Starting phenix.real_space_refine on Fri Oct 10 13:18:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tld_41367/10_2025/8tld_41367.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tld_41367/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8tld_41367/10_2025/8tld_41367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tld_41367/10_2025/8tld_41367.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tld_41367/10_2025/8tld_41367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tld_41367/10_2025/8tld_41367.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.50, per 1000 atoms: 0.25 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: 0.50 Conformation dependent library (CDL) restraints added in 328.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.22 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: 0.94 Time building geometry restraints manager: 0.64 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: 0.530 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.240 Find NCS groups from input model: 0.050 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.360 ------------------------------------------------------------------------------- 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 : 12.31 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (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 ARG 0.018 0.001 ARG C 110 TYR 0.009 0.001 TYR F 172 PHE 0.024 0.002 PHE D 116 TRP 0.032 0.002 TRP F 322 HIS 0.006 0.001 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 6116) covalent geometry : angle 0.73239 ( 8308) SS BOND : bond 0.00319 ( 8) SS BOND : angle 0.68439 ( 16) hydrogen bonds : bond 0.19589 ( 262) hydrogen bonds : angle 7.41462 ( 768) link_NAG-ASN : bond 0.01686 ( 5) link_NAG-ASN : angle 4.76115 ( 15) *********************** 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 : 0.228 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: 0.7840 (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: 0.0925 time to fit residues: 14.9911 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 : 0.231 ------------------------------------------------------------------------------- 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 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.148654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.131394 restraints weight = 9849.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.134299 restraints weight = 5979.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.136310 restraints weight = 4099.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.137662 restraints weight = 3069.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.138584 restraints weight = 2478.015| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.0973 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= 0.183 Angle : 0.666 12.406 8339 Z= 0.338 Chirality : 0.046 0.377 946 Planarity : 0.006 0.094 1054 Dihedral : 6.812 55.045 903 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.17 % Favored : 95.41 % Rotamer: Outliers : 4.07 % Allowed : 22.02 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.32), residues: 719 helix: 0.72 (0.41), residues: 164 sheet: 0.56 (0.35), residues: 234 loop : -0.85 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 174 TYR 0.014 0.002 TYR E 376 PHE 0.015 0.002 PHE F 198 TRP 0.018 0.002 TRP F 322 HIS 0.004 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 6116) covalent geometry : angle 0.63332 ( 8308) SS BOND : bond 0.00469 ( 8) SS BOND : angle 0.94641 ( 16) hydrogen bonds : bond 0.04219 ( 262) hydrogen bonds : angle 5.51387 ( 768) link_NAG-ASN : bond 0.01445 ( 5) link_NAG-ASN : angle 4.83624 ( 15) *********************** 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 163 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 PRO cc_start: 0.6975 (Cg_exo) cc_final: 0.6741 (Cg_endo) REVERT: C 88 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7270 (tp) REVERT: F 40 VAL cc_start: 0.8282 (t) cc_final: 0.8044 (m) REVERT: F 273 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6665 (mt-10) REVERT: F 292 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7165 (t0) REVERT: F 322 TRP cc_start: 0.7972 (m100) cc_final: 0.7339 (m-10) REVERT: F 324 GLU cc_start: 0.7599 (tp30) cc_final: 0.7310 (tp30) outliers start: 27 outliers final: 9 residues processed: 148 average time/residue: 0.0842 time to fit residues: 15.9717 Evaluate side-chains 143 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL 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 259 GLU 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 29 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 49 optimal weight: 0.0370 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.149200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131795 restraints weight = 9728.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.134740 restraints weight = 5921.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.136745 restraints weight = 4067.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.138151 restraints weight = 3057.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.139108 restraints weight = 2456.191| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6129 Z= 0.139 Angle : 0.595 12.265 8339 Z= 0.303 Chirality : 0.043 0.343 946 Planarity : 0.006 0.071 1054 Dihedral : 6.590 54.056 903 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.92 % Favored : 96.66 % Rotamer: Outliers : 4.07 % Allowed : 21.12 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.32), residues: 719 helix: 1.11 (0.42), residues: 158 sheet: 0.61 (0.35), residues: 230 loop : -0.72 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 174 TYR 0.014 0.001 TYR F 272 PHE 0.011 0.002 PHE F 198 TRP 0.011 0.001 TRP F 322 HIS 0.003 0.001 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6116) covalent geometry : angle 0.56875 ( 8308) SS BOND : bond 0.00349 ( 8) SS BOND : angle 0.69845 ( 16) hydrogen bonds : bond 0.03751 ( 262) hydrogen bonds : angle 5.14139 ( 768) link_NAG-ASN : bond 0.01334 ( 5) link_NAG-ASN : angle 4.17409 ( 15) *********************** 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 155 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7794 (m) REVERT: D 112 ARG cc_start: 0.7422 (mmt-90) cc_final: 0.7003 (mpt180) REVERT: F 40 VAL cc_start: 0.8361 (t) cc_final: 0.8139 (m) REVERT: F 273 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6846 (mt-10) REVERT: F 292 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7135 (t0) REVERT: F 322 TRP cc_start: 0.7921 (m100) cc_final: 0.7445 (m-10) outliers start: 27 outliers final: 14 residues processed: 142 average time/residue: 0.0928 time to fit residues: 16.7406 Evaluate side-chains 139 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 84 THR 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 259 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 309 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.148378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.130950 restraints weight = 9711.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.134084 restraints weight = 5805.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.136165 restraints weight = 3931.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137603 restraints weight = 2921.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.138552 restraints weight = 2327.757| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.1513 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= 0.166 Angle : 0.609 12.328 8339 Z= 0.309 Chirality : 0.044 0.338 946 Planarity : 0.005 0.061 1054 Dihedral : 6.455 56.640 903 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.59 % Favored : 94.99 % Rotamer: Outliers : 5.43 % Allowed : 20.66 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.32), residues: 719 helix: 0.94 (0.41), residues: 164 sheet: 0.59 (0.35), residues: 230 loop : -0.77 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 174 TYR 0.013 0.002 TYR E 376 PHE 0.014 0.002 PHE F 198 TRP 0.016 0.002 TRP F 50 HIS 0.004 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 6116) covalent geometry : angle 0.58622 ( 8308) SS BOND : bond 0.00433 ( 8) SS BOND : angle 0.77906 ( 16) hydrogen bonds : bond 0.03619 ( 262) hydrogen bonds : angle 5.05298 ( 768) link_NAG-ASN : bond 0.01304 ( 5) link_NAG-ASN : angle 3.93564 ( 15) *********************** 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 167 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.8252 (t) cc_final: 0.7984 (p) REVERT: C 84 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7790 (m) REVERT: D 112 ARG cc_start: 0.7401 (mmt-90) cc_final: 0.6993 (mpt180) REVERT: F 40 VAL cc_start: 0.8397 (t) cc_final: 0.8182 (m) REVERT: F 220 LYS cc_start: 0.6911 (OUTLIER) cc_final: 0.6648 (pttt) REVERT: F 273 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6817 (mt-10) REVERT: F 292 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7126 (t0) REVERT: F 322 TRP cc_start: 0.7950 (m100) cc_final: 0.7389 (m-10) outliers start: 36 outliers final: 23 residues processed: 148 average time/residue: 0.0849 time to fit residues: 16.3459 Evaluate side-chains 155 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR 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 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 28 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 156 THR 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 Chi-restraints excluded: chain F residue 309 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 0.0970 chunk 57 optimal weight: 0.2980 chunk 67 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3888 r_free = 0.3888 target = 0.149925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.132624 restraints weight = 9802.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.135768 restraints weight = 5838.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.137869 restraints weight = 3944.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.139317 restraints weight = 2910.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.140355 restraints weight = 2302.616| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6129 Z= 0.134 Angle : 0.588 12.310 8339 Z= 0.298 Chirality : 0.043 0.324 946 Planarity : 0.005 0.066 1054 Dihedral : 6.308 56.845 903 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.48 % Favored : 96.11 % Rotamer: Outliers : 4.07 % Allowed : 22.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.32), residues: 719 helix: 1.05 (0.41), residues: 164 sheet: 0.60 (0.35), residues: 230 loop : -0.69 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 174 TYR 0.010 0.001 TYR F 172 PHE 0.020 0.002 PHE D 123 TRP 0.016 0.001 TRP F 50 HIS 0.003 0.001 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6116) covalent geometry : angle 0.56458 ( 8308) SS BOND : bond 0.00393 ( 8) SS BOND : angle 0.70144 ( 16) hydrogen bonds : bond 0.03336 ( 262) hydrogen bonds : angle 4.91593 ( 768) link_NAG-ASN : bond 0.01269 ( 5) link_NAG-ASN : angle 3.87327 ( 15) *********************** 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 150 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.8162 (t) cc_final: 0.7892 (p) REVERT: C 84 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7766 (m) REVERT: D 112 ARG cc_start: 0.7328 (mmt-90) cc_final: 0.6926 (mpt180) REVERT: D 123 PHE cc_start: 0.7245 (t80) cc_final: 0.6100 (t80) REVERT: E 377 ARG cc_start: 0.8082 (ptt-90) cc_final: 0.7473 (ttp80) REVERT: F 220 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6632 (pttt) REVERT: F 273 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6785 (mt-10) REVERT: F 292 ASN cc_start: 0.8241 (t0) cc_final: 0.7184 (t0) REVERT: F 317 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6907 (ttm170) REVERT: F 322 TRP cc_start: 0.7933 (m100) cc_final: 0.7329 (m-10) outliers start: 27 outliers final: 19 residues processed: 138 average time/residue: 0.0806 time to fit residues: 14.5719 Evaluate side-chains 143 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 F residue 28 ILE Chi-restraints excluded: chain F residue 46 VAL 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 259 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 309 ARG Chi-restraints excluded: chain F residue 317 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 60 optimal weight: 1.9990 chunk 62 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.0166 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.148105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.130855 restraints weight = 9699.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133924 restraints weight = 5851.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.135988 restraints weight = 3979.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.137425 restraints weight = 2963.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.138389 restraints weight = 2357.634| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 6129 Z= 0.186 Angle : 0.634 12.193 8339 Z= 0.320 Chirality : 0.044 0.325 946 Planarity : 0.005 0.065 1054 Dihedral : 6.248 55.733 901 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.45 % Favored : 95.13 % Rotamer: Outliers : 5.58 % Allowed : 22.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.32), residues: 719 helix: 1.04 (0.41), residues: 164 sheet: 0.45 (0.35), residues: 230 loop : -0.78 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 52 TYR 0.014 0.002 TYR E 376 PHE 0.017 0.002 PHE F 198 TRP 0.018 0.002 TRP F 50 HIS 0.005 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 6116) covalent geometry : angle 0.61261 ( 8308) SS BOND : bond 0.00529 ( 8) SS BOND : angle 0.90133 ( 16) hydrogen bonds : bond 0.03627 ( 262) hydrogen bonds : angle 5.02345 ( 768) link_NAG-ASN : bond 0.01263 ( 5) link_NAG-ASN : angle 3.79606 ( 15) *********************** 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 166 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 112 ARG cc_start: 0.7103 (mmt-90) cc_final: 0.6765 (mpt180) REVERT: E 421 TYR cc_start: 0.8366 (m-80) cc_final: 0.7592 (m-80) REVERT: F 206 LYS cc_start: 0.7983 (mtmm) cc_final: 0.7781 (mtmm) REVERT: F 220 LYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6710 (pttt) REVERT: F 273 GLU cc_start: 0.7369 (mt-10) cc_final: 0.6496 (mt-10) REVERT: F 292 ASN cc_start: 0.8358 (t0) cc_final: 0.7243 (t0) REVERT: F 322 TRP cc_start: 0.7915 (m100) cc_final: 0.7208 (m-10) outliers start: 37 outliers final: 29 residues processed: 150 average time/residue: 0.0857 time to fit residues: 16.4764 Evaluate side-chains 156 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 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 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 40 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 61 VAL 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 220 LYS Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 309 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 53 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.148202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.130667 restraints weight = 9770.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.133823 restraints weight = 5861.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.135946 restraints weight = 3988.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.137432 restraints weight = 2947.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.138231 restraints weight = 2338.247| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 6129 Z= 0.169 Angle : 0.642 12.153 8339 Z= 0.322 Chirality : 0.045 0.319 946 Planarity : 0.006 0.097 1054 Dihedral : 6.472 56.111 901 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.31 % Favored : 95.27 % Rotamer: Outliers : 5.13 % Allowed : 23.23 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.32), residues: 719 helix: 1.09 (0.41), residues: 164 sheet: 0.43 (0.34), residues: 230 loop : -0.78 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 174 TYR 0.012 0.002 TYR E 376 PHE 0.014 0.002 PHE F 198 TRP 0.018 0.002 TRP F 50 HIS 0.004 0.001 HIS D 61 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 6116) covalent geometry : angle 0.62054 ( 8308) SS BOND : bond 0.00478 ( 8) SS BOND : angle 0.81467 ( 16) hydrogen bonds : bond 0.03502 ( 262) hydrogen bonds : angle 4.93406 ( 768) link_NAG-ASN : bond 0.01287 ( 5) link_NAG-ASN : angle 3.92864 ( 15) *********************** 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 159 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7749 (m) REVERT: D 42 ARG cc_start: 0.5779 (OUTLIER) cc_final: 0.4826 (ttm110) REVERT: D 112 ARG cc_start: 0.7264 (mmt-90) cc_final: 0.6904 (mpt180) REVERT: D 127 MET cc_start: 0.6576 (mmp) cc_final: 0.6304 (mmm) REVERT: E 421 TYR cc_start: 0.8351 (m-80) cc_final: 0.7554 (m-80) REVERT: F 220 LYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6689 (pttt) REVERT: F 273 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6595 (mt-10) REVERT: F 292 ASN cc_start: 0.8297 (t0) cc_final: 0.7166 (t0) REVERT: F 322 TRP cc_start: 0.7940 (m100) cc_final: 0.7221 (m-10) outliers start: 34 outliers final: 25 residues processed: 144 average time/residue: 0.0834 time to fit residues: 15.5641 Evaluate side-chains 150 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 78 MET 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 61 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 220 LYS Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 309 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 20 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.148692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131245 restraints weight = 9662.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.134409 restraints weight = 5807.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136521 restraints weight = 3937.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.138017 restraints weight = 2916.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.139086 restraints weight = 2309.190| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 6129 Z= 0.143 Angle : 0.618 12.206 8339 Z= 0.311 Chirality : 0.044 0.314 946 Planarity : 0.005 0.063 1054 Dihedral : 6.295 56.096 901 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.17 % Favored : 95.41 % Rotamer: Outliers : 4.68 % Allowed : 23.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.32), residues: 719 helix: 1.16 (0.41), residues: 164 sheet: 0.53 (0.35), residues: 230 loop : -0.79 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 174 TYR 0.012 0.001 TYR F 185 PHE 0.028 0.002 PHE D 123 TRP 0.018 0.002 TRP F 50 HIS 0.005 0.001 HIS D 61 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6116) covalent geometry : angle 0.59440 ( 8308) SS BOND : bond 0.00414 ( 8) SS BOND : angle 0.72996 ( 16) hydrogen bonds : bond 0.03332 ( 262) hydrogen bonds : angle 4.84391 ( 768) link_NAG-ASN : bond 0.01213 ( 5) link_NAG-ASN : angle 3.97452 ( 15) *********************** 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 157 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.8139 (t) cc_final: 0.7889 (p) REVERT: C 84 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7754 (m) REVERT: D 112 ARG cc_start: 0.7178 (mmt-90) cc_final: 0.6857 (mpt180) REVERT: D 123 PHE cc_start: 0.7155 (t80) cc_final: 0.6327 (t80) REVERT: D 127 MET cc_start: 0.6567 (mmp) cc_final: 0.6078 (mmp) REVERT: F 220 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6670 (pttt) REVERT: F 273 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6680 (mt-10) REVERT: F 292 ASN cc_start: 0.8271 (t0) cc_final: 0.7202 (t0) REVERT: F 317 ARG cc_start: 0.7151 (ttm170) cc_final: 0.6901 (ttm170) REVERT: F 322 TRP cc_start: 0.7949 (m100) cc_final: 0.7189 (m-10) outliers start: 31 outliers final: 24 residues processed: 143 average time/residue: 0.0844 time to fit residues: 15.5634 Evaluate side-chains 148 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 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 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 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 289 LEU Chi-restraints excluded: chain F residue 309 ARG 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 9 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.148082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.130473 restraints weight = 9749.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133630 restraints weight = 5860.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.135759 restraints weight = 3979.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.137165 restraints weight = 2955.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.138269 restraints weight = 2370.738| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 6129 Z= 0.174 Angle : 0.645 12.105 8339 Z= 0.323 Chirality : 0.044 0.311 946 Planarity : 0.005 0.061 1054 Dihedral : 6.256 55.357 901 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.45 % Favored : 95.13 % Rotamer: Outliers : 4.83 % Allowed : 23.53 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.32), residues: 719 helix: 1.11 (0.41), residues: 164 sheet: 0.51 (0.35), residues: 230 loop : -0.84 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 174 TYR 0.012 0.002 TYR E 376 PHE 0.023 0.002 PHE D 123 TRP 0.015 0.002 TRP F 50 HIS 0.004 0.001 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 6116) covalent geometry : angle 0.62375 ( 8308) SS BOND : bond 0.00512 ( 8) SS BOND : angle 0.86153 ( 16) hydrogen bonds : bond 0.03490 ( 262) hydrogen bonds : angle 4.90336 ( 768) link_NAG-ASN : bond 0.01217 ( 5) link_NAG-ASN : angle 3.88706 ( 15) *********************** 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 153 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7781 (m) REVERT: D 42 ARG cc_start: 0.5904 (OUTLIER) cc_final: 0.4920 (ttm110) REVERT: D 123 PHE cc_start: 0.7187 (t80) cc_final: 0.6426 (t80) REVERT: D 127 MET cc_start: 0.6573 (mmp) cc_final: 0.6080 (mmp) REVERT: E 377 ARG cc_start: 0.8122 (ptt-90) cc_final: 0.7633 (ttp80) REVERT: E 421 TYR cc_start: 0.8425 (m-80) cc_final: 0.7804 (m-80) REVERT: F 68 LYS cc_start: 0.5571 (OUTLIER) cc_final: 0.5345 (tptm) REVERT: F 193 ASN cc_start: 0.7701 (m-40) cc_final: 0.7451 (m110) REVERT: F 220 LYS cc_start: 0.7008 (OUTLIER) cc_final: 0.6746 (pttt) REVERT: F 273 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6198 (mt-10) REVERT: F 292 ASN cc_start: 0.8292 (t0) cc_final: 0.7210 (t0) REVERT: F 322 TRP cc_start: 0.7981 (m100) cc_final: 0.7169 (m-10) outliers start: 32 outliers final: 27 residues processed: 138 average time/residue: 0.0878 time to fit residues: 15.7449 Evaluate side-chains 150 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 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 D residue 91 ASN 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 68 LYS 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 289 LEU Chi-restraints excluded: chain F residue 309 ARG 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 18 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 F 45 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.148444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.131026 restraints weight = 9732.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134116 restraints weight = 5917.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.136187 restraints weight = 4043.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.137610 restraints weight = 3022.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.138642 restraints weight = 2421.067| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.2157 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= 0.166 Angle : 0.655 12.078 8339 Z= 0.328 Chirality : 0.044 0.310 946 Planarity : 0.006 0.096 1054 Dihedral : 6.257 55.431 901 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.45 % Favored : 95.13 % Rotamer: Outliers : 4.98 % Allowed : 23.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.32), residues: 719 helix: 1.10 (0.41), residues: 164 sheet: 0.51 (0.35), residues: 230 loop : -0.84 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 174 TYR 0.011 0.002 TYR E 376 PHE 0.024 0.002 PHE D 123 TRP 0.025 0.002 TRP E 434 HIS 0.004 0.001 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 6116) covalent geometry : angle 0.63293 ( 8308) SS BOND : bond 0.00478 ( 8) SS BOND : angle 0.79940 ( 16) hydrogen bonds : bond 0.03487 ( 262) hydrogen bonds : angle 4.90372 ( 768) link_NAG-ASN : bond 0.01219 ( 5) link_NAG-ASN : angle 4.02682 ( 15) ********************** 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 151 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7826 (m) REVERT: D 42 ARG cc_start: 0.5927 (OUTLIER) cc_final: 0.4941 (ttm110) REVERT: D 123 PHE cc_start: 0.7209 (t80) cc_final: 0.6450 (t80) REVERT: D 127 MET cc_start: 0.6574 (mmp) cc_final: 0.6086 (mmp) REVERT: E 377 ARG cc_start: 0.8113 (ptt-90) cc_final: 0.7637 (ttp80) REVERT: E 421 TYR cc_start: 0.8449 (m-80) cc_final: 0.7846 (m-80) REVERT: F 68 LYS cc_start: 0.5568 (OUTLIER) cc_final: 0.5353 (tptm) REVERT: F 193 ASN cc_start: 0.7683 (m-40) cc_final: 0.7464 (m110) REVERT: F 220 LYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6719 (pttt) REVERT: F 273 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6217 (mt-10) REVERT: F 292 ASN cc_start: 0.8284 (t0) cc_final: 0.7190 (t0) REVERT: F 322 TRP cc_start: 0.7971 (m100) cc_final: 0.7157 (m-10) outliers start: 33 outliers final: 27 residues processed: 135 average time/residue: 0.0805 time to fit residues: 14.1585 Evaluate side-chains 150 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 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 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 68 LYS 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 220 LYS Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 309 ARG 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 35 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 45 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.144652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126837 restraints weight = 9860.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.129921 restraints weight = 6047.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.131976 restraints weight = 4175.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.133413 restraints weight = 3163.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.134406 restraints weight = 2541.654| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.120 6129 Z= 0.293 Angle : 0.761 11.737 8339 Z= 0.383 Chirality : 0.047 0.321 946 Planarity : 0.007 0.114 1054 Dihedral : 6.602 54.302 901 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.42 % Favored : 94.16 % Rotamer: Outliers : 4.83 % Allowed : 23.53 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.31), residues: 719 helix: 0.70 (0.40), residues: 169 sheet: 0.22 (0.35), residues: 225 loop : -1.07 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 174 TYR 0.017 0.003 TYR E 376 PHE 0.026 0.003 PHE F 198 TRP 0.019 0.003 TRP F 322 HIS 0.007 0.002 HIS F 119 Details of bonding type rmsd covalent geometry : bond 0.00663 ( 6116) covalent geometry : angle 0.74335 ( 8308) SS BOND : bond 0.00755 ( 8) SS BOND : angle 1.27267 ( 16) hydrogen bonds : bond 0.04265 ( 262) hydrogen bonds : angle 5.25582 ( 768) link_NAG-ASN : bond 0.01263 ( 5) link_NAG-ASN : angle 3.81236 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1205.62 seconds wall clock time: 21 minutes 31.61 seconds (1291.61 seconds total)