideal model delta sigma weight residual 121.54 125.59 -4.05 1.91e+00 2.74e-01 4.50e+00 angle pdb=" CA GLU A 222 " pdb=" CB GLU A 222 " pdb=" CG GLU A 222 " ideal model delta sigma weight residual 114.10 118.09 -3.99 2.00e+00 2.50e-01 3.98e+00 ... (remaining 27602 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.09: 6598 25.09 - 50.18: 475 50.18 - 75.27: 151 75.27 - 100.35: 12 100.35 - 125.44: 3 Dihedral angle restraints: 7239 sinusoidal: 4355 harmonic: 2884 Sorted by residual: dihedral pdb=" C4' C D 48 " pdb=" C3' C D 48 " pdb=" O3' C D 48 " pdb=" P A D 49 " ideal model delta sinusoidal sigma weight residual -110.00 10.20 -120.20 1 3.50e+01 8.16e-04 1.18e+01 dihedral pdb=" CA ASP A 587 " pdb=" CB ASP A 587 " pdb=" CG ASP A 587 " pdb=" OD1 ASP A 587 " ideal model delta sinusoidal sigma weight residual -30.00 -88.33 58.33 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" O4' G D 45 " pdb=" C1' G D 45 " pdb=" N9 G D 45 " pdb=" C4 G D 45 " ideal model delta sinusoidal sigma weight residual 68.00 115.46 -47.46 1 1.70e+01 3.46e-03 1.08e+01 ... (remaining 7236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 852 0.026 - 0.051: 300 0.051 - 0.077: 69 0.077 - 0.103: 41 0.103 - 0.129: 37 Chirality restraints: 1299 Sorted by residual: chirality pdb=" CA VAL A 393 " pdb=" N VAL A 393 " pdb=" C VAL A 393 " pdb=" CB VAL A 393 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE A 229 " pdb=" N ILE A 229 " pdb=" C ILE A 229 " pdb=" CB ILE A 229 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA ILE A1204 " pdb=" N ILE A1204 " pdb=" C ILE A1204 " pdb=" CB ILE A1204 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 1296 not shown) Planarity restraints: 2016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A1207 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" CG ASP A1207 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP A1207 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A1207 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1207 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C ASP A1207 " -0.027 2.00e-02 2.50e+03 pdb=" O ASP A1207 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY A1208 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A1013 " -0.024 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO A1014 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A1014 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1014 " -0.021 5.00e-02 4.00e+02 ... (remaining 2013 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.81: 25 1.81 - 2.51: 11068 2.51 - 3.21: 45244 3.21 - 3.90: 57311 3.90 - 4.60: 87927 Nonbonded interactions: 201575 Sorted by model distance: nonbonded pdb=" HE1 HIS A 973 " pdb="ZN ZN A1501 " model vdw 1.116 1.408 nonbonded pdb=" OE1 GLU A1219 " pdb=" H GLU A1219 " model vdw 1.613 2.450 nonbonded pdb=" OD1 ASN A 567 " pdb=" H ASP A 570 " model vdw 1.620 2.450 nonbonded pdb=" O LEU A 214 " pdb="HE21 GLN A 218 " model vdw 1.628 2.450 nonbonded pdb=" HZ2 LYS A 976 " pdb=" OD1 ASP A 977 " model vdw 1.633 2.450 ... (remaining 201570 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 group one per residue 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: 2.360 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: 0.250 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 48.400 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5878 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 : 0.002 0.031 8060 Z= 0.141 Angle : 0.478 8.923 11169 Z= 0.245 Chirality : 0.035 0.129 1299 Planarity : 0.003 0.037 1217 Dihedral : 19.509 125.444 3359 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.14 % Allowed : 19.27 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.30), residues: 807 helix: 2.97 (0.28), residues: 337 sheet: 0.08 (0.56), residues: 86 loop : 0.04 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 555 HIS 0.002 0.001 HIS A 422 PHE 0.007 0.001 PHE A 955 TYR 0.010 0.001 TYR A1245 ARG 0.005 0.000 ARG A 970 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 107 average time/residue: 0.4524 time to fit residues: 65.9112 Evaluate side-chains 108 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN A1193 GLN B 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8060 Z= 0.271 Angle : 0.542 5.897 11169 Z= 0.286 Chirality : 0.038 0.149 1299 Planarity : 0.004 0.040 1217 Dihedral : 18.951 122.400 1711 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.36 % Allowed : 18.32 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.29), residues: 807 helix: 2.43 (0.28), residues: 341 sheet: -0.27 (0.54), residues: 86 loop : -0.18 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 555 HIS 0.004 0.001 HIS A 973 PHE 0.017 0.002 PHE A1154 TYR 0.015 0.002 TYR A 562 ARG 0.004 0.001 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1141 ASP cc_start: 0.5864 (OUTLIER) cc_final: 0.4161 (m-30) REVERT: A 1248 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.7010 (tm-30) outliers start: 10 outliers final: 5 residues processed: 124 average time/residue: 0.4631 time to fit residues: 77.2136 Evaluate side-chains 122 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1248 GLU Chi-restraints excluded: chain A residue 1276 ILE Chi-restraints excluded: chain A residue 1292 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 0.3980 chunk 70 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A1193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6026 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8060 Z= 0.236 Angle : 0.529 9.717 11169 Z= 0.276 Chirality : 0.037 0.144 1299 Planarity : 0.004 0.042 1217 Dihedral : 18.911 123.858 1709 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.17 % Allowed : 18.72 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.29), residues: 807 helix: 1.89 (0.28), residues: 353 sheet: -0.13 (0.57), residues: 81 loop : -0.30 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 555 HIS 0.005 0.001 HIS A 260 PHE 0.016 0.001 PHE A 462 TYR 0.013 0.002 TYR A 562 ARG 0.003 0.000 ARG A 623 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ILE cc_start: 0.8099 (pt) cc_final: 0.7676 (tt) REVERT: A 1141 ASP cc_start: 0.5714 (OUTLIER) cc_final: 0.4132 (m-30) REVERT: A 1310 VAL cc_start: 0.8161 (p) cc_final: 0.7936 (t) outliers start: 16 outliers final: 13 residues processed: 130 average time/residue: 0.4474 time to fit residues: 78.7211 Evaluate side-chains 129 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1322 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8060 Z= 0.275 Angle : 0.554 6.203 11169 Z= 0.291 Chirality : 0.038 0.146 1299 Planarity : 0.004 0.047 1217 Dihedral : 18.934 124.775 1709 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.26 % Allowed : 18.32 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.29), residues: 807 helix: 1.63 (0.28), residues: 354 sheet: -0.27 (0.57), residues: 81 loop : -0.43 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 555 HIS 0.005 0.001 HIS A 973 PHE 0.018 0.002 PHE A 462 TYR 0.013 0.002 TYR A 562 ARG 0.004 0.000 ARG A 623 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 ASP cc_start: 0.7371 (m-30) cc_final: 0.7131 (m-30) REVERT: A 365 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7409 (tp40) REVERT: A 384 ASP cc_start: 0.7570 (t0) cc_final: 0.7354 (t0) REVERT: A 1141 ASP cc_start: 0.5883 (OUTLIER) cc_final: 0.4125 (m-30) REVERT: A 1310 VAL cc_start: 0.8187 (p) cc_final: 0.7969 (t) outliers start: 24 outliers final: 14 residues processed: 135 average time/residue: 0.4843 time to fit residues: 88.5586 Evaluate side-chains 130 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1322 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 71 optimal weight: 0.0870 chunk 58 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A1193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8060 Z= 0.220 Angle : 0.526 7.880 11169 Z= 0.274 Chirality : 0.037 0.133 1299 Planarity : 0.004 0.046 1217 Dihedral : 18.896 124.696 1709 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.44 % Allowed : 19.00 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.81 (0.29), residues: 807 helix: 1.79 (0.28), residues: 353 sheet: -0.32 (0.58), residues: 81 loop : -0.44 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 555 HIS 0.004 0.001 HIS A 973 PHE 0.016 0.001 PHE A 462 TYR 0.010 0.002 TYR A1245 ARG 0.003 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ILE cc_start: 0.8120 (pt) cc_final: 0.7698 (tt) REVERT: A 356 ASP cc_start: 0.7386 (m-30) cc_final: 0.7133 (m-30) REVERT: A 365 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7369 (tp40) REVERT: A 1141 ASP cc_start: 0.5754 (OUTLIER) cc_final: 0.4096 (m-30) REVERT: A 1298 ASN cc_start: 0.6574 (m-40) cc_final: 0.6360 (m110) REVERT: A 1310 VAL cc_start: 0.8133 (p) cc_final: 0.7925 (t) outliers start: 18 outliers final: 14 residues processed: 132 average time/residue: 0.4505 time to fit residues: 79.9221 Evaluate side-chains 131 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1258 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.9980 chunk 16 optimal weight: 0.0770 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8060 Z= 0.222 Angle : 0.535 7.864 11169 Z= 0.278 Chirality : 0.037 0.134 1299 Planarity : 0.004 0.048 1217 Dihedral : 18.911 124.182 1709 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.71 % Allowed : 18.59 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.29), residues: 807 helix: 1.77 (0.28), residues: 353 sheet: -0.36 (0.58), residues: 81 loop : -0.43 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 555 HIS 0.004 0.001 HIS A 973 PHE 0.015 0.001 PHE A 462 TYR 0.011 0.002 TYR A1245 ARG 0.006 0.000 ARG A 970 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ILE cc_start: 0.8113 (pt) cc_final: 0.7691 (tt) REVERT: A 356 ASP cc_start: 0.7418 (m-30) cc_final: 0.7128 (m-30) REVERT: A 365 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7376 (tp40) REVERT: A 561 PHE cc_start: 0.6793 (t80) cc_final: 0.6453 (t80) REVERT: A 1141 ASP cc_start: 0.5812 (OUTLIER) cc_final: 0.4929 (m-30) REVERT: A 1298 ASN cc_start: 0.6565 (m-40) cc_final: 0.6152 (m110) outliers start: 20 outliers final: 16 residues processed: 135 average time/residue: 0.4819 time to fit residues: 85.3965 Evaluate side-chains 132 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1322 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A1193 GLN ** A1298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6077 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8060 Z= 0.221 Angle : 0.531 8.362 11169 Z= 0.277 Chirality : 0.037 0.134 1299 Planarity : 0.005 0.063 1217 Dihedral : 18.925 123.790 1709 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.85 % Allowed : 18.59 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.77 (0.29), residues: 807 helix: 1.70 (0.28), residues: 353 sheet: -0.37 (0.58), residues: 81 loop : -0.41 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 555 HIS 0.004 0.001 HIS A 973 PHE 0.015 0.001 PHE A 462 TYR 0.011 0.002 TYR A1245 ARG 0.005 0.000 ARG A1294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ILE cc_start: 0.8101 (pt) cc_final: 0.7679 (tt) REVERT: A 365 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7378 (tp40) REVERT: A 382 PHE cc_start: 0.6715 (m-80) cc_final: 0.6463 (m-80) REVERT: A 561 PHE cc_start: 0.6820 (t80) cc_final: 0.6513 (t80) REVERT: A 1141 ASP cc_start: 0.5787 (OUTLIER) cc_final: 0.4931 (m-30) REVERT: A 1294 ARG cc_start: 0.6014 (OUTLIER) cc_final: 0.5745 (ttm-80) outliers start: 21 outliers final: 16 residues processed: 133 average time/residue: 0.4950 time to fit residues: 87.0984 Evaluate side-chains 129 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain A residue 1258 ILE Chi-restraints excluded: chain A residue 1294 ARG Chi-restraints excluded: chain A residue 1322 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 73 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8060 Z= 0.211 Angle : 0.528 7.820 11169 Z= 0.274 Chirality : 0.037 0.131 1299 Planarity : 0.004 0.048 1217 Dihedral : 18.926 123.481 1709 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.44 % Allowed : 18.86 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.29), residues: 807 helix: 1.76 (0.28), residues: 353 sheet: -0.39 (0.58), residues: 81 loop : -0.40 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 555 HIS 0.004 0.001 HIS A 973 PHE 0.014 0.001 PHE A 462 TYR 0.011 0.002 TYR A1245 ARG 0.004 0.000 ARG A1294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ILE cc_start: 0.8139 (pt) cc_final: 0.7682 (tt) REVERT: A 365 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7415 (tp40) REVERT: A 382 PHE cc_start: 0.6691 (m-80) cc_final: 0.6463 (m-80) REVERT: A 561 PHE cc_start: 0.6850 (t80) cc_final: 0.6560 (t80) REVERT: A 1141 ASP cc_start: 0.5768 (OUTLIER) cc_final: 0.4916 (m-30) outliers start: 18 outliers final: 13 residues processed: 130 average time/residue: 0.4727 time to fit residues: 81.3169 Evaluate side-chains 125 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1258 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 77 optimal weight: 0.0980 chunk 51 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 0.3980 chunk 57 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8060 Z= 0.214 Angle : 0.544 8.884 11169 Z= 0.285 Chirality : 0.037 0.163 1299 Planarity : 0.004 0.054 1217 Dihedral : 18.933 123.245 1709 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.31 % Allowed : 19.27 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.29), residues: 807 helix: 1.67 (0.28), residues: 353 sheet: -0.39 (0.59), residues: 81 loop : -0.41 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 555 HIS 0.004 0.001 HIS A 973 PHE 0.014 0.001 PHE A 462 TYR 0.011 0.002 TYR A1245 ARG 0.006 0.000 ARG A1294 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ILE cc_start: 0.8131 (pt) cc_final: 0.7680 (tt) REVERT: A 382 PHE cc_start: 0.6660 (m-80) cc_final: 0.6431 (m-80) REVERT: A 561 PHE cc_start: 0.6882 (t80) cc_final: 0.6597 (t80) REVERT: A 1141 ASP cc_start: 0.5777 (OUTLIER) cc_final: 0.4067 (m-30) outliers start: 17 outliers final: 12 residues processed: 126 average time/residue: 0.4979 time to fit residues: 82.7544 Evaluate side-chains 121 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1005 CYS Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1258 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8060 Z= 0.300 Angle : 0.602 8.038 11169 Z= 0.318 Chirality : 0.039 0.154 1299 Planarity : 0.005 0.051 1217 Dihedral : 19.009 123.758 1709 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.04 % Allowed : 19.40 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.29), residues: 807 helix: 1.23 (0.27), residues: 354 sheet: -0.55 (0.59), residues: 81 loop : -0.55 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 555 HIS 0.006 0.001 HIS A 973 PHE 0.020 0.002 PHE A 955 TYR 0.015 0.002 TYR A 562 ARG 0.005 0.001 ARG A 560 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 212 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 591 is missing expected H atoms. Skipping. Residue MET 1063 is missing expected H atoms. Skipping. Residue LYS 1325 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ILE cc_start: 0.8190 (pt) cc_final: 0.7721 (tt) REVERT: A 382 PHE cc_start: 0.6803 (m-80) cc_final: 0.6542 (m-80) REVERT: A 413 ASN cc_start: 0.6176 (t160) cc_final: 0.5885 (t0) REVERT: A 561 PHE cc_start: 0.6906 (t80) cc_final: 0.6630 (t80) outliers start: 15 outliers final: 12 residues processed: 123 average time/residue: 0.4656 time to fit residues: 76.9249 Evaluate side-chains 122 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1258 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 70 optimal weight: 0.3980 chunk 8 optimal weight: 0.0670 chunk 12 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.209273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.179762 restraints weight = 39495.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.182802 restraints weight = 18423.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.184310 restraints weight = 11759.796| |-----------------------------------------------------------------------------| r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6092 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8060 Z= 0.200 Angle : 0.549 9.187 11169 Z= 0.288 Chirality : 0.037 0.139 1299 Planarity : 0.004 0.047 1217 Dihedral : 18.940 123.964 1709 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.76 % Allowed : 19.95 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.29), residues: 807 helix: 1.40 (0.28), residues: 355 sheet: -0.49 (0.60), residues: 81 loop : -0.48 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 555 HIS 0.004 0.001 HIS A 973 PHE 0.014 0.001 PHE A 462 TYR 0.011 0.002 TYR A 948 ARG 0.003 0.000 ARG A1294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4187.32 seconds wall clock time: 75 minutes 28.17 seconds (4528.17 seconds total)