Starting phenix.real_space_refine on Thu Jun 5 10:05:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tld_41367/06_2025/8tld_41367.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tld_41367/06_2025/8tld_41367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tld_41367/06_2025/8tld_41367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tld_41367/06_2025/8tld_41367.map" model { file = "/net/cci-nas-00/data/ceres_data/8tld_41367/06_2025/8tld_41367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tld_41367/06_2025/8tld_41367.cif" } resolution = 3.6 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= 0.026 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 27 5.16 5 C 3776 2.51 5 N 1040 2.21 5 O 1139 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 5982 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 758 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 9, 'TRANS': 84} Chain breaks: 1 Chain: "C" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 862 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "D" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 879 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "E" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 942 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "F" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2471 Classifications: {'peptide': 308} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 291} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.99, per 1000 atoms: 0.67 Number of scatterers: 5982 At special positions: 0 Unit cell: (80.972, 112.316, 124.07, 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 27 16.00 O 1139 8.00 N 1040 7.00 C 3776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 45 " distance=2.03 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS D 106 " distance=2.03 Simple disulfide: pdb=" SG CYS C 106 " - pdb=" SG CYS D 64 " distance=2.03 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 155 " distance=2.03 Simple disulfide: pdb=" SG CYS F 182 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 269 " - pdb=" SG CYS F 316 " 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 C 200 " - " ASN C 48 " " NAG F 501 " - " ASN F 35 " " NAG F 502 " - " ASN F 131 " " NAG F 503 " - " ASN F 216 " " NAG F 504 " - " ASN F 244 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 816.5 milliseconds 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 11 sheets defined 24.9% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'B' and resid 27 through 33 Processing helix chain 'B' and resid 51 through 55 removed outlier: 3.859A pdb=" N ARG B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 51 through 55' Processing helix chain 'C' and resid 26 through 41 Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 64 through 78 Processing helix chain 'C' and resid 84 through 105 removed outlier: 3.673A pdb=" N ASN C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 130 Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.536A pdb=" N LEU D 45 " --> pdb=" O HIS D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 63 removed outlier: 3.721A pdb=" N LEU D 63 " --> pdb=" O ASN D 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 60 through 63' Processing helix chain 'D' and resid 64 through 79 Processing helix chain 'D' and resid 83 through 106 removed outlier: 4.037A pdb=" N ARG D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 130 Processing helix chain 'E' and resid 382 through 386 Processing helix chain 'F' and resid 232 through 237 Processing sheet with id=AA1, first strand: chain 'B' and resid 34 through 37 Processing sheet with id=AA2, first strand: chain 'B' and resid 59 through 64 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 55 removed outlier: 4.293A pdb=" N GLU D 109 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER F 95 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 55 removed outlier: 4.293A pdb=" N GLU D 109 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER F 95 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 344 through 350 Processing sheet with id=AA6, first strand: chain 'E' and resid 387 through 392 Processing sheet with id=AA7, first strand: chain 'F' and resid 34 through 42 removed outlier: 5.518A pdb=" N ASN F 35 " --> pdb=" O LYS F 51 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS F 51 " --> pdb=" O ASN F 35 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS F 39 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR F 41 " --> pdb=" O GLN F 45 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN F 45 " --> pdb=" O THR F 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 130 through 140 removed outlier: 5.696A pdb=" N ASN F 131 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU F 158 " --> pdb=" O ASN F 131 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL F 151 " --> pdb=" O ARG F 200 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG F 200 " --> pdb=" O VAL F 151 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ILE F 194 " --> pdb=" O TRP F 157 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER F 186 " --> pdb=" O ILE F 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 178 through 181 Processing sheet with id=AB1, first strand: chain 'F' and resid 246 through 250 Processing sheet with id=AB2, first strand: chain 'F' and resid 284 through 289 280 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 1.65 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: 1954 1.34 - 1.46: 1304 1.46 - 1.58: 2820 1.58 - 1.70: 2 1.70 - 1.82: 36 Bond restraints: 6116 Sorted by residual: bond pdb=" CG PRO C 54 " pdb=" CD PRO C 54 " ideal model delta sigma weight residual 1.503 1.296 0.207 3.40e-02 8.65e+02 3.70e+01 bond pdb=" CB PRO C 54 " pdb=" CG PRO C 54 " ideal model delta sigma weight residual 1.492 1.668 -0.176 5.00e-02 4.00e+02 1.23e+01 bond pdb=" N PRO C 54 " pdb=" CD PRO C 54 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" N PRO C 54 " pdb=" CA PRO C 54 " ideal model delta sigma weight residual 1.469 1.438 0.030 1.28e-02 6.10e+03 5.64e+00 bond pdb=" C1 NAG F 503 " pdb=" O5 NAG F 503 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.14e+00 ... (remaining 6111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 8264 3.60 - 7.20: 37 7.20 - 10.81: 5 10.81 - 14.41: 1 14.41 - 18.01: 1 Bond angle restraints: 8308 Sorted by residual: angle pdb=" CA PRO C 54 " pdb=" N PRO C 54 " pdb=" CD PRO C 54 " ideal model delta sigma weight residual 112.00 93.99 18.01 1.40e+00 5.10e-01 1.65e+02 angle pdb=" N PRO C 54 " pdb=" CD PRO C 54 " pdb=" CG PRO C 54 " ideal model delta sigma weight residual 103.20 90.46 12.74 1.50e+00 4.44e-01 7.21e+01 angle pdb=" CA PRO C 54 " pdb=" CB PRO C 54 " pdb=" CG PRO C 54 " ideal model delta sigma weight residual 104.50 94.84 9.66 1.90e+00 2.77e-01 2.59e+01 angle pdb=" CA PRO F 261 " pdb=" N PRO F 261 " pdb=" CD PRO F 261 " ideal model delta sigma weight residual 112.00 106.01 5.99 1.40e+00 5.10e-01 1.83e+01 angle pdb=" C GLU D 24 " pdb=" N ILE D 25 " pdb=" CA ILE D 25 " ideal model delta sigma weight residual 122.13 129.53 -7.40 1.85e+00 2.92e-01 1.60e+01 ... (remaining 8303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 3192 17.71 - 35.41: 429 35.41 - 53.12: 121 53.12 - 70.82: 18 70.82 - 88.53: 12 Dihedral angle restraints: 3772 sinusoidal: 1622 harmonic: 2150 Sorted by residual: dihedral pdb=" CA GLN C 102 " pdb=" C GLN C 102 " pdb=" N LYS C 103 " pdb=" CA LYS C 103 " ideal model delta harmonic sigma weight residual 180.00 152.91 27.09 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ASN C 48 " pdb=" C ASN C 48 " pdb=" N GLU C 49 " pdb=" CA GLU C 49 " ideal model delta harmonic sigma weight residual -180.00 -154.26 -25.74 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CB CYS C 64 " pdb=" SG CYS C 64 " pdb=" SG CYS D 106 " pdb=" CB CYS D 106 " ideal model delta sinusoidal sigma weight residual -86.00 -45.06 -40.94 1 1.00e+01 1.00e-02 2.35e+01 ... (remaining 3769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 874 0.084 - 0.167: 70 0.167 - 0.251: 1 0.251 - 0.334: 0 0.334 - 0.418: 1 Chirality restraints: 946 Sorted by residual: chirality pdb=" C1 NAG C 200 " pdb=" ND2 ASN C 48 " pdb=" C2 NAG C 200 " pdb=" O5 NAG C 200 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" CA ASN D 60 " pdb=" N ASN D 60 " pdb=" C ASN D 60 " pdb=" CB ASN D 60 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" C1 NAG F 501 " pdb=" ND2 ASN F 35 " pdb=" C2 NAG F 501 " pdb=" O5 NAG F 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 6.89e-01 ... (remaining 943 not shown) Planarity restraints: 1059 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 53 " -0.102 5.00e-02 4.00e+02 1.39e-01 3.07e+01 pdb=" N PRO C 54 " 0.239 5.00e-02 4.00e+02 pdb=" CA PRO C 54 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO C 54 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 110 " -0.371 9.50e-02 1.11e+02 1.67e-01 1.80e+01 pdb=" NE ARG C 110 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 110 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG C 110 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 110 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 260 " 0.063 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO F 261 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO F 261 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO F 261 " 0.050 5.00e-02 4.00e+02 ... (remaining 1056 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 343 2.72 - 3.27: 5661 3.27 - 3.81: 9630 3.81 - 4.36: 11263 4.36 - 4.90: 19145 Nonbonded interactions: 46042 Sorted by model distance: nonbonded pdb=" O PRO E 343 " pdb=" OG SER E 429 " model vdw 2.181 3.040 nonbonded pdb=" OG1 THR D 34 " pdb=" OD1 ASN D 91 " model vdw 2.183 3.040 nonbonded pdb=" OD2 ASP B 104 " pdb=" NH1 ARG C 87 " model vdw 2.185 3.120 nonbonded pdb=" NZ LYS F 260 " pdb=" O PHE F 265 " model vdw 2.198 3.120 nonbonded pdb=" O THR C 50 " pdb=" NH1 ARG C 52 " model vdw 2.211 3.120 ... (remaining 46037 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 Found NCS groups: ncs_group { reference = (chain 'C' and resid 25 through 131) selection = (chain 'D' and resid 25 through 131) } 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 17.400 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 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 0.207 6129 Z= 0.205 Angle : 0.759 18.009 8339 Z= 0.412 Chirality : 0.045 0.418 946 Planarity : 0.009 0.167 1054 Dihedral : 17.428 88.526 2348 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.76 % Favored : 95.83 % Rotamer: Outliers : 0.60 % Allowed : 24.13 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.17 (0.32), residues: 719 helix: 0.48 (0.41), residues: 169 sheet: 0.65 (0.36), residues: 226 loop : -0.96 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 322 HIS 0.006 0.001 HIS C 61 PHE 0.024 0.002 PHE D 116 TYR 0.009 0.001 TYR F 172 ARG 0.018 0.001 ARG C 110 Details of bonding type rmsd link_NAG-ASN : bond 0.01686 ( 5) link_NAG-ASN : angle 4.76115 ( 15) hydrogen bonds : bond 0.19589 ( 262) hydrogen bonds : angle 7.41462 ( 768) SS BOND : bond 0.00319 ( 8) SS BOND : angle 0.68439 ( 16) covalent geometry : bond 0.00532 ( 6116) covalent geometry : angle 0.73239 ( 8308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: D 123 PHE cc_start: 0.7327 (t80) cc_final: 0.6906 (t80) REVERT: F 186 SER cc_start: 0.8080 (m) cc_final: 0.7838 (p) REVERT: F 292 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.6940 (t0) REVERT: F 324 GLU cc_start: 0.7743 (tp30) cc_final: 0.7373 (tp30) outliers start: 4 outliers final: 0 residues processed: 127 average time/residue: 0.2087 time to fit residues: 33.7033 Evaluate side-chains 124 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 292 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 0.3980 chunk 35 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.0770 chunk 33 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.149677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.132037 restraints weight = 9674.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.135100 restraints weight = 5761.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.137202 restraints weight = 3891.922| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6129 Z= 0.151 Angle : 0.638 12.369 8339 Z= 0.325 Chirality : 0.045 0.371 946 Planarity : 0.006 0.089 1054 Dihedral : 6.731 54.288 903 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.76 % Favored : 95.83 % Rotamer: Outliers : 3.02 % Allowed : 23.68 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.17 (0.32), residues: 719 helix: 1.03 (0.42), residues: 158 sheet: 0.78 (0.36), residues: 227 loop : -0.79 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 322 HIS 0.004 0.001 HIS F 277 PHE 0.012 0.002 PHE F 198 TYR 0.012 0.001 TYR E 376 ARG 0.007 0.001 ARG F 174 Details of bonding type rmsd link_NAG-ASN : bond 0.01489 ( 5) link_NAG-ASN : angle 4.90878 ( 15) hydrogen bonds : bond 0.04145 ( 262) hydrogen bonds : angle 5.52571 ( 768) SS BOND : bond 0.00373 ( 8) SS BOND : angle 0.79716 ( 16) covalent geometry : bond 0.00351 ( 6116) covalent geometry : angle 0.60368 ( 8308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 PRO cc_start: 0.6862 (Cg_exo) cc_final: 0.6637 (Cg_endo) REVERT: D 112 ARG cc_start: 0.7470 (mmt-90) cc_final: 0.7005 (mpt180) REVERT: D 123 PHE cc_start: 0.6986 (t80) cc_final: 0.6746 (t80) REVERT: F 40 VAL cc_start: 0.8316 (t) cc_final: 0.8067 (m) REVERT: F 292 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7052 (t0) REVERT: F 324 GLU cc_start: 0.7664 (tp30) cc_final: 0.7349 (tp30) outliers start: 20 outliers final: 9 residues processed: 147 average time/residue: 0.2368 time to fit residues: 44.3137 Evaluate side-chains 142 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 292 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 4 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN D 81 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.147096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.129657 restraints weight = 9827.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.132573 restraints weight = 5968.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.134569 restraints weight = 4108.434| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 6129 Z= 0.205 Angle : 0.652 12.144 8339 Z= 0.332 Chirality : 0.045 0.356 946 Planarity : 0.006 0.072 1054 Dihedral : 6.731 54.618 903 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.03 % Favored : 95.55 % Rotamer: Outliers : 4.37 % Allowed : 22.17 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.00 (0.32), residues: 719 helix: 0.80 (0.41), residues: 164 sheet: 0.61 (0.35), residues: 230 loop : -0.83 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 322 HIS 0.007 0.001 HIS F 106 PHE 0.017 0.002 PHE F 198 TYR 0.014 0.002 TYR E 376 ARG 0.004 0.001 ARG C 112 Details of bonding type rmsd link_NAG-ASN : bond 0.01379 ( 5) link_NAG-ASN : angle 4.21790 ( 15) hydrogen bonds : bond 0.04162 ( 262) hydrogen bonds : angle 5.31573 ( 768) SS BOND : bond 0.00561 ( 8) SS BOND : angle 0.95477 ( 16) covalent geometry : bond 0.00469 ( 6116) covalent geometry : angle 0.62707 ( 8308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7793 (m) REVERT: D 112 ARG cc_start: 0.7488 (mmt-90) cc_final: 0.7056 (mpt180) REVERT: D 123 PHE cc_start: 0.7080 (t80) cc_final: 0.6834 (t80) REVERT: F 40 VAL cc_start: 0.8388 (t) cc_final: 0.8164 (m) REVERT: F 45 GLN cc_start: 0.7230 (mt0) cc_final: 0.7016 (mt0) REVERT: F 292 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.7143 (t0) REVERT: F 322 TRP cc_start: 0.7922 (m100) cc_final: 0.7650 (m-10) outliers start: 29 outliers final: 19 residues processed: 146 average time/residue: 0.2098 time to fit residues: 38.7470 Evaluate side-chains 151 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 131 TRP Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 433 SER Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 292 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** 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 = 0.3871 r_free = 0.3871 target = 0.148758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.131893 restraints weight = 9790.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.134849 restraints weight = 5990.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136854 restraints weight = 4116.727| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 6129 Z= 0.171 Angle : 0.613 12.233 8339 Z= 0.311 Chirality : 0.044 0.338 946 Planarity : 0.005 0.063 1054 Dihedral : 6.516 55.667 903 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.03 % Favored : 95.55 % Rotamer: Outliers : 4.98 % Allowed : 22.17 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.01 (0.31), residues: 719 helix: 0.87 (0.41), residues: 164 sheet: 0.56 (0.35), residues: 230 loop : -0.81 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 322 HIS 0.004 0.001 HIS C 61 PHE 0.014 0.002 PHE F 198 TYR 0.013 0.002 TYR E 376 ARG 0.004 0.000 ARG F 59 Details of bonding type rmsd link_NAG-ASN : bond 0.01305 ( 5) link_NAG-ASN : angle 3.96824 ( 15) hydrogen bonds : bond 0.03739 ( 262) hydrogen bonds : angle 5.15505 ( 768) SS BOND : bond 0.00477 ( 8) SS BOND : angle 0.83163 ( 16) covalent geometry : bond 0.00388 ( 6116) covalent geometry : angle 0.58892 ( 8308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.8312 (t) cc_final: 0.8070 (p) REVERT: C 84 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7915 (m) REVERT: D 123 PHE cc_start: 0.7194 (t80) cc_final: 0.6900 (t80) REVERT: E 421 TYR cc_start: 0.8389 (m-80) cc_final: 0.7752 (m-80) REVERT: F 40 VAL cc_start: 0.8321 (t) cc_final: 0.8099 (m) REVERT: F 292 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7219 (t0) REVERT: F 322 TRP cc_start: 0.7903 (m100) cc_final: 0.7593 (m-10) outliers start: 33 outliers final: 19 residues processed: 149 average time/residue: 0.1924 time to fit residues: 36.6113 Evaluate side-chains 151 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 131 TRP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 433 SER Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 292 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 46 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** 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 = 0.3855 r_free = 0.3855 target = 0.147486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.129890 restraints weight = 9722.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.133082 restraints weight = 5805.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135241 restraints weight = 3915.780| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 6129 Z= 0.202 Angle : 0.648 12.176 8339 Z= 0.330 Chirality : 0.045 0.333 946 Planarity : 0.006 0.063 1054 Dihedral : 6.491 55.952 903 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.73 % Favored : 94.85 % Rotamer: Outliers : 5.13 % Allowed : 22.17 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.09 (0.31), residues: 719 helix: 0.87 (0.41), residues: 164 sheet: 0.45 (0.34), residues: 230 loop : -0.88 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 322 HIS 0.005 0.001 HIS F 106 PHE 0.017 0.002 PHE F 198 TYR 0.014 0.002 TYR E 376 ARG 0.008 0.001 ARG F 59 Details of bonding type rmsd link_NAG-ASN : bond 0.01313 ( 5) link_NAG-ASN : angle 3.85562 ( 15) hydrogen bonds : bond 0.03839 ( 262) hydrogen bonds : angle 5.16539 ( 768) SS BOND : bond 0.00586 ( 8) SS BOND : angle 0.94401 ( 16) covalent geometry : bond 0.00459 ( 6116) covalent geometry : angle 0.62723 ( 8308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 112 ARG cc_start: 0.7230 (mpt180) cc_final: 0.7021 (mpt180) REVERT: D 123 PHE cc_start: 0.7078 (t80) cc_final: 0.6767 (t80) REVERT: E 421 TYR cc_start: 0.8359 (m-80) cc_final: 0.7577 (m-80) REVERT: F 39 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6989 (ttmm) REVERT: F 292 ASN cc_start: 0.8295 (t0) cc_final: 0.7187 (t0) REVERT: F 309 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.6246 (mtm110) REVERT: F 317 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6857 (ttm170) REVERT: F 322 TRP cc_start: 0.7946 (m100) cc_final: 0.7456 (m-10) outliers start: 34 outliers final: 23 residues processed: 155 average time/residue: 0.1941 time to fit residues: 38.8140 Evaluate side-chains 156 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 433 SER Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 309 ARG Chi-restraints excluded: chain F residue 317 ARG Chi-restraints excluded: chain F residue 326 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.148737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.131758 restraints weight = 9557.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.134736 restraints weight = 5847.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.136747 restraints weight = 4013.207| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 6129 Z= 0.143 Angle : 0.608 12.302 8339 Z= 0.307 Chirality : 0.044 0.322 946 Planarity : 0.005 0.064 1054 Dihedral : 6.399 56.487 901 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.48 % Favored : 96.11 % Rotamer: Outliers : 5.73 % Allowed : 22.02 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.06 (0.31), residues: 719 helix: 1.01 (0.41), residues: 164 sheet: 0.48 (0.34), residues: 230 loop : -0.75 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 50 HIS 0.005 0.001 HIS D 61 PHE 0.012 0.002 PHE F 198 TYR 0.014 0.002 TYR C 119 ARG 0.005 0.000 ARG F 174 Details of bonding type rmsd link_NAG-ASN : bond 0.01270 ( 5) link_NAG-ASN : angle 4.10048 ( 15) hydrogen bonds : bond 0.03479 ( 262) hydrogen bonds : angle 4.99876 ( 768) SS BOND : bond 0.00427 ( 8) SS BOND : angle 0.71939 ( 16) covalent geometry : bond 0.00330 ( 6116) covalent geometry : angle 0.58234 ( 8308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.8201 (t) cc_final: 0.7954 (p) REVERT: C 84 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7847 (m) REVERT: D 123 PHE cc_start: 0.7140 (t80) cc_final: 0.6884 (t80) REVERT: E 421 TYR cc_start: 0.8388 (m-80) cc_final: 0.7652 (m-80) REVERT: F 292 ASN cc_start: 0.8251 (t0) cc_final: 0.7216 (t0) REVERT: F 317 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7034 (ttm170) outliers start: 38 outliers final: 27 residues processed: 143 average time/residue: 0.1815 time to fit residues: 33.8265 Evaluate side-chains 149 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 433 SER Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 317 ARG Chi-restraints excluded: chain F residue 326 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 23 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 61 optimal weight: 0.0570 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.148311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.131358 restraints weight = 9604.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134392 restraints weight = 5872.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.136409 restraints weight = 4021.877| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 6129 Z= 0.146 Angle : 0.606 12.312 8339 Z= 0.305 Chirality : 0.044 0.318 946 Planarity : 0.005 0.062 1054 Dihedral : 6.227 56.494 901 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.31 % Favored : 95.27 % Rotamer: Outliers : 5.13 % Allowed : 22.93 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.10 (0.32), residues: 719 helix: 1.06 (0.41), residues: 164 sheet: 0.51 (0.35), residues: 230 loop : -0.74 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 50 HIS 0.004 0.001 HIS D 61 PHE 0.013 0.002 PHE F 198 TYR 0.011 0.001 TYR F 272 ARG 0.005 0.000 ARG F 174 Details of bonding type rmsd link_NAG-ASN : bond 0.01244 ( 5) link_NAG-ASN : angle 3.95917 ( 15) hydrogen bonds : bond 0.03424 ( 262) hydrogen bonds : angle 4.92978 ( 768) SS BOND : bond 0.00438 ( 8) SS BOND : angle 0.73102 ( 16) covalent geometry : bond 0.00338 ( 6116) covalent geometry : angle 0.58300 ( 8308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.8213 (t) cc_final: 0.7966 (p) REVERT: C 84 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7860 (m) REVERT: D 42 ARG cc_start: 0.5860 (OUTLIER) cc_final: 0.4889 (ttm110) REVERT: D 123 PHE cc_start: 0.7172 (t80) cc_final: 0.6884 (t80) REVERT: F 90 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7817 (mt) REVERT: F 292 ASN cc_start: 0.8303 (t0) cc_final: 0.7295 (t0) REVERT: F 317 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7076 (ttm170) outliers start: 34 outliers final: 26 residues processed: 144 average time/residue: 0.1850 time to fit residues: 34.6099 Evaluate side-chains 149 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 317 ARG Chi-restraints excluded: chain F residue 326 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** 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 = 0.3859 r_free = 0.3859 target = 0.147757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.130452 restraints weight = 9624.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133570 restraints weight = 5815.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.135658 restraints weight = 3956.503| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 6129 Z= 0.183 Angle : 0.646 12.267 8339 Z= 0.324 Chirality : 0.044 0.320 946 Planarity : 0.006 0.075 1054 Dihedral : 6.291 55.724 901 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.73 % Favored : 94.85 % Rotamer: Outliers : 5.13 % Allowed : 23.08 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.04 (0.32), residues: 719 helix: 0.90 (0.40), residues: 169 sheet: 0.46 (0.35), residues: 230 loop : -0.86 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 322 HIS 0.004 0.001 HIS F 106 PHE 0.017 0.002 PHE F 198 TYR 0.013 0.002 TYR E 376 ARG 0.006 0.001 ARG F 174 Details of bonding type rmsd link_NAG-ASN : bond 0.01244 ( 5) link_NAG-ASN : angle 3.86966 ( 15) hydrogen bonds : bond 0.03630 ( 262) hydrogen bonds : angle 5.01587 ( 768) SS BOND : bond 0.00533 ( 8) SS BOND : angle 0.89688 ( 16) covalent geometry : bond 0.00423 ( 6116) covalent geometry : angle 0.62472 ( 8308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7736 (m) REVERT: D 42 ARG cc_start: 0.5996 (OUTLIER) cc_final: 0.5222 (ttm110) REVERT: D 123 PHE cc_start: 0.7059 (t80) cc_final: 0.6726 (t80) REVERT: D 127 MET cc_start: 0.6556 (mmp) cc_final: 0.6303 (mmp) REVERT: E 421 TYR cc_start: 0.8400 (m-80) cc_final: 0.7812 (m-80) REVERT: F 90 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7903 (mt) REVERT: F 220 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6759 (pttt) REVERT: F 272 TYR cc_start: 0.7693 (m-80) cc_final: 0.7400 (m-80) REVERT: F 292 ASN cc_start: 0.8317 (t0) cc_final: 0.7144 (t0) outliers start: 34 outliers final: 28 residues processed: 149 average time/residue: 0.2551 time to fit residues: 49.9483 Evaluate side-chains 155 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 433 SER Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 326 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.0370 chunk 62 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN E 331 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.148962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.131648 restraints weight = 9708.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.134801 restraints weight = 5844.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.136912 restraints weight = 3961.854| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 6129 Z= 0.135 Angle : 0.613 12.322 8339 Z= 0.308 Chirality : 0.043 0.314 946 Planarity : 0.005 0.063 1054 Dihedral : 6.217 56.327 901 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.62 % Favored : 95.97 % Rotamer: Outliers : 4.98 % Allowed : 23.53 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.15 (0.32), residues: 719 helix: 1.15 (0.41), residues: 164 sheet: 0.53 (0.35), residues: 231 loop : -0.74 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 322 HIS 0.004 0.001 HIS D 61 PHE 0.012 0.002 PHE F 198 TYR 0.014 0.001 TYR F 185 ARG 0.006 0.000 ARG F 174 Details of bonding type rmsd link_NAG-ASN : bond 0.01196 ( 5) link_NAG-ASN : angle 3.96981 ( 15) hydrogen bonds : bond 0.03328 ( 262) hydrogen bonds : angle 4.89156 ( 768) SS BOND : bond 0.00374 ( 8) SS BOND : angle 0.69408 ( 16) covalent geometry : bond 0.00313 ( 6116) covalent geometry : angle 0.58970 ( 8308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.8192 (t) cc_final: 0.7952 (p) REVERT: C 84 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7869 (m) REVERT: D 42 ARG cc_start: 0.5854 (OUTLIER) cc_final: 0.4850 (ttm110) REVERT: D 112 ARG cc_start: 0.7492 (mmt-90) cc_final: 0.7168 (mpt180) REVERT: D 123 PHE cc_start: 0.7185 (t80) cc_final: 0.6907 (t80) REVERT: E 421 TYR cc_start: 0.8455 (m-80) cc_final: 0.7883 (m-80) REVERT: F 90 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7825 (mt) REVERT: F 292 ASN cc_start: 0.8301 (t0) cc_final: 0.7273 (t0) outliers start: 33 outliers final: 27 residues processed: 142 average time/residue: 0.1964 time to fit residues: 36.0188 Evaluate side-chains 149 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 326 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 21 optimal weight: 0.0670 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.0270 chunk 27 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 6 optimal weight: 0.0000 overall best weight: 0.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.150234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.132988 restraints weight = 9646.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.136098 restraints weight = 5826.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.138194 restraints weight = 3945.119| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6129 Z= 0.115 Angle : 0.618 12.372 8339 Z= 0.307 Chirality : 0.043 0.309 946 Planarity : 0.005 0.063 1054 Dihedral : 6.169 56.465 901 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.34 % Favored : 96.24 % Rotamer: Outliers : 4.52 % Allowed : 24.28 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.28 (0.32), residues: 719 helix: 1.20 (0.41), residues: 164 sheet: 0.76 (0.36), residues: 225 loop : -0.73 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 50 HIS 0.004 0.001 HIS D 61 PHE 0.012 0.001 PHE F 198 TYR 0.014 0.001 TYR F 173 ARG 0.006 0.000 ARG F 174 Details of bonding type rmsd link_NAG-ASN : bond 0.01171 ( 5) link_NAG-ASN : angle 4.01969 ( 15) hydrogen bonds : bond 0.03199 ( 262) hydrogen bonds : angle 4.81757 ( 768) SS BOND : bond 0.00324 ( 8) SS BOND : angle 0.66937 ( 16) covalent geometry : bond 0.00268 ( 6116) covalent geometry : angle 0.59427 ( 8308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.8117 (t) cc_final: 0.7899 (p) REVERT: C 84 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7712 (m) REVERT: C 112 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.6179 (tpp80) REVERT: D 42 ARG cc_start: 0.5751 (OUTLIER) cc_final: 0.4809 (ttm110) REVERT: D 123 PHE cc_start: 0.7020 (t80) cc_final: 0.6773 (t80) REVERT: F 45 GLN cc_start: 0.7236 (tt0) cc_final: 0.6991 (tt0) REVERT: F 88 THR cc_start: 0.7355 (t) cc_final: 0.6592 (m) REVERT: F 90 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7860 (mt) REVERT: F 193 ASN cc_start: 0.7645 (m-40) cc_final: 0.7132 (m110) REVERT: F 292 ASN cc_start: 0.8248 (t0) cc_final: 0.7174 (t0) REVERT: F 322 TRP cc_start: 0.7851 (m100) cc_final: 0.7522 (m-10) outliers start: 30 outliers final: 24 residues processed: 140 average time/residue: 0.2313 time to fit residues: 42.1619 Evaluate side-chains 145 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 326 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 55 optimal weight: 0.0570 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** 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 = 0.3881 r_free = 0.3881 target = 0.149449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.132093 restraints weight = 9767.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.135251 restraints weight = 5922.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.137376 restraints weight = 4025.352| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 6129 Z= 0.138 Angle : 0.620 12.266 8339 Z= 0.310 Chirality : 0.043 0.308 946 Planarity : 0.005 0.062 1054 Dihedral : 6.248 55.915 901 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.76 % Favored : 95.83 % Rotamer: Outliers : 4.68 % Allowed : 24.13 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.27 (0.32), residues: 719 helix: 1.18 (0.41), residues: 164 sheet: 0.78 (0.36), residues: 225 loop : -0.74 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 434 HIS 0.004 0.001 HIS D 61 PHE 0.015 0.002 PHE F 198 TYR 0.013 0.001 TYR F 173 ARG 0.006 0.000 ARG F 174 Details of bonding type rmsd link_NAG-ASN : bond 0.01164 ( 5) link_NAG-ASN : angle 3.92463 ( 15) hydrogen bonds : bond 0.03281 ( 262) hydrogen bonds : angle 4.86242 ( 768) SS BOND : bond 0.00406 ( 8) SS BOND : angle 0.73420 ( 16) covalent geometry : bond 0.00321 ( 6116) covalent geometry : angle 0.59779 ( 8308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2448.47 seconds wall clock time: 43 minutes 48.04 seconds (2628.04 seconds total)