Starting phenix.real_space_refine on Thu Jul 2 03:55:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pm4_17757/07_2026/8pm4_17757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pm4_17757/07_2026/8pm4_17757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pm4_17757/07_2026/8pm4_17757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pm4_17757/07_2026/8pm4_17757.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pm4_17757/07_2026/8pm4_17757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pm4_17757/07_2026/8pm4_17757.map" } resolution = 2.93 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= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 95 5.49 5 S 12 5.16 5 C 3790 2.51 5 N 1276 2.21 5 O 1451 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6624 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4611 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 575} Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 2, 'ASP:plan': 11, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1112 Classifications: {'RNA': 52} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 23, 'rna3p_pyr': 22} Link IDs: {'rna2p': 6, 'rna3p': 45} Chain: "C" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 558 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 343 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Time building chain proxies: 1.28, per 1000 atoms: 0.19 Number of scatterers: 6624 At special positions: 0 Unit cell: (99, 90.2, 101.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 95 15.00 O 1451 8.00 N 1276 7.00 C 3790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 580 " 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 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 287.7 milliseconds 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1148 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 56.8% alpha, 14.2% beta 34 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 18 through 53 removed outlier: 3.593A pdb=" N ALA A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 84 Processing helix chain 'A' and resid 91 through 119 removed outlier: 4.112A pdb=" N ALA A 95 " --> pdb=" O HIS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 145 Processing helix chain 'A' and resid 151 through 175 Processing helix chain 'A' and resid 206 through 212 Processing helix chain 'A' and resid 228 through 235 removed outlier: 3.935A pdb=" N THR A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 368 through 404 removed outlier: 4.020A pdb=" N GLU A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 425 through 439 removed outlier: 4.208A pdb=" N PHE A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR A 439 " --> pdb=" O GLN A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 491 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 508 through 511 Processing helix chain 'A' and resid 514 through 529 Processing helix chain 'A' and resid 529 through 544 Processing helix chain 'A' and resid 588 through 604 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 195 removed outlier: 5.704A pdb=" N ILE A 283 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS A 306 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 285 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ALA A 299 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 3 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N THR A 263 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER A 254 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU A 265 " --> pdb=" O CYS A 252 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 353 through 355 removed outlier: 3.673A pdb=" N ALA A 335 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A 334 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 319 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ASP A 497 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N VAL A 321 " --> pdb=" O ASP A 497 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 578 through 579 310 hydrogen bonds defined for protein. 912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 174 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1471 1.33 - 1.45: 1988 1.45 - 1.57: 3297 1.57 - 1.69: 188 1.69 - 1.81: 19 Bond restraints: 6963 Sorted by residual: bond pdb=" C3' DT C -6 " pdb=" O3' DT C -6 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" O4' DG C -9 " pdb=" C1' DG C -9 " ideal model delta sigma weight residual 1.420 1.384 0.036 1.10e-02 8.26e+03 1.10e+01 bond pdb=" C3' DG C 5 " pdb=" C2' DG C 5 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.38e+00 bond pdb=" C3' DG C -17 " pdb=" O3' DG C -17 " ideal model delta sigma weight residual 1.435 1.398 0.037 1.30e-02 5.92e+03 8.20e+00 bond pdb=" O4' DC C -2 " pdb=" C1' DC C -2 " ideal model delta sigma weight residual 1.420 1.389 0.031 1.10e-02 8.26e+03 8.15e+00 ... (remaining 6958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 9314 1.36 - 2.72: 520 2.72 - 4.08: 71 4.08 - 5.44: 6 5.44 - 6.80: 2 Bond angle restraints: 9913 Sorted by residual: angle pdb=" O4' DG C -15 " pdb=" C4' DG C -15 " pdb=" C3' DG C -15 " ideal model delta sigma weight residual 106.00 102.64 3.36 6.00e-01 2.78e+00 3.14e+01 angle pdb=" N3 DT D -1 " pdb=" C4 DT D -1 " pdb=" O4 DT D -1 " ideal model delta sigma weight residual 119.90 122.75 -2.85 6.00e-01 2.78e+00 2.25e+01 angle pdb=" O4' DG D -7 " pdb=" C4' DG D -7 " pdb=" C3' DG D -7 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.23e+01 angle pdb=" N3 DT C -11 " pdb=" C4 DT C -11 " pdb=" O4 DT C -11 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT D -2 " pdb=" C4 DT D -2 " pdb=" O4 DT D -2 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 9908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.50: 3691 27.50 - 54.99: 354 54.99 - 82.49: 104 82.49 - 109.99: 1 109.99 - 137.49: 1 Dihedral angle restraints: 4151 sinusoidal: 2388 harmonic: 1763 Sorted by residual: dihedral pdb=" CA ARG A 88 " pdb=" C ARG A 88 " pdb=" N PRO A 89 " pdb=" CA PRO A 89 " ideal model delta harmonic sigma weight residual -180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CB CYS A 563 " pdb=" SG CYS A 563 " pdb=" SG CYS A 580 " pdb=" CB CYS A 580 " ideal model delta sinusoidal sigma weight residual -86.00 -118.48 32.48 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CA ASP A 147 " pdb=" C ASP A 147 " pdb=" N GLY A 148 " pdb=" CA GLY A 148 " ideal model delta harmonic sigma weight residual 180.00 -161.41 -18.59 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 4148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1047 0.076 - 0.151: 118 0.151 - 0.227: 6 0.227 - 0.303: 0 0.303 - 0.378: 1 Chirality restraints: 1172 Sorted by residual: chirality pdb=" P DC D 0 " pdb=" OP1 DC D 0 " pdb=" OP2 DC D 0 " pdb=" O5' DC D 0 " both_signs ideal model delta sigma weight residual True 2.34 -2.71 -0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" C1' G B 2 " pdb=" O4' G B 2 " pdb=" C2' G B 2 " pdb=" N9 G B 2 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C3' DG C -12 " pdb=" C4' DG C -12 " pdb=" O3' DG C -12 " pdb=" C2' DG C -12 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1169 not shown) Planarity restraints: 929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 10 " -0.031 2.00e-02 2.50e+03 1.32e-02 4.79e+00 pdb=" N9 A B 10 " 0.026 2.00e-02 2.50e+03 pdb=" C8 A B 10 " 0.007 2.00e-02 2.50e+03 pdb=" N7 A B 10 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A B 10 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A B 10 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A B 10 " -0.010 2.00e-02 2.50e+03 pdb=" N1 A B 10 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A B 10 " 0.005 2.00e-02 2.50e+03 pdb=" N3 A B 10 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A B 10 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 4 " 0.028 2.00e-02 2.50e+03 1.37e-02 4.22e+00 pdb=" N1 U B 4 " -0.026 2.00e-02 2.50e+03 pdb=" C2 U B 4 " -0.000 2.00e-02 2.50e+03 pdb=" O2 U B 4 " -0.007 2.00e-02 2.50e+03 pdb=" N3 U B 4 " 0.004 2.00e-02 2.50e+03 pdb=" C4 U B 4 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U B 4 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U B 4 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U B 4 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 2 " 0.029 2.00e-02 2.50e+03 1.17e-02 4.12e+00 pdb=" N9 G B 2 " -0.025 2.00e-02 2.50e+03 pdb=" C8 G B 2 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G B 2 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G B 2 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 2 " 0.005 2.00e-02 2.50e+03 pdb=" O6 G B 2 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G B 2 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G B 2 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G B 2 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 2 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G B 2 " -0.004 2.00e-02 2.50e+03 ... (remaining 926 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1088 2.76 - 3.29: 6209 3.29 - 3.83: 12435 3.83 - 4.36: 14656 4.36 - 4.90: 22918 Nonbonded interactions: 57306 Sorted by model distance: nonbonded pdb=" NH1 ARG A 241 " pdb=" OP2 C B -5 " model vdw 2.220 3.120 nonbonded pdb=" NZ LYS A 460 " pdb=" OE2 GLU A 464 " model vdw 2.253 3.120 nonbonded pdb=" NH2 ARG A 393 " pdb=" O TRP A 423 " model vdw 2.254 3.120 nonbonded pdb=" OE2 GLU A 452 " pdb=" NH2 ARG A 455 " model vdw 2.264 3.120 nonbonded pdb=" NH2 ARG A 173 " pdb=" O ALA A 179 " model vdw 2.268 3.120 ... (remaining 57301 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.620 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:8.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 : 0.007 0.045 6964 Z= 0.543 Angle : 0.679 6.801 9915 Z= 0.536 Chirality : 0.048 0.378 1172 Planarity : 0.006 0.046 929 Dihedral : 20.606 137.486 3000 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.32 % Allowed : 9.45 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: 1.17 (0.33), residues: 602 helix: 1.89 (0.28), residues: 321 sheet: -0.65 (0.51), residues: 89 loop : -0.33 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 249 TYR 0.012 0.002 TYR A 42 PHE 0.007 0.002 PHE A 487 TRP 0.014 0.002 TRP A 226 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00747 / 0.54 ( 6963) covalent geometry : angle 0.67838 / 0.54 ( 9913) SS BOND : bond 0.00330 / 0.17 ( 1) SS BOND : angle 1.50477 / 0.88 ( 2) hydrogen bonds : bond 0.10344 / 7.03 ( 399) hydrogen bonds : angle 4.59758 / 3.42 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 400 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6596 (mp) outliers start: 6 outliers final: 0 residues processed: 56 average time/residue: 0.4505 time to fit residues: 26.7600 Evaluate side-chains 39 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.151246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.118123 restraints weight = 8248.519| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.53 r_work: 0.3413 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6964 Z= 0.153 Angle : 0.536 5.665 9915 Z= 0.316 Chirality : 0.040 0.196 1172 Planarity : 0.005 0.037 929 Dihedral : 22.520 140.326 1979 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.86 % Allowed : 12.53 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: 1.71 (0.33), residues: 602 helix: 2.27 (0.27), residues: 322 sheet: -0.08 (0.60), residues: 74 loop : -0.18 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 83 TYR 0.026 0.002 TYR A 587 PHE 0.005 0.001 PHE A 155 TRP 0.015 0.001 TRP A 454 HIS 0.007 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 ( 6963) covalent geometry : angle 0.53523 / 0.32 ( 9913) SS BOND : bond 0.00008 / 0.00 ( 1) SS BOND : angle 2.07458 / 1.19 ( 2) hydrogen bonds : bond 0.04966 / 3.49 ( 399) hydrogen bonds : angle 3.82494 / 2.85 ( 1086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: A 276 MET cc_start: 0.9139 (mmt) cc_final: 0.8905 (mmt) REVERT: A 400 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6603 (mp) REVERT: A 560 HIS cc_start: 0.7732 (t-170) cc_final: 0.7250 (t-170) outliers start: 13 outliers final: 3 residues processed: 54 average time/residue: 0.3590 time to fit residues: 20.8474 Evaluate side-chains 47 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 400 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.0050 chunk 64 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.151088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.117624 restraints weight = 8139.848| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.53 r_work: 0.3415 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6964 Z= 0.161 Angle : 0.524 5.914 9915 Z= 0.307 Chirality : 0.040 0.198 1172 Planarity : 0.004 0.035 929 Dihedral : 22.425 140.977 1979 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.76 % Allowed : 15.60 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: 1.89 (0.34), residues: 602 helix: 2.39 (0.27), residues: 322 sheet: 0.17 (0.61), residues: 73 loop : -0.11 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 543 TYR 0.025 0.002 TYR A 587 PHE 0.005 0.001 PHE A 155 TRP 0.012 0.001 TRP A 454 HIS 0.008 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 ( 6963) covalent geometry : angle 0.52330 / 0.31 ( 9913) SS BOND : bond 0.00066 / 0.03 ( 1) SS BOND : angle 1.79162 / 1.03 ( 2) hydrogen bonds : bond 0.04762 / 3.36 ( 399) hydrogen bonds : angle 3.71096 / 2.78 ( 1086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6956 (mmp) cc_final: 0.6672 (mmm) REVERT: A 276 MET cc_start: 0.9181 (mmt) cc_final: 0.8970 (mmt) REVERT: A 400 LEU cc_start: 0.7187 (mp) cc_final: 0.6674 (mp) REVERT: A 494 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8093 (tt) REVERT: A 560 HIS cc_start: 0.7829 (t-170) cc_final: 0.7309 (t-170) outliers start: 8 outliers final: 4 residues processed: 56 average time/residue: 0.4028 time to fit residues: 24.0708 Evaluate side-chains 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 556 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 59 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 35 optimal weight: 0.0570 chunk 2 optimal weight: 1.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 565 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.153238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.120005 restraints weight = 8218.748| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.54 r_work: 0.3448 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6964 Z= 0.130 Angle : 0.487 4.817 9915 Z= 0.290 Chirality : 0.038 0.202 1172 Planarity : 0.004 0.034 929 Dihedral : 22.323 139.991 1977 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.76 % Allowed : 16.04 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: 2.14 (0.34), residues: 602 helix: 2.61 (0.28), residues: 322 sheet: 0.38 (0.62), residues: 73 loop : -0.08 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 83 TYR 0.028 0.002 TYR A 587 PHE 0.005 0.001 PHE A 155 TRP 0.011 0.001 TRP A 454 HIS 0.010 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.13 ( 6963) covalent geometry : angle 0.48642 / 0.29 ( 9913) SS BOND : bond 0.00069 / 0.04 ( 1) SS BOND : angle 1.46397 / 0.85 ( 2) hydrogen bonds : bond 0.04354 / 3.04 ( 399) hydrogen bonds : angle 3.53017 / 2.66 ( 1086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7052 (mmp) cc_final: 0.6824 (mmm) REVERT: A 276 MET cc_start: 0.9116 (mmt) cc_final: 0.8891 (mmt) REVERT: A 560 HIS cc_start: 0.7732 (t-170) cc_final: 0.7205 (t-170) outliers start: 8 outliers final: 2 residues processed: 54 average time/residue: 0.4972 time to fit residues: 28.4329 Evaluate side-chains 48 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 565 HIS ** 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 = 0.3925 r_free = 0.3925 target = 0.148594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.114683 restraints weight = 8253.732| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.58 r_work: 0.3372 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6964 Z= 0.255 Angle : 0.577 5.731 9915 Z= 0.331 Chirality : 0.043 0.214 1172 Planarity : 0.005 0.046 929 Dihedral : 22.291 139.201 1977 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.98 % Allowed : 15.38 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: 1.75 (0.34), residues: 602 helix: 2.24 (0.28), residues: 322 sheet: 0.07 (0.61), residues: 73 loop : -0.10 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 476 TYR 0.019 0.002 TYR A 587 PHE 0.009 0.002 PHE A 487 TRP 0.010 0.002 TRP A 454 HIS 0.009 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.26 ( 6963) covalent geometry : angle 0.57604 / 0.33 ( 9913) SS BOND : bond 0.00132 / 0.07 ( 1) SS BOND : angle 1.77280 / 1.02 ( 2) hydrogen bonds : bond 0.05044 / 3.56 ( 399) hydrogen bonds : angle 3.74783 / 2.79 ( 1086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 400 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.6048 (mp) REVERT: A 494 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8172 (tt) REVERT: A 560 HIS cc_start: 0.7777 (t-170) cc_final: 0.7313 (t-170) outliers start: 9 outliers final: 4 residues processed: 53 average time/residue: 0.4280 time to fit residues: 24.1431 Evaluate side-chains 51 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 556 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 565 HIS ** 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 = 0.3950 r_free = 0.3950 target = 0.150479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.117044 restraints weight = 8290.839| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.55 r_work: 0.3403 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6964 Z= 0.177 Angle : 0.526 5.412 9915 Z= 0.306 Chirality : 0.040 0.213 1172 Planarity : 0.004 0.033 929 Dihedral : 22.316 139.456 1977 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.76 % Allowed : 17.36 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: 1.88 (0.34), residues: 602 helix: 2.38 (0.28), residues: 322 sheet: 0.06 (0.61), residues: 73 loop : -0.07 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 476 TYR 0.030 0.002 TYR A 587 PHE 0.005 0.002 PHE A 155 TRP 0.012 0.001 TRP A 454 HIS 0.005 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.18 ( 6963) covalent geometry : angle 0.52531 / 0.31 ( 9913) SS BOND : bond 0.00179 / 0.09 ( 1) SS BOND : angle 1.66149 / 0.96 ( 2) hydrogen bonds : bond 0.04579 / 3.23 ( 399) hydrogen bonds : angle 3.63348 / 2.73 ( 1086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7212 (mmp) cc_final: 0.6887 (mmm) REVERT: A 276 MET cc_start: 0.9087 (mmt) cc_final: 0.8881 (mmt) REVERT: A 400 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.5985 (mp) REVERT: A 560 HIS cc_start: 0.7778 (t-170) cc_final: 0.7497 (t70) outliers start: 8 outliers final: 2 residues processed: 54 average time/residue: 0.3936 time to fit residues: 22.5323 Evaluate side-chains 48 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 400 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 51 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 565 HIS ** 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 = 0.3892 r_free = 0.3892 target = 0.145731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.111785 restraints weight = 8304.734| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.59 r_work: 0.3327 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 6964 Z= 0.386 Angle : 0.687 6.923 9915 Z= 0.385 Chirality : 0.049 0.230 1172 Planarity : 0.006 0.050 929 Dihedral : 22.365 138.898 1977 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.98 % Allowed : 18.02 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: 1.03 (0.34), residues: 602 helix: 1.64 (0.27), residues: 322 sheet: -0.51 (0.58), residues: 80 loop : -0.27 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 83 TYR 0.032 0.004 TYR A 486 PHE 0.011 0.003 PHE A 487 TRP 0.012 0.003 TRP A 226 HIS 0.006 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00834 / 0.39 ( 6963) covalent geometry : angle 0.68621 / 0.38 ( 9913) SS BOND : bond 0.00229 / 0.12 ( 1) SS BOND : angle 2.23902 / 1.29 ( 2) hydrogen bonds : bond 0.05864 / 4.14 ( 399) hydrogen bonds : angle 4.08758 / 3.02 ( 1086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7769 (mmp) cc_final: 0.7554 (mmm) REVERT: A 301 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8707 (tt) REVERT: A 330 HIS cc_start: 0.8029 (m-70) cc_final: 0.7813 (m-70) outliers start: 9 outliers final: 2 residues processed: 51 average time/residue: 0.4692 time to fit residues: 25.3952 Evaluate side-chains 44 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 397 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 52 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 565 HIS ** 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 = 0.3952 r_free = 0.3952 target = 0.150869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.117374 restraints weight = 8227.965| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.54 r_work: 0.3410 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6964 Z= 0.143 Angle : 0.528 5.784 9915 Z= 0.309 Chirality : 0.039 0.215 1172 Planarity : 0.004 0.034 929 Dihedral : 22.412 139.640 1977 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.76 % Allowed : 18.02 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: 1.65 (0.34), residues: 602 helix: 2.21 (0.28), residues: 322 sheet: -0.19 (0.58), residues: 79 loop : -0.16 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 83 TYR 0.031 0.002 TYR A 486 PHE 0.005 0.001 PHE A 155 TRP 0.015 0.001 TRP A 454 HIS 0.007 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 ( 6963) covalent geometry : angle 0.52742 / 0.31 ( 9913) SS BOND : bond 0.00445 / 0.23 ( 1) SS BOND : angle 1.65293 / 0.95 ( 2) hydrogen bonds : bond 0.04523 / 3.18 ( 399) hydrogen bonds : angle 3.70607 / 2.78 ( 1086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6415 (mtm-85) REVERT: A 141 TYR cc_start: 0.8589 (t80) cc_final: 0.8012 (t80) REVERT: A 330 HIS cc_start: 0.7896 (m-70) cc_final: 0.7633 (m-70) outliers start: 8 outliers final: 3 residues processed: 57 average time/residue: 0.3841 time to fit residues: 23.3076 Evaluate side-chains 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 556 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 51 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 12 optimal weight: 0.0770 chunk 16 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 565 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.153122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.120319 restraints weight = 8279.491| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.53 r_work: 0.3449 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6964 Z= 0.128 Angle : 0.505 5.636 9915 Z= 0.295 Chirality : 0.038 0.217 1172 Planarity : 0.004 0.035 929 Dihedral : 22.258 139.760 1977 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.32 % Allowed : 18.90 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: 2.02 (0.34), residues: 602 helix: 2.54 (0.28), residues: 322 sheet: 0.12 (0.59), residues: 79 loop : -0.12 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 83 TYR 0.034 0.002 TYR A 486 PHE 0.005 0.001 PHE A 155 TRP 0.016 0.001 TRP A 454 HIS 0.011 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.13 ( 6963) covalent geometry : angle 0.50436 / 0.30 ( 9913) SS BOND : bond 0.00343 / 0.18 ( 1) SS BOND : angle 1.44072 / 0.83 ( 2) hydrogen bonds : bond 0.04246 / 2.96 ( 399) hydrogen bonds : angle 3.55843 / 2.69 ( 1086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6271 (mtm-85) REVERT: A 330 HIS cc_start: 0.7863 (m-70) cc_final: 0.7592 (m-70) outliers start: 6 outliers final: 2 residues processed: 52 average time/residue: 0.4962 time to fit residues: 27.5245 Evaluate side-chains 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 397 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 64 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 565 HIS ** 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 = 0.3940 r_free = 0.3940 target = 0.150017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.116412 restraints weight = 8247.070| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.54 r_work: 0.3390 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6964 Z= 0.209 Angle : 0.560 7.878 9915 Z= 0.318 Chirality : 0.042 0.300 1172 Planarity : 0.005 0.034 929 Dihedral : 22.230 138.344 1977 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.88 % Allowed : 19.78 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: 1.81 (0.34), residues: 602 helix: 2.33 (0.28), residues: 322 sheet: 0.00 (0.59), residues: 79 loop : -0.12 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 249 TYR 0.035 0.003 TYR A 486 PHE 0.005 0.002 PHE A 155 TRP 0.011 0.002 TRP A 454 HIS 0.010 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 ( 6963) covalent geometry : angle 0.55956 / 0.32 ( 9913) SS BOND : bond 0.00308 / 0.16 ( 1) SS BOND : angle 1.62154 / 0.94 ( 2) hydrogen bonds : bond 0.04698 / 3.31 ( 399) hydrogen bonds : angle 3.72364 / 2.78 ( 1086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6318 (mtm-85) REVERT: A 330 HIS cc_start: 0.7922 (m-70) cc_final: 0.7702 (m-70) outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 0.5426 time to fit residues: 25.1601 Evaluate side-chains 43 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 397 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 565 HIS ** 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 = 0.3981 r_free = 0.3981 target = 0.153169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.120315 restraints weight = 8220.545| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.53 r_work: 0.3449 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6964 Z= 0.129 Angle : 0.518 10.050 9915 Z= 0.297 Chirality : 0.040 0.315 1172 Planarity : 0.004 0.035 929 Dihedral : 22.256 138.898 1977 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.88 % Allowed : 20.00 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 are not related in a simple way. whole: 2.00 (0.34), residues: 602 helix: 2.50 (0.28), residues: 322 sheet: 0.16 (0.59), residues: 79 loop : -0.10 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 83 TYR 0.036 0.002 TYR A 486 PHE 0.005 0.001 PHE A 155 TRP 0.015 0.001 TRP A 454 HIS 0.011 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 ( 6963) covalent geometry : angle 0.51768 / 0.30 ( 9913) SS BOND : bond 0.00335 / 0.18 ( 1) SS BOND : angle 1.39352 / 0.80 ( 2) hydrogen bonds : bond 0.04202 / 2.93 ( 399) hydrogen bonds : angle 3.59621 / 2.70 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1787.95 seconds wall clock time: 31 minutes 16.41 seconds (1876.41 seconds total)