Starting phenix.real_space_refine on Fri Aug 22 17:32:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pm4_17757/08_2025/8pm4_17757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pm4_17757/08_2025/8pm4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8pm4_17757/08_2025/8pm4_17757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pm4_17757/08_2025/8pm4_17757.map" model { file = "/net/cci-nas-00/data/ceres_data/8pm4_17757/08_2025/8pm4_17757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pm4_17757/08_2025/8pm4_17757.cif" } 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-2.0-5787/lib/python3.9/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: 1.54, per 1000 atoms: 0.23 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: 0.39 Conformation dependent library (CDL) restraints added in 195.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.86 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: 1.01 Time building geometry restraints manager: 0.54 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=" O4' DG C -9 " pdb=" C1' DG C -9 " ideal model delta sigma weight residual 1.414 1.384 0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" P DC D 0 " pdb=" OP2 DC D 0 " ideal model delta sigma weight residual 1.480 1.509 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" P DC D 0 " pdb=" OP1 DC D 0 " ideal model delta sigma weight residual 1.480 1.508 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" CG LEU A 288 " pdb=" CD1 LEU A 288 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.85e+00 bond pdb=" CB ARG A 219 " pdb=" CG ARG A 219 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.81e+00 ... (remaining 6958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 9430 1.36 - 2.72: 416 2.72 - 4.08: 59 4.08 - 5.44: 6 5.44 - 6.80: 2 Bond angle restraints: 9913 Sorted by residual: angle pdb=" N GLY A 148 " pdb=" CA GLY A 148 " pdb=" C GLY A 148 " ideal model delta sigma weight residual 113.18 119.98 -6.80 2.37e+00 1.78e-01 8.24e+00 angle pdb=" C2' G B 2 " pdb=" C1' G B 2 " pdb=" N9 G B 2 " ideal model delta sigma weight residual 112.00 115.70 -3.70 1.50e+00 4.44e-01 6.07e+00 angle pdb=" C2' A B 10 " pdb=" C1' A B 10 " pdb=" N9 A B 10 " ideal model delta sigma weight residual 112.00 115.33 -3.33 1.50e+00 4.44e-01 4.93e+00 angle pdb=" C4' DC D 0 " pdb=" O4' DC D 0 " pdb=" C1' DC D 0 " ideal model delta sigma weight residual 109.70 106.56 3.14 1.50e+00 4.44e-01 4.37e+00 angle pdb=" C ARG A 85 " pdb=" N THR A 86 " pdb=" CA THR A 86 " ideal model delta sigma weight residual 122.08 118.92 3.16 1.53e+00 4.27e-01 4.26e+00 ... (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 - 0.074: 1062 0.074 - 0.147: 107 0.147 - 0.221: 1 0.221 - 0.294: 1 0.294 - 0.368: 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 2.35 -2.71 -0.37 2.00e-01 2.50e+01 3.38e+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=" C1' A B 10 " pdb=" O4' A B 10 " pdb=" C2' A B 10 " pdb=" N9 A B 10 " both_signs ideal model delta sigma weight residual False 2.46 2.30 0.15 2.00e-01 2.50e+01 5.98e-01 ... (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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.220 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:8.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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= 0.329 Angle : 0.634 6.801 9915 Z= 0.352 Chirality : 0.044 0.368 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 aren 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 covalent geometry : bond 0.00718 ( 6963) covalent geometry : angle 0.63386 ( 9913) SS BOND : bond 0.00330 ( 1) SS BOND : angle 1.50477 ( 2) hydrogen bonds : bond 0.10344 ( 399) hydrogen bonds : angle 4.59758 ( 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 : 0.181 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: 0.4384 time to fit residues: 25.9726 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 : 0.137 ------------------------------------------------------------------------------- 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: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.152306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.119151 restraints weight = 8250.641| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.54 r_work: 0.3428 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6964 Z= 0.150 Angle : 0.516 5.115 9915 Z= 0.287 Chirality : 0.036 0.190 1172 Planarity : 0.004 0.036 929 Dihedral : 22.312 141.149 1979 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.02 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 aren not related in a simple way. whole: 1.91 (0.34), residues: 602 helix: 2.47 (0.27), residues: 322 sheet: -0.06 (0.58), residues: 79 loop : -0.13 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 83 TYR 0.021 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 covalent geometry : bond 0.00312 ( 6963) covalent geometry : angle 0.51540 ( 9913) SS BOND : bond 0.00057 ( 1) SS BOND : angle 1.82923 ( 2) hydrogen bonds : bond 0.04400 ( 399) hydrogen bonds : angle 3.67837 ( 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 60 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 276 MET cc_start: 0.9159 (mmt) cc_final: 0.8939 (mmt) REVERT: A 400 LEU cc_start: 0.7118 (mp) cc_final: 0.6645 (mp) REVERT: A 560 HIS cc_start: 0.7773 (t-170) cc_final: 0.7414 (t-170) outliers start: 13 outliers final: 3 residues processed: 55 average time/residue: 0.4437 time to fit residues: 25.9609 Evaluate side-chains 46 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 4 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.150182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.116737 restraints weight = 8151.524| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.52 r_work: 0.3398 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6964 Z= 0.207 Angle : 0.534 5.011 9915 Z= 0.296 Chirality : 0.038 0.195 1172 Planarity : 0.004 0.034 929 Dihedral : 22.180 139.490 1977 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.20 % Allowed : 14.95 % 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 aren not related in a simple way. whole: 1.83 (0.34), residues: 602 helix: 2.38 (0.27), residues: 322 sheet: -0.09 (0.58), residues: 79 loop : -0.13 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 83 TYR 0.023 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 covalent geometry : bond 0.00450 ( 6963) covalent geometry : angle 0.53332 ( 9913) SS BOND : bond 0.00071 ( 1) SS BOND : angle 1.66943 ( 2) hydrogen bonds : bond 0.04525 ( 399) hydrogen bonds : angle 3.70740 ( 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 57 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 400 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6716 (mp) REVERT: A 494 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8137 (tt) REVERT: A 560 HIS cc_start: 0.7793 (t-170) cc_final: 0.7314 (t-170) outliers start: 10 outliers final: 3 residues processed: 53 average time/residue: 0.4955 time to fit residues: 27.6720 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 : 0.151 ------------------------------------------------------------------------------- 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: 0.9980 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.152448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.119097 restraints weight = 8242.132| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.54 r_work: 0.3431 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6964 Z= 0.147 Angle : 0.497 4.903 9915 Z= 0.276 Chirality : 0.036 0.179 1172 Planarity : 0.004 0.035 929 Dihedral : 22.118 139.560 1977 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.20 % Allowed : 15.16 % 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 aren not related in a simple way. whole: 2.11 (0.34), residues: 602 helix: 2.65 (0.28), residues: 321 sheet: 0.06 (0.59), residues: 79 loop : -0.08 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 83 TYR 0.024 0.002 TYR A 587 PHE 0.005 0.001 PHE A 155 TRP 0.012 0.001 TRP A 454 HIS 0.009 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6963) covalent geometry : angle 0.49694 ( 9913) SS BOND : bond 0.00084 ( 1) SS BOND : angle 1.37355 ( 2) hydrogen bonds : bond 0.04097 ( 399) hydrogen bonds : angle 3.51536 ( 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 60 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 125 ARG cc_start: 0.7302 (mtp85) cc_final: 0.7085 (mtp180) REVERT: A 560 HIS cc_start: 0.7727 (t-170) cc_final: 0.7378 (t-170) outliers start: 10 outliers final: 4 residues processed: 55 average time/residue: 0.4538 time to fit residues: 26.3272 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 : 0.194 ------------------------------------------------------------------------------- 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 556 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.152549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.119350 restraints weight = 8225.107| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.53 r_work: 0.3436 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6964 Z= 0.151 Angle : 0.498 6.037 9915 Z= 0.276 Chirality : 0.036 0.180 1172 Planarity : 0.004 0.033 929 Dihedral : 22.054 138.417 1977 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.30 % Allowed : 14.51 % 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 aren not related in a simple way. whole: 2.20 (0.34), residues: 602 helix: 2.69 (0.28), residues: 322 sheet: 0.12 (0.60), residues: 79 loop : 0.01 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 0.009 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6963) covalent geometry : angle 0.49810 ( 9913) SS BOND : bond 0.00136 ( 1) SS BOND : angle 1.31414 ( 2) hydrogen bonds : bond 0.04013 ( 399) hydrogen bonds : angle 3.46672 ( 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 65 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.6410 (mpp80) REVERT: A 125 ARG cc_start: 0.7307 (mtp85) cc_final: 0.7086 (mtp180) REVERT: A 144 TYR cc_start: 0.8882 (m-80) cc_final: 0.8680 (m-80) REVERT: A 276 MET cc_start: 0.9081 (mmt) cc_final: 0.8877 (mmt) REVERT: A 560 HIS cc_start: 0.7771 (t-170) cc_final: 0.7389 (t-170) outliers start: 15 outliers final: 4 residues processed: 60 average time/residue: 0.4652 time to fit residues: 29.5518 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 : 0.142 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3959 r_free = 0.3959 target = 0.151334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.117958 restraints weight = 8296.982| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.54 r_work: 0.3413 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6964 Z= 0.186 Angle : 0.526 7.739 9915 Z= 0.287 Chirality : 0.038 0.188 1172 Planarity : 0.004 0.034 929 Dihedral : 22.045 138.070 1977 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.98 % Allowed : 16.70 % Favored : 81.32 % 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 aren not related in a simple way. whole: 2.12 (0.34), residues: 602 helix: 2.59 (0.28), residues: 322 sheet: 0.10 (0.60), residues: 79 loop : 0.04 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 83 TYR 0.027 0.002 TYR A 587 PHE 0.005 0.002 PHE A 155 TRP 0.010 0.001 TRP A 454 HIS 0.009 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 6963) covalent geometry : angle 0.52605 ( 9913) SS BOND : bond 0.00166 ( 1) SS BOND : angle 1.43278 ( 2) hydrogen bonds : bond 0.04184 ( 399) hydrogen bonds : angle 3.52720 ( 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 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6524 (mpp80) REVERT: A 125 ARG cc_start: 0.7316 (mtp85) cc_final: 0.7091 (mtp180) REVERT: A 560 HIS cc_start: 0.7799 (t-170) cc_final: 0.7323 (t-170) outliers start: 9 outliers final: 3 residues processed: 50 average time/residue: 0.5260 time to fit residues: 27.7213 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 : 0.119 ------------------------------------------------------------------------------- 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 556 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 51 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.146677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.112746 restraints weight = 8286.242| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.57 r_work: 0.3340 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 6964 Z= 0.360 Angle : 0.655 7.359 9915 Z= 0.353 Chirality : 0.045 0.220 1172 Planarity : 0.006 0.051 929 Dihedral : 22.157 137.665 1977 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.20 % Allowed : 17.36 % 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 aren not related in a simple way. whole: 1.43 (0.34), residues: 602 helix: 1.99 (0.28), residues: 322 sheet: -0.37 (0.57), residues: 80 loop : -0.12 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 83 TYR 0.032 0.003 TYR A 486 PHE 0.010 0.002 PHE A 487 TRP 0.011 0.002 TRP A 226 HIS 0.010 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00793 ( 6963) covalent geometry : angle 0.65470 ( 9913) SS BOND : bond 0.00206 ( 1) SS BOND : angle 1.98442 ( 2) hydrogen bonds : bond 0.05279 ( 399) hydrogen bonds : angle 3.94171 ( 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 54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 125 ARG cc_start: 0.7373 (mtp85) cc_final: 0.7129 (mtp180) REVERT: A 301 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8404 (mt) REVERT: A 330 HIS cc_start: 0.7974 (m-70) cc_final: 0.7766 (m-70) REVERT: A 458 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6818 (t70) outliers start: 10 outliers final: 4 residues processed: 51 average time/residue: 0.5708 time to fit residues: 30.9324 Evaluate side-chains 46 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 301 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 458 ASP 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: 0.9980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 31 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.152586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119565 restraints weight = 8224.361| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.53 r_work: 0.3435 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6964 Z= 0.136 Angle : 0.522 7.066 9915 Z= 0.285 Chirality : 0.036 0.187 1172 Planarity : 0.004 0.033 929 Dihedral : 22.122 139.417 1977 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.94 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 aren not related in a simple way. whole: 2.02 (0.34), residues: 602 helix: 2.58 (0.28), residues: 321 sheet: -0.04 (0.63), residues: 68 loop : -0.10 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 83 TYR 0.033 0.002 TYR A 486 PHE 0.005 0.001 PHE A 155 TRP 0.014 0.001 TRP A 454 HIS 0.011 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6963) covalent geometry : angle 0.52218 ( 9913) SS BOND : bond 0.00343 ( 1) SS BOND : angle 1.24760 ( 2) hydrogen bonds : bond 0.04083 ( 399) hydrogen bonds : angle 3.56306 ( 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: 6 poor density : 48 time to evaluate : 0.216 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 51 average time/residue: 0.5790 time to fit residues: 31.2820 Evaluate side-chains 42 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 51 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 57 optimal weight: 0.0060 chunk 2 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.155264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.122055 restraints weight = 8299.609| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.55 r_work: 0.3471 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6964 Z= 0.127 Angle : 0.502 5.977 9915 Z= 0.274 Chirality : 0.036 0.199 1172 Planarity : 0.004 0.033 929 Dihedral : 21.934 137.081 1977 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.54 % Allowed : 19.12 % 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 aren not related in a simple way. whole: 2.26 (0.34), residues: 602 helix: 2.77 (0.28), residues: 322 sheet: 0.28 (0.65), residues: 68 loop : -0.08 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 543 TYR 0.033 0.002 TYR A 486 PHE 0.005 0.001 PHE A 155 TRP 0.014 0.001 TRP A 454 HIS 0.013 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6963) covalent geometry : angle 0.50157 ( 9913) SS BOND : bond 0.00239 ( 1) SS BOND : angle 1.12431 ( 2) hydrogen bonds : bond 0.03808 ( 399) hydrogen bonds : angle 3.43415 ( 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: 7 poor density : 43 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.5826 (mtm-85) outliers start: 7 outliers final: 2 residues processed: 49 average time/residue: 0.5983 time to fit residues: 31.0349 Evaluate side-chains 40 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 556 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 64 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3975 r_free = 0.3975 target = 0.152885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.119497 restraints weight = 8227.270| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.54 r_work: 0.3435 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6964 Z= 0.168 Angle : 0.538 8.943 9915 Z= 0.289 Chirality : 0.038 0.329 1172 Planarity : 0.004 0.033 929 Dihedral : 21.932 136.378 1977 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.54 % Allowed : 19.34 % 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 aren not related in a simple way. whole: 2.18 (0.34), residues: 602 helix: 2.62 (0.28), residues: 323 sheet: 0.24 (0.60), residues: 79 loop : 0.02 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 83 TYR 0.034 0.003 TYR A 587 PHE 0.005 0.002 PHE A 155 TRP 0.012 0.001 TRP A 454 HIS 0.013 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6963) covalent geometry : angle 0.53733 ( 9913) SS BOND : bond 0.00847 ( 1) SS BOND : angle 1.59629 ( 2) hydrogen bonds : bond 0.04048 ( 399) hydrogen bonds : angle 3.53330 ( 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 51 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7424 (mp0) REVERT: A 85 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.5863 (mtm-85) outliers start: 7 outliers final: 4 residues processed: 51 average time/residue: 0.6588 time to fit residues: 35.3536 Evaluate side-chains 45 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU 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 556 LEU 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: 0.8980 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.154483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.121449 restraints weight = 8237.620| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.53 r_work: 0.3460 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6964 Z= 0.133 Angle : 0.522 8.767 9915 Z= 0.282 Chirality : 0.037 0.339 1172 Planarity : 0.004 0.041 929 Dihedral : 21.948 136.730 1977 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.10 % Allowed : 19.56 % 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 aren not related in a simple way. whole: 2.25 (0.34), residues: 602 helix: 2.68 (0.28), residues: 323 sheet: 0.39 (0.65), residues: 68 loop : 0.01 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 83 TYR 0.038 0.003 TYR A 587 PHE 0.005 0.001 PHE A 155 TRP 0.014 0.001 TRP A 454 HIS 0.013 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6963) covalent geometry : angle 0.52173 ( 9913) SS BOND : bond 0.00633 ( 1) SS BOND : angle 1.28507 ( 2) hydrogen bonds : bond 0.03872 ( 399) hydrogen bonds : angle 3.46867 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1991.58 seconds wall clock time: 34 minutes 46.39 seconds (2086.39 seconds total)