Starting phenix.real_space_refine on Tue Aug 4 19:51:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pm4_17757/08_2026/8pm4_17757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pm4_17757/08_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_17757/08_2026/8pm4_17757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pm4_17757/08_2026/8pm4_17757.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pm4_17757/08_2026/8pm4_17757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pm4_17757/08_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-2.2rc3-6140/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: 1.95, per 1000 atoms: 0.29 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: 0.65 Conformation dependent library (CDL) restraints added in 316.7 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: 0.92 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: 1.12 Time building geometry restraints manager: 0.85 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: 9171 1.36 - 2.72: 605 2.72 - 4.08: 129 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=" O5' U B -7 " pdb=" C5' U B -7 " pdb=" C4' U B -7 " ideal model delta sigma weight residual 109.40 113.10 -3.70 8.00e-01 1.56e+00 2.14e+01 angle pdb=" O5' U B 4 " pdb=" C5' U B 4 " pdb=" C4' U B 4 " ideal model delta sigma weight residual 109.40 113.08 -3.68 8.00e-01 1.56e+00 2.12e+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: 994 0.076 - 0.151: 170 0.151 - 0.227: 6 0.227 - 0.303: 1 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 2.47 2.23 0.24 2.00e-01 2.50e+01 1.42e+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: 0.530 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.060 Find NCS groups from input model: 0.020 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:8.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.530 ------------------------------------------------------------------------------- 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 : 0.008 0.045 6964 Z= 0.553 Angle : 0.746 6.801 9915 Z= 0.588 Chirality : 0.055 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 0.00751 / 0.55 ( 6963) covalent geometry : angle 0.74548 / 0.59 ( 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 : 0.162 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: 0.3859 time to fit residues: 22.8974 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 : 0.141 ------------------------------------------------------------------------------- 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: 20.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 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 = 0.3963 r_free = 0.3963 target = 0.151430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.118243 restraints weight = 8251.649| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.53 r_work: 0.3415 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.0859 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 : 0.545 5.552 9915 Z= 0.319 Chirality : 0.041 0.204 1172 Planarity : 0.005 0.037 929 Dihedral : 22.481 140.527 1979 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.35 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: 1.72 (0.33), residues: 602 helix: 2.28 (0.27), residues: 322 sheet: -0.07 (0.60), residues: 74 loop : -0.18 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 119 TYR 0.026 0.001 TYR A 587 PHE 0.005 0.001 PHE A 155 TRP 0.014 0.001 TRP A 454 HIS 0.006 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 ( 6963) covalent geometry : angle 0.54404 / 0.32 ( 9913) SS BOND : bond 0.00028 / 0.01 ( 1) SS BOND : angle 2.06561 / 1.19 ( 2) hydrogen bonds : bond 0.04997 / 3.50 ( 399) hydrogen bonds : angle 3.81729 / 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 58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 276 MET cc_start: 0.9144 (mmt) cc_final: 0.8919 (mmt) REVERT: A 400 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6586 (mp) REVERT: A 560 HIS cc_start: 0.7752 (t-170) cc_final: 0.7289 (t-170) outliers start: 13 outliers final: 3 residues processed: 53 average time/residue: 0.3268 time to fit residues: 18.6008 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 : 0.182 ------------------------------------------------------------------------------- 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: 0.9990 chunk 5 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 17 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.150549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.117243 restraints weight = 8136.834| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.52 r_work: 0.3409 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6964 Z= 0.174 Angle : 0.537 5.244 9915 Z= 0.312 Chirality : 0.040 0.216 1172 Planarity : 0.004 0.035 929 Dihedral : 22.374 140.583 1979 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.42 % Allowed : 14.73 % Favored : 82.86 % 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: 1.86 (0.34), residues: 602 helix: 2.36 (0.27), residues: 322 sheet: 0.08 (0.61), residues: 73 loop : -0.09 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 83 TYR 0.026 0.002 TYR A 587 PHE 0.005 0.001 PHE A 155 TRP 0.011 0.001 TRP A 454 HIS 0.008 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 ( 6963) covalent geometry : angle 0.53610 / 0.31 ( 9913) SS BOND : bond 0.00084 / 0.04 ( 1) SS BOND : angle 1.83181 / 1.06 ( 2) hydrogen bonds : bond 0.04888 / 3.45 ( 399) hydrogen bonds : angle 3.73531 / 2.79 ( 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 60 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 276 MET cc_start: 0.9192 (mmt) cc_final: 0.8989 (mmt) REVERT: A 400 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6706 (mp) REVERT: A 494 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8125 (tt) REVERT: A 560 HIS cc_start: 0.7843 (t-170) cc_final: 0.7341 (t-170) outliers start: 11 outliers final: 3 residues processed: 55 average time/residue: 0.3500 time to fit residues: 20.5449 Evaluate side-chains 50 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 59 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.0040 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.153199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.120014 restraints weight = 8237.649| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.54 r_work: 0.3445 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6964 Z= 0.130 Angle : 0.500 4.961 9915 Z= 0.294 Chirality : 0.038 0.219 1172 Planarity : 0.004 0.035 929 Dihedral : 22.309 139.812 1979 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.76 % Allowed : 16.26 % Favored : 81.98 % 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: 2.09 (0.34), residues: 602 helix: 2.55 (0.28), residues: 322 sheet: 0.32 (0.62), residues: 73 loop : -0.07 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 83 TYR 0.029 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 0.00237 / 0.13 ( 6963) covalent geometry : angle 0.49922 / 0.29 ( 9913) SS BOND : bond 0.00077 / 0.04 ( 1) SS BOND : angle 1.50931 / 0.87 ( 2) hydrogen bonds : bond 0.04422 / 3.08 ( 399) hydrogen bonds : angle 3.55776 / 2.68 ( 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 : 0.125 Fit side-chains revert: symmetry clash REVERT: A 276 MET cc_start: 0.9124 (mmt) cc_final: 0.8895 (mmt) REVERT: A 386 ASP cc_start: 0.7847 (m-30) cc_final: 0.7642 (m-30) REVERT: A 600 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7425 (mtp85) outliers start: 8 outliers final: 2 residues processed: 54 average time/residue: 0.3813 time to fit residues: 21.8209 Evaluate side-chains 47 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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: 0.9980 chunk 24 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.150475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.116845 restraints weight = 8237.947| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.55 r_work: 0.3401 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6964 Z= 0.192 Angle : 0.545 5.078 9915 Z= 0.311 Chirality : 0.041 0.227 1172 Planarity : 0.005 0.038 929 Dihedral : 22.239 139.166 1977 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: 1.96 (0.34), residues: 602 helix: 2.45 (0.28), residues: 322 sheet: 0.13 (0.61), residues: 73 loop : -0.08 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 338 TYR 0.020 0.002 TYR A 587 PHE 0.006 0.002 PHE A 487 TRP 0.010 0.001 TRP A 454 HIS 0.009 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 ( 6963) covalent geometry : angle 0.54481 / 0.31 ( 9913) SS BOND : bond 0.00345 / 0.18 ( 1) SS BOND : angle 1.66504 / 0.96 ( 2) hydrogen bonds : bond 0.04735 / 3.33 ( 399) hydrogen bonds : angle 3.61821 / 2.71 ( 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 54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 400 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.6009 (mp) REVERT: A 494 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8125 (tt) outliers start: 9 outliers final: 3 residues processed: 52 average time/residue: 0.4322 time to fit residues: 23.8304 Evaluate side-chains 46 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.152791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119625 restraints weight = 8273.074| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.54 r_work: 0.3442 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1433 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= 0.132 Angle : 0.498 4.978 9915 Z= 0.291 Chirality : 0.038 0.227 1172 Planarity : 0.004 0.033 929 Dihedral : 22.231 139.153 1977 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.86 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: 2.16 (0.34), residues: 602 helix: 2.64 (0.28), residues: 322 sheet: 0.21 (0.61), residues: 73 loop : -0.04 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 83 TYR 0.029 0.002 TYR A 587 PHE 0.005 0.001 PHE A 155 TRP 0.012 0.001 TRP A 454 HIS 0.006 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.13 ( 6963) covalent geometry : angle 0.49785 / 0.29 ( 9913) SS BOND : bond 0.00226 / 0.12 ( 1) SS BOND : angle 1.43775 / 0.83 ( 2) hydrogen bonds : bond 0.04326 / 3.02 ( 399) hydrogen bonds : angle 3.49062 / 2.63 ( 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 55 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6054 (mtm-85) REVERT: A 400 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.5971 (mp) REVERT: A 560 HIS cc_start: 0.7539 (t-170) cc_final: 0.7113 (t70) outliers start: 8 outliers final: 2 residues processed: 53 average time/residue: 0.4333 time to fit residues: 24.2811 Evaluate side-chains 51 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.119 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.146842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.112883 restraints weight = 8276.019| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.54 r_work: 0.3341 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1173 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= 0.351 Angle : 0.681 6.616 9915 Z= 0.373 Chirality : 0.049 0.244 1172 Planarity : 0.006 0.046 929 Dihedral : 22.245 138.427 1977 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.98 % Allowed : 17.58 % Favored : 80.44 % 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: 1.33 (0.34), residues: 602 helix: 1.91 (0.28), residues: 322 sheet: -0.40 (0.57), residues: 80 loop : -0.17 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 476 TYR 0.026 0.003 TYR A 587 PHE 0.012 0.003 PHE A 487 TRP 0.011 0.002 TRP A 226 HIS 0.006 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.35 ( 6963) covalent geometry : angle 0.68011 / 0.37 ( 9913) SS BOND : bond 0.00268 / 0.14 ( 1) SS BOND : angle 1.96413 / 1.14 ( 2) hydrogen bonds : bond 0.05612 / 3.96 ( 399) hydrogen bonds : angle 3.95548 / 2.93 ( 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 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 16 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7902 (tp40) REVERT: A 276 MET cc_start: 0.9145 (mmt) cc_final: 0.8934 (mmt) REVERT: A 297 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8643 (mp) REVERT: A 330 HIS cc_start: 0.7867 (m-70) cc_final: 0.7629 (m-70) REVERT: A 494 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8182 (tt) outliers start: 9 outliers final: 2 residues processed: 51 average time/residue: 0.4399 time to fit residues: 23.7882 Evaluate side-chains 43 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 52 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.151730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.118467 restraints weight = 8196.906| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.54 r_work: 0.3423 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6964 Z= 0.132 Angle : 0.515 5.481 9915 Z= 0.301 Chirality : 0.039 0.232 1172 Planarity : 0.004 0.034 929 Dihedral : 22.287 139.132 1977 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.10 % Allowed : 18.46 % Favored : 80.44 % 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: 1.87 (0.34), residues: 602 helix: 2.40 (0.28), residues: 322 sheet: -0.10 (0.58), residues: 79 loop : -0.06 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 83 TYR 0.032 0.002 TYR A 486 PHE 0.005 0.001 PHE A 155 TRP 0.014 0.001 TRP A 454 HIS 0.005 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 ( 6963) covalent geometry : angle 0.51500 / 0.30 ( 9913) SS BOND : bond 0.00316 / 0.17 ( 1) SS BOND : angle 1.56151 / 0.90 ( 2) hydrogen bonds : bond 0.04458 / 3.13 ( 399) hydrogen bonds : angle 3.62651 / 2.73 ( 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 54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6374 (mtm-85) outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 0.4359 time to fit residues: 24.6245 Evaluate side-chains 45 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.149981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.116657 restraints weight = 8285.835| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.54 r_work: 0.3398 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6964 Z= 0.187 Angle : 0.549 5.669 9915 Z= 0.312 Chirality : 0.041 0.237 1172 Planarity : 0.004 0.033 929 Dihedral : 22.224 139.028 1977 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: 1.82 (0.34), residues: 602 helix: 2.36 (0.28), residues: 322 sheet: -0.15 (0.58), residues: 79 loop : -0.09 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 83 TYR 0.035 0.003 TYR A 486 PHE 0.005 0.002 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 0.00385 / 0.19 ( 6963) covalent geometry : angle 0.54858 / 0.31 ( 9913) SS BOND : bond 0.00246 / 0.13 ( 1) SS BOND : angle 1.63065 / 0.94 ( 2) hydrogen bonds : bond 0.04689 / 3.31 ( 399) hydrogen bonds : angle 3.67447 / 2.75 ( 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 50 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7698 (mm) cc_final: 0.7493 (mm) REVERT: A 85 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6404 (mtm-85) REVERT: A 250 MET cc_start: 0.8594 (ttm) cc_final: 0.8373 (mtp) REVERT: A 330 HIS cc_start: 0.7899 (m-70) cc_final: 0.7653 (m-70) outliers start: 8 outliers final: 3 residues processed: 49 average time/residue: 0.5046 time to fit residues: 26.1395 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 : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 297 LEU 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: 2.9990 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.151075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117547 restraints weight = 8200.602| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.55 r_work: 0.3410 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6964 Z= 0.163 Angle : 0.536 5.178 9915 Z= 0.306 Chirality : 0.040 0.235 1172 Planarity : 0.004 0.033 929 Dihedral : 22.212 138.870 1977 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.54 % Allowed : 18.02 % Favored : 80.44 % 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: 1.85 (0.34), residues: 602 helix: 2.41 (0.28), residues: 322 sheet: -0.14 (0.58), residues: 79 loop : -0.11 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 83 TYR 0.038 0.003 TYR A 486 PHE 0.005 0.001 PHE A 155 TRP 0.013 0.001 TRP A 454 HIS 0.008 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 ( 6963) covalent geometry : angle 0.53592 / 0.31 ( 9913) SS BOND : bond 0.00273 / 0.14 ( 1) SS BOND : angle 1.57546 / 0.91 ( 2) hydrogen bonds : bond 0.04515 / 3.18 ( 399) hydrogen bonds : angle 3.63666 / 2.73 ( 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 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6356 (mtm-85) REVERT: A 330 HIS cc_start: 0.7874 (m-70) cc_final: 0.7632 (m-70) outliers start: 7 outliers final: 3 residues processed: 48 average time/residue: 0.4953 time to fit residues: 25.1107 Evaluate side-chains 46 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 297 LEU 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: 8.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 57 optimal weight: 0.0050 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.155028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.121831 restraints weight = 8218.106| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.55 r_work: 0.3468 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6964 Z= 0.120 Angle : 0.500 6.886 9915 Z= 0.289 Chirality : 0.038 0.278 1172 Planarity : 0.004 0.034 929 Dihedral : 22.171 138.795 1977 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: 2.15 (0.34), residues: 602 helix: 2.73 (0.28), residues: 321 sheet: 0.19 (0.64), residues: 68 loop : -0.18 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 83 TYR 0.038 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 0.00214 / 0.12 ( 6963) covalent geometry : angle 0.49979 / 0.29 ( 9913) SS BOND : bond 0.00259 / 0.14 ( 1) SS BOND : angle 1.39608 / 0.81 ( 2) hydrogen bonds : bond 0.04136 / 2.86 ( 399) hydrogen bonds : angle 3.49114 / 2.64 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1694.13 seconds wall clock time: 29 minutes 33.93 seconds (1773.93 seconds total)