Starting phenix.real_space_refine on Sun Jun 8 10:25:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fx2_50841/06_2025/9fx2_50841.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fx2_50841/06_2025/9fx2_50841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fx2_50841/06_2025/9fx2_50841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fx2_50841/06_2025/9fx2_50841.map" model { file = "/net/cci-nas-00/data/ceres_data/9fx2_50841/06_2025/9fx2_50841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fx2_50841/06_2025/9fx2_50841.cif" } resolution = 3.3 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= 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 5974 2.51 5 N 1515 2.21 5 O 1794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9311 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1170, 9241 Classifications: {'peptide': 1170} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1116} Chain breaks: 4 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.26, per 1000 atoms: 0.67 Number of scatterers: 9311 At special positions: 0 Unit cell: (91.874, 126.812, 116.46, 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 28 16.00 O 1794 8.00 N 1515 7.00 C 5974 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 636 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 41 " " NAG A1302 " - " ASN A 118 " " NAG A1303 " - " ASN A1244 " " NAG A1304 " - " ASN A 365 " " NAG A1305 " - " ASN A 419 " Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.2 seconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 18 sheets defined 21.5% alpha, 36.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.239A pdb=" N SER A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 387 removed outlier: 3.628A pdb=" N ARG A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 526 Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 606 through 618 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.908A pdb=" N PHE A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 914 removed outlier: 3.700A pdb=" N LEU A 914 " --> pdb=" O GLY A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 943 Proline residue: A 931 - end of helix Processing helix chain 'A' and resid 946 through 967 Processing helix chain 'A' and resid 977 through 981 Processing helix chain 'A' and resid 985 through 1000 Processing helix chain 'A' and resid 1006 through 1020 removed outlier: 3.879A pdb=" N HIS A1020 " --> pdb=" O TRP A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1040 Processing helix chain 'A' and resid 1044 through 1057 Processing helix chain 'A' and resid 1058 through 1062 removed outlier: 3.574A pdb=" N LYS A1061 " --> pdb=" O GLY A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1082 Processing helix chain 'A' and resid 1085 through 1099 Processing helix chain 'A' and resid 1102 through 1114 removed outlier: 4.475A pdb=" N GLU A1106 " --> pdb=" O PRO A1102 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A1114 " --> pdb=" O MET A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1155 Processing helix chain 'A' and resid 1158 through 1160 No H-bonds generated for 'chain 'A' and resid 1158 through 1160' Processing helix chain 'A' and resid 1161 through 1171 Processing helix chain 'A' and resid 1181 through 1198 removed outlier: 3.833A pdb=" N THR A1185 " --> pdb=" O THR A1181 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A1186 " --> pdb=" O GLN A1182 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET A1198 " --> pdb=" O PHE A1194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 7.432A pdb=" N THR A 43 " --> pdb=" O PRO A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 removed outlier: 4.580A pdb=" N TYR A 102 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 74 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 135 Processing sheet with id=AA4, first strand: chain 'A' and resid 139 through 140 removed outlier: 5.290A pdb=" N LEU A 164 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 229 through 234 Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 240 removed outlier: 6.281A pdb=" N CYS A 239 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 349 through 354 Processing sheet with id=AA8, first strand: chain 'A' and resid 413 through 420 Processing sheet with id=AA9, first strand: chain 'A' and resid 468 through 471 Processing sheet with id=AB1, first strand: chain 'A' and resid 505 through 512 removed outlier: 6.451A pdb=" N VAL A 500 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL A 509 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR A 498 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS A 511 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A 496 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 559 through 563 Processing sheet with id=AB3, first strand: chain 'A' and resid 567 through 568 Processing sheet with id=AB4, first strand: chain 'A' and resid 567 through 568 Processing sheet with id=AB5, first strand: chain 'A' and resid 748 through 752 Processing sheet with id=AB6, first strand: chain 'A' and resid 757 through 759 removed outlier: 6.133A pdb=" N VAL A 758 " --> pdb=" O LYS A 852 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 856 through 868 removed outlier: 4.404A pdb=" N VAL A 895 " --> pdb=" O LEU A1235 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 875 through 882 removed outlier: 6.311A pdb=" N GLY A1211 " --> pdb=" O SER A1216 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER A1216 " --> pdb=" O GLY A1211 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1116 through 1117 removed outlier: 3.566A pdb=" N PHE A1123 " --> pdb=" O GLU A1116 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1236 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: 4.62 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2940 1.34 - 1.46: 2180 1.46 - 1.58: 4339 1.58 - 1.70: 0 1.70 - 1.82: 49 Bond restraints: 9508 Sorted by residual: bond pdb=" C THR A 421 " pdb=" N VAL A 422 " ideal model delta sigma weight residual 1.329 1.480 -0.151 1.13e-02 7.83e+03 1.78e+02 bond pdb=" N ASN A 388 " pdb=" CA ASN A 388 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.27e-02 6.20e+03 6.30e+00 bond pdb=" N ASN A 365 " pdb=" CA ASN A 365 " ideal model delta sigma weight residual 1.456 1.484 -0.027 1.24e-02 6.50e+03 4.88e+00 bond pdb=" N PHE A 366 " pdb=" CA PHE A 366 " ideal model delta sigma weight residual 1.455 1.484 -0.028 1.30e-02 5.92e+03 4.79e+00 bond pdb=" N LEU A 364 " pdb=" CA LEU A 364 " ideal model delta sigma weight residual 1.461 1.484 -0.023 1.19e-02 7.06e+03 3.85e+00 ... (remaining 9503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 12696 2.46 - 4.92: 172 4.92 - 7.37: 37 7.37 - 9.83: 9 9.83 - 12.29: 3 Bond angle restraints: 12917 Sorted by residual: angle pdb=" CA LYS A 417 " pdb=" CB LYS A 417 " pdb=" CG LYS A 417 " ideal model delta sigma weight residual 114.10 123.57 -9.47 2.00e+00 2.50e-01 2.24e+01 angle pdb=" O VAL A 415 " pdb=" C VAL A 415 " pdb=" N GLN A 416 " ideal model delta sigma weight residual 123.20 127.73 -4.53 1.06e+00 8.90e-01 1.83e+01 angle pdb=" CB LYS A 417 " pdb=" CG LYS A 417 " pdb=" CD LYS A 417 " ideal model delta sigma weight residual 111.30 121.08 -9.78 2.30e+00 1.89e-01 1.81e+01 angle pdb=" CA MET A 957 " pdb=" CB MET A 957 " pdb=" CG MET A 957 " ideal model delta sigma weight residual 114.10 122.56 -8.46 2.00e+00 2.50e-01 1.79e+01 angle pdb=" CA VAL A 415 " pdb=" C VAL A 415 " pdb=" N GLN A 416 " ideal model delta sigma weight residual 116.38 111.70 4.68 1.13e+00 7.83e-01 1.72e+01 ... (remaining 12912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5095 17.89 - 35.78: 516 35.78 - 53.68: 116 53.68 - 71.57: 36 71.57 - 89.46: 7 Dihedral angle restraints: 5770 sinusoidal: 2351 harmonic: 3419 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 636 " pdb=" CB CYS A 636 " ideal model delta sinusoidal sigma weight residual -86.00 -151.66 65.66 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CA MET A 625 " pdb=" C MET A 625 " pdb=" N PHE A 626 " pdb=" CA PHE A 626 " ideal model delta harmonic sigma weight residual 180.00 155.14 24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA LEU A 48 " pdb=" C LEU A 48 " pdb=" N LEU A 49 " pdb=" CA LEU A 49 " ideal model delta harmonic sigma weight residual 180.00 -158.43 -21.57 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 5767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 1515 0.180 - 0.361: 1 0.361 - 0.541: 0 0.541 - 0.721: 0 0.721 - 0.902: 1 Chirality restraints: 1517 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 419 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" CB ILE A1052 " pdb=" CA ILE A1052 " pdb=" CG1 ILE A1052 " pdb=" CG2 ILE A1052 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA ILE A 750 " pdb=" N ILE A 750 " pdb=" C ILE A 750 " pdb=" CB ILE A 750 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 1514 not shown) Planarity restraints: 1633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " 0.189 2.00e-02 2.50e+03 1.59e-01 3.16e+02 pdb=" C7 NAG A1304 " -0.048 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " 0.133 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " -0.266 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 415 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C VAL A 415 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL A 415 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 416 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 419 " -0.002 2.00e-02 2.50e+03 1.53e-02 2.94e+00 pdb=" CG ASN A 419 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 419 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 419 " 0.021 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " -0.016 2.00e-02 2.50e+03 ... (remaining 1630 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1930 2.79 - 3.32: 8342 3.32 - 3.84: 15295 3.84 - 4.37: 17556 4.37 - 4.90: 30500 Nonbonded interactions: 73623 Sorted by model distance: nonbonded pdb=" NZ LYS A 161 " pdb=" OE2 GLU A 729 " model vdw 2.260 3.120 nonbonded pdb=" OG SER A 72 " pdb=" OE2 GLU A 75 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR A 860 " pdb=" OE1 GLN A 862 " model vdw 2.296 3.040 nonbonded pdb=" OD1 ASP A 136 " pdb=" OH TYR A 140 " model vdw 2.298 3.040 nonbonded pdb=" ND2 ASN A 388 " pdb=" ND2 ASN A 419 " model vdw 2.300 3.200 ... (remaining 73618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.640 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.151 9514 Z= 0.238 Angle : 0.844 22.118 12934 Z= 0.416 Chirality : 0.054 0.902 1517 Planarity : 0.005 0.159 1628 Dihedral : 15.544 89.461 3555 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.90 % Favored : 98.02 % Rotamer: Outliers : 0.19 % Allowed : 17.73 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.11 (0.24), residues: 1160 helix: 0.62 (0.35), residues: 209 sheet: 0.52 (0.24), residues: 476 loop : -0.53 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1167 HIS 0.001 0.000 HIS A 51 PHE 0.014 0.001 PHE A 366 TYR 0.010 0.001 TYR A1002 ARG 0.004 0.001 ARG A 149 Details of bonding type rmsd link_NAG-ASN : bond 0.01670 ( 5) link_NAG-ASN : angle 7.79127 ( 15) hydrogen bonds : bond 0.10309 ( 438) hydrogen bonds : angle 5.14194 ( 1236) SS BOND : bond 0.00122 ( 1) SS BOND : angle 1.56947 ( 2) covalent geometry : bond 0.00461 ( 9508) covalent geometry : angle 0.80113 (12917) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8381 (mm) outliers start: 2 outliers final: 0 residues processed: 35 average time/residue: 0.2250 time to fit residues: 12.2241 Evaluate side-chains 32 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 388 ASN A1157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.065592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.041118 restraints weight = 40416.202| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 4.12 r_work: 0.2765 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9514 Z= 0.186 Angle : 0.561 15.333 12934 Z= 0.277 Chirality : 0.046 0.642 1517 Planarity : 0.003 0.041 1628 Dihedral : 5.545 51.995 1350 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.33 % Favored : 97.59 % Rotamer: Outliers : 1.72 % Allowed : 17.25 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.46 (0.25), residues: 1160 helix: 1.19 (0.35), residues: 218 sheet: 0.69 (0.24), residues: 484 loop : -0.48 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1124 HIS 0.002 0.001 HIS A1225 PHE 0.030 0.001 PHE A 996 TYR 0.010 0.001 TYR A1002 ARG 0.004 0.000 ARG A1060 Details of bonding type rmsd link_NAG-ASN : bond 0.00814 ( 5) link_NAG-ASN : angle 5.29530 ( 15) hydrogen bonds : bond 0.03154 ( 438) hydrogen bonds : angle 4.66360 ( 1236) SS BOND : bond 0.00230 ( 1) SS BOND : angle 2.00669 ( 2) covalent geometry : bond 0.00406 ( 9508) covalent geometry : angle 0.53053 (12917) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 29 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7854 (mp0) outliers start: 18 outliers final: 12 residues processed: 46 average time/residue: 0.1904 time to fit residues: 13.8782 Evaluate side-chains 42 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1165 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 113 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.063521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.039047 restraints weight = 41696.013| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 4.10 r_work: 0.2692 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 9514 Z= 0.328 Angle : 0.659 11.877 12934 Z= 0.332 Chirality : 0.046 0.506 1517 Planarity : 0.004 0.043 1628 Dihedral : 5.573 49.142 1348 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.10 % Allowed : 17.16 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.41 (0.25), residues: 1160 helix: 1.28 (0.35), residues: 221 sheet: 0.57 (0.24), residues: 482 loop : -0.46 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1028 HIS 0.005 0.001 HIS A1225 PHE 0.018 0.002 PHE A 366 TYR 0.014 0.002 TYR A1002 ARG 0.008 0.001 ARG A 149 Details of bonding type rmsd link_NAG-ASN : bond 0.00735 ( 5) link_NAG-ASN : angle 4.32852 ( 15) hydrogen bonds : bond 0.03528 ( 438) hydrogen bonds : angle 5.02904 ( 1236) SS BOND : bond 0.00609 ( 1) SS BOND : angle 3.66809 ( 2) covalent geometry : bond 0.00713 ( 9508) covalent geometry : angle 0.64078 (12917) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 29 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8975 (t0) cc_final: 0.8725 (t0) REVERT: A 125 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.7957 (mp0) REVERT: A 848 MET cc_start: 0.9035 (mmm) cc_final: 0.8769 (mmm) REVERT: A 875 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.8167 (t) REVERT: A 1110 MET cc_start: 0.8941 (ppp) cc_final: 0.8539 (ppp) REVERT: A 1258 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.7796 (m-40) outliers start: 43 outliers final: 27 residues processed: 70 average time/residue: 0.1822 time to fit residues: 20.2671 Evaluate side-chains 59 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 29 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1258 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 57 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 13 optimal weight: 0.0170 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.065370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.041058 restraints weight = 40636.481| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 4.12 r_work: 0.2769 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9514 Z= 0.100 Angle : 0.504 11.104 12934 Z= 0.252 Chirality : 0.045 0.468 1517 Planarity : 0.003 0.041 1628 Dihedral : 5.053 50.713 1348 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.38 % Allowed : 19.45 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.71 (0.25), residues: 1160 helix: 1.58 (0.35), residues: 221 sheet: 0.72 (0.24), residues: 485 loop : -0.28 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1124 HIS 0.001 0.000 HIS A 347 PHE 0.015 0.001 PHE A 764 TYR 0.009 0.001 TYR A 756 ARG 0.002 0.000 ARG A 823 Details of bonding type rmsd link_NAG-ASN : bond 0.00613 ( 5) link_NAG-ASN : angle 3.75256 ( 15) hydrogen bonds : bond 0.02680 ( 438) hydrogen bonds : angle 4.54447 ( 1236) SS BOND : bond 0.00900 ( 1) SS BOND : angle 1.69125 ( 2) covalent geometry : bond 0.00213 ( 9508) covalent geometry : angle 0.48709 (12917) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 30 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8834 (t0) cc_final: 0.8536 (t0) REVERT: A 125 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8101 (mp0) REVERT: A 1110 MET cc_start: 0.8977 (ppp) cc_final: 0.8597 (ppp) outliers start: 25 outliers final: 16 residues processed: 55 average time/residue: 0.1997 time to fit residues: 16.7927 Evaluate side-chains 45 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 28 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1228 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 109 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.065026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.040675 restraints weight = 40599.850| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 4.11 r_work: 0.2755 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9514 Z= 0.143 Angle : 0.513 10.550 12934 Z= 0.257 Chirality : 0.044 0.436 1517 Planarity : 0.003 0.041 1628 Dihedral : 4.924 50.526 1348 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.29 % Allowed : 19.64 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.83 (0.25), residues: 1160 helix: 1.77 (0.35), residues: 222 sheet: 0.77 (0.24), residues: 485 loop : -0.21 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1124 HIS 0.001 0.000 HIS A1011 PHE 0.014 0.001 PHE A 764 TYR 0.009 0.001 TYR A1002 ARG 0.002 0.000 ARG A 149 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 5) link_NAG-ASN : angle 3.58808 ( 15) hydrogen bonds : bond 0.02756 ( 438) hydrogen bonds : angle 4.51400 ( 1236) SS BOND : bond 0.00214 ( 1) SS BOND : angle 1.80647 ( 2) covalent geometry : bond 0.00313 ( 9508) covalent geometry : angle 0.49833 (12917) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 29 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8826 (t0) cc_final: 0.8577 (t0) REVERT: A 125 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: A 848 MET cc_start: 0.9099 (mmm) cc_final: 0.8856 (mmm) REVERT: A 1110 MET cc_start: 0.8951 (ppp) cc_final: 0.8542 (ppp) outliers start: 24 outliers final: 18 residues processed: 53 average time/residue: 0.1811 time to fit residues: 15.2948 Evaluate side-chains 48 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 29 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 63 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 92 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.065527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.041181 restraints weight = 40363.477| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 4.11 r_work: 0.2769 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9514 Z= 0.108 Angle : 0.505 10.085 12934 Z= 0.249 Chirality : 0.044 0.407 1517 Planarity : 0.003 0.041 1628 Dihedral : 4.741 50.973 1348 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.19 % Allowed : 19.73 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.96 (0.25), residues: 1160 helix: 1.97 (0.35), residues: 220 sheet: 0.78 (0.24), residues: 489 loop : -0.11 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 639 HIS 0.001 0.000 HIS A 51 PHE 0.012 0.001 PHE A 764 TYR 0.008 0.001 TYR A 534 ARG 0.001 0.000 ARG A1166 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 5) link_NAG-ASN : angle 3.34624 ( 15) hydrogen bonds : bond 0.02568 ( 438) hydrogen bonds : angle 4.36582 ( 1236) SS BOND : bond 0.00082 ( 1) SS BOND : angle 1.42817 ( 2) covalent geometry : bond 0.00236 ( 9508) covalent geometry : angle 0.49213 (12917) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 29 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: A 1110 MET cc_start: 0.8951 (ppp) cc_final: 0.8530 (ppp) outliers start: 23 outliers final: 19 residues processed: 51 average time/residue: 0.2030 time to fit residues: 17.1277 Evaluate side-chains 49 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 29 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 35 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 115 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1035 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.064863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.040302 restraints weight = 40120.429| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 4.06 r_work: 0.2716 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9514 Z= 0.194 Angle : 0.547 9.900 12934 Z= 0.271 Chirality : 0.044 0.387 1517 Planarity : 0.003 0.041 1628 Dihedral : 4.845 51.019 1348 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.05 % Allowed : 19.26 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.96 (0.25), residues: 1160 helix: 1.92 (0.35), residues: 222 sheet: 0.73 (0.24), residues: 485 loop : -0.01 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1124 HIS 0.002 0.001 HIS A1225 PHE 0.013 0.001 PHE A 764 TYR 0.009 0.001 TYR A1147 ARG 0.003 0.000 ARG A 149 Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 5) link_NAG-ASN : angle 3.32718 ( 15) hydrogen bonds : bond 0.02822 ( 438) hydrogen bonds : angle 4.51798 ( 1236) SS BOND : bond 0.00393 ( 1) SS BOND : angle 2.26544 ( 2) covalent geometry : bond 0.00425 ( 9508) covalent geometry : angle 0.53510 (12917) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 29 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: A 794 MET cc_start: 0.8510 (tpp) cc_final: 0.8247 (tpp) REVERT: A 848 MET cc_start: 0.9116 (mmm) cc_final: 0.8862 (mmm) REVERT: A 1035 HIS cc_start: 0.8855 (OUTLIER) cc_final: 0.8169 (m90) REVERT: A 1110 MET cc_start: 0.8965 (ppp) cc_final: 0.8553 (ppp) outliers start: 32 outliers final: 25 residues processed: 61 average time/residue: 0.1779 time to fit residues: 17.7706 Evaluate side-chains 56 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 29 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 1035 HIS Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 106 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 67 optimal weight: 0.0470 chunk 87 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1035 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.065333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.040736 restraints weight = 40617.826| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 4.10 r_work: 0.2735 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9514 Z= 0.130 Angle : 0.522 9.821 12934 Z= 0.258 Chirality : 0.044 0.381 1517 Planarity : 0.003 0.041 1628 Dihedral : 4.785 51.449 1348 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.76 % Allowed : 19.54 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 1.02 (0.25), residues: 1160 helix: 2.02 (0.35), residues: 217 sheet: 0.79 (0.24), residues: 489 loop : -0.02 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1124 HIS 0.004 0.001 HIS A1035 PHE 0.013 0.001 PHE A 764 TYR 0.008 0.001 TYR A 756 ARG 0.001 0.000 ARG A 823 Details of bonding type rmsd link_NAG-ASN : bond 0.00589 ( 5) link_NAG-ASN : angle 3.24497 ( 15) hydrogen bonds : bond 0.02666 ( 438) hydrogen bonds : angle 4.42987 ( 1236) SS BOND : bond 0.00013 ( 1) SS BOND : angle 1.54647 ( 2) covalent geometry : bond 0.00284 ( 9508) covalent geometry : angle 0.50989 (12917) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 29 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: A 794 MET cc_start: 0.8557 (tpp) cc_final: 0.8297 (tpp) REVERT: A 848 MET cc_start: 0.9085 (mmm) cc_final: 0.8850 (mmm) REVERT: A 1035 HIS cc_start: 0.9033 (OUTLIER) cc_final: 0.8330 (m90) REVERT: A 1110 MET cc_start: 0.8967 (ppp) cc_final: 0.8543 (ppp) outliers start: 29 outliers final: 24 residues processed: 58 average time/residue: 0.2007 time to fit residues: 18.8057 Evaluate side-chains 55 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 29 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 1035 HIS Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 100 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1086 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.065143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.040632 restraints weight = 39754.536| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 4.04 r_work: 0.2731 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9514 Z= 0.150 Angle : 0.532 9.757 12934 Z= 0.262 Chirality : 0.044 0.376 1517 Planarity : 0.003 0.042 1628 Dihedral : 4.774 51.231 1348 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.76 % Allowed : 19.54 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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 (0.25), residues: 1160 helix: 2.03 (0.35), residues: 220 sheet: 0.78 (0.24), residues: 485 loop : -0.04 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1124 HIS 0.002 0.000 HIS A1225 PHE 0.013 0.001 PHE A 764 TYR 0.008 0.001 TYR A1002 ARG 0.002 0.000 ARG A 149 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 5) link_NAG-ASN : angle 3.23249 ( 15) hydrogen bonds : bond 0.02682 ( 438) hydrogen bonds : angle 4.42372 ( 1236) SS BOND : bond 0.00107 ( 1) SS BOND : angle 1.75595 ( 2) covalent geometry : bond 0.00330 ( 9508) covalent geometry : angle 0.52020 (12917) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 29 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: A 794 MET cc_start: 0.8600 (tpp) cc_final: 0.8339 (tpp) REVERT: A 848 MET cc_start: 0.9107 (mmm) cc_final: 0.8880 (mmm) REVERT: A 1110 MET cc_start: 0.8951 (ppp) cc_final: 0.8535 (ppp) outliers start: 29 outliers final: 25 residues processed: 58 average time/residue: 0.1753 time to fit residues: 16.7081 Evaluate side-chains 55 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 29 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 24 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 57 optimal weight: 0.0970 chunk 86 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.065171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.040630 restraints weight = 40628.387| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 4.08 r_work: 0.2731 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9514 Z= 0.147 Angle : 0.537 9.656 12934 Z= 0.264 Chirality : 0.044 0.367 1517 Planarity : 0.003 0.042 1628 Dihedral : 4.744 51.256 1348 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.67 % Allowed : 19.92 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 1.04 (0.26), residues: 1160 helix: 2.03 (0.35), residues: 220 sheet: 0.80 (0.24), residues: 487 loop : 0.00 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 639 HIS 0.001 0.000 HIS A1225 PHE 0.013 0.001 PHE A 764 TYR 0.008 0.001 TYR A 756 ARG 0.002 0.000 ARG A 149 Details of bonding type rmsd link_NAG-ASN : bond 0.00610 ( 5) link_NAG-ASN : angle 3.16172 ( 15) hydrogen bonds : bond 0.02665 ( 438) hydrogen bonds : angle 4.42921 ( 1236) SS BOND : bond 0.00063 ( 1) SS BOND : angle 1.61866 ( 2) covalent geometry : bond 0.00321 ( 9508) covalent geometry : angle 0.52655 (12917) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 30 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: A 794 MET cc_start: 0.8574 (tpp) cc_final: 0.8283 (tpp) REVERT: A 848 MET cc_start: 0.9104 (mmm) cc_final: 0.8891 (mmm) REVERT: A 1110 MET cc_start: 0.8944 (ppp) cc_final: 0.8530 (ppp) REVERT: A 1143 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7674 (mm-30) outliers start: 28 outliers final: 26 residues processed: 58 average time/residue: 0.1722 time to fit residues: 16.1827 Evaluate side-chains 57 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 30 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 0.0270 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1035 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.065072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.040575 restraints weight = 40172.224| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 4.06 r_work: 0.2727 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9514 Z= 0.148 Angle : 0.536 9.571 12934 Z= 0.263 Chirality : 0.044 0.357 1517 Planarity : 0.003 0.042 1628 Dihedral : 4.723 51.254 1348 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.67 % Allowed : 19.92 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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 (0.26), residues: 1160 helix: 2.04 (0.35), residues: 217 sheet: 0.81 (0.24), residues: 487 loop : 0.05 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1124 HIS 0.001 0.000 HIS A1225 PHE 0.013 0.001 PHE A 764 TYR 0.008 0.001 TYR A 756 ARG 0.002 0.000 ARG A 149 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 5) link_NAG-ASN : angle 3.10210 ( 15) hydrogen bonds : bond 0.02678 ( 438) hydrogen bonds : angle 4.41560 ( 1236) SS BOND : bond 0.00218 ( 1) SS BOND : angle 1.91193 ( 2) covalent geometry : bond 0.00324 ( 9508) covalent geometry : angle 0.52540 (12917) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5224.77 seconds wall clock time: 92 minutes 25.88 seconds (5545.88 seconds total)