Starting phenix.real_space_refine on Sun Apr 27 20:12:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pm4_17757/04_2025/8pm4_17757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pm4_17757/04_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_17757/04_2025/8pm4_17757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pm4_17757/04_2025/8pm4_17757.map" model { file = "/net/cci-nas-00/data/ceres_data/8pm4_17757/04_2025/8pm4_17757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pm4_17757/04_2025/8pm4_17757.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 2, 'GLU:plan': 12, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 11} 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: 4.76, per 1000 atoms: 0.72 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: 1.96 Conformation dependent library (CDL) restraints added in 701.5 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: 2.47 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: 2.79 Time building geometry restraints manager: 2.28 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: 0.440 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.070 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.970 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.014 0.002 TRP A 226 HIS 0.003 0.001 HIS A 183 PHE 0.007 0.002 PHE A 487 TYR 0.012 0.002 TYR A 42 ARG 0.004 0.001 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.10344 ( 399) hydrogen bonds : angle 4.59758 ( 1086) SS BOND : bond 0.00330 ( 1) SS BOND : angle 1.50477 ( 2) covalent geometry : bond 0.00718 ( 6963) covalent geometry : angle 0.63386 ( 9913) *********************** 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 : 0.613 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: 1.0977 time to fit residues: 65.4290 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 : 0.617 ------------------------------------------------------------------------------- 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 57 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.151623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118555 restraints weight = 8115.828| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.52 r_work: 0.3422 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6964 Z= 0.162 Angle : 0.520 5.116 9915 Z= 0.289 Chirality : 0.037 0.189 1172 Planarity : 0.004 0.036 929 Dihedral : 22.302 141.408 1979 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.30 % Allowed : 11.87 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.34), residues: 602 helix: 2.43 (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 TRP 0.014 0.001 TRP A 454 HIS 0.006 0.001 HIS A 565 PHE 0.005 0.001 PHE A 155 TYR 0.021 0.001 TYR A 587 ARG 0.005 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.04471 ( 399) hydrogen bonds : angle 3.69196 ( 1086) SS BOND : bond 0.00103 ( 1) SS BOND : angle 1.74138 ( 2) covalent geometry : bond 0.00343 ( 6963) covalent geometry : angle 0.51902 ( 9913) *********************** 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 62 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 276 MET cc_start: 0.9171 (mmt) cc_final: 0.8953 (mmt) REVERT: A 386 ASP cc_start: 0.7877 (m-30) cc_final: 0.7671 (m-30) REVERT: A 400 LEU cc_start: 0.7126 (mp) cc_final: 0.6649 (mp) REVERT: A 494 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8079 (tt) REVERT: A 560 HIS cc_start: 0.7790 (t-170) cc_final: 0.7466 (t-170) outliers start: 15 outliers final: 3 residues processed: 57 average time/residue: 1.0272 time to fit residues: 62.3722 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 : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 494 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 66 optimal weight: 2.9990 chunk 56 optimal weight: 0.0770 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 35 optimal weight: 0.0020 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.6152 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.150335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.116931 restraints weight = 8196.216| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.52 r_work: 0.3401 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6964 Z= 0.200 Angle : 0.529 5.006 9915 Z= 0.294 Chirality : 0.038 0.194 1172 Planarity : 0.004 0.035 929 Dihedral : 22.184 139.567 1977 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.34), residues: 602 helix: 2.41 (0.27), residues: 322 sheet: -0.13 (0.58), residues: 79 loop : -0.12 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 454 HIS 0.008 0.001 HIS A 565 PHE 0.005 0.001 PHE A 155 TYR 0.023 0.002 TYR A 587 ARG 0.005 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.04482 ( 399) hydrogen bonds : angle 3.68657 ( 1086) SS BOND : bond 0.00056 ( 1) SS BOND : angle 1.65684 ( 2) covalent geometry : bond 0.00434 ( 6963) covalent geometry : angle 0.52851 ( 9913) *********************** 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: 9 poor density : 48 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 400 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6712 (mp) REVERT: A 494 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8135 (tt) REVERT: A 560 HIS cc_start: 0.7770 (t-170) cc_final: 0.7420 (t-170) outliers start: 9 outliers final: 3 residues processed: 53 average time/residue: 1.0754 time to fit residues: 60.6589 Evaluate side-chains 51 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.0670 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.152380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.118982 restraints weight = 8298.696| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.55 r_work: 0.3428 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1319 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= 0.145 Angle : 0.492 4.839 9915 Z= 0.274 Chirality : 0.035 0.181 1172 Planarity : 0.004 0.034 929 Dihedral : 22.130 139.523 1977 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.34), residues: 602 helix: 2.68 (0.28), residues: 321 sheet: 0.03 (0.59), residues: 79 loop : -0.11 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 454 HIS 0.008 0.001 HIS A 565 PHE 0.005 0.001 PHE A 155 TYR 0.024 0.002 TYR A 587 ARG 0.006 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 399) hydrogen bonds : angle 3.50926 ( 1086) SS BOND : bond 0.00090 ( 1) SS BOND : angle 1.38105 ( 2) covalent geometry : bond 0.00304 ( 6963) covalent geometry : angle 0.49134 ( 9913) *********************** 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 61 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 125 ARG cc_start: 0.7303 (mtp85) cc_final: 0.7082 (mtp180) REVERT: A 560 HIS cc_start: 0.7710 (t-170) cc_final: 0.7348 (t-170) outliers start: 9 outliers final: 4 residues processed: 57 average time/residue: 1.1472 time to fit residues: 69.3159 Evaluate side-chains 50 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 12 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.148427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.114868 restraints weight = 8235.455| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.54 r_work: 0.3370 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 6964 Z= 0.268 Angle : 0.569 5.097 9915 Z= 0.313 Chirality : 0.040 0.201 1172 Planarity : 0.005 0.036 929 Dihedral : 22.146 138.540 1977 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.64 % Allowed : 16.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.34), residues: 602 helix: 2.31 (0.28), residues: 322 sheet: -0.21 (0.58), residues: 80 loop : -0.10 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 454 HIS 0.008 0.001 HIS A 565 PHE 0.006 0.002 PHE A 155 TYR 0.026 0.003 TYR A 587 ARG 0.006 0.001 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 399) hydrogen bonds : angle 3.74531 ( 1086) SS BOND : bond 0.00184 ( 1) SS BOND : angle 1.76085 ( 2) covalent geometry : bond 0.00585 ( 6963) covalent geometry : angle 0.56815 ( 9913) *********************** 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 60 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 16 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7890 (tp40) REVERT: A 494 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8161 (tt) REVERT: A 560 HIS cc_start: 0.7862 (t-170) cc_final: 0.7359 (t-170) outliers start: 12 outliers final: 3 residues processed: 58 average time/residue: 1.1112 time to fit residues: 68.4853 Evaluate side-chains 48 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 54 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.152284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.119230 restraints weight = 8126.488| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.52 r_work: 0.3434 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1461 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= 0.147 Angle : 0.501 4.830 9915 Z= 0.277 Chirality : 0.036 0.178 1172 Planarity : 0.004 0.033 929 Dihedral : 22.105 139.408 1977 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.34), residues: 602 helix: 2.61 (0.28), residues: 322 sheet: 0.05 (0.59), residues: 79 loop : -0.03 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 454 HIS 0.010 0.001 HIS A 565 PHE 0.005 0.001 PHE A 155 TYR 0.025 0.002 TYR A 486 ARG 0.007 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 399) hydrogen bonds : angle 3.48892 ( 1086) SS BOND : bond 0.00090 ( 1) SS BOND : angle 1.37904 ( 2) covalent geometry : bond 0.00311 ( 6963) covalent geometry : angle 0.50032 ( 9913) *********************** 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 62 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6378 (mtm-85) REVERT: A 125 ARG cc_start: 0.7313 (mtp85) cc_final: 0.7089 (mtp180) outliers start: 10 outliers final: 1 residues processed: 58 average time/residue: 1.1339 time to fit residues: 69.6492 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 : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 300 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 35 optimal weight: 0.0770 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 overall best weight: 1.2742 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.151195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.118200 restraints weight = 8124.295| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.51 r_work: 0.3417 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 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 : 0.004 0.029 6964 Z= 0.170 Angle : 0.516 4.789 9915 Z= 0.284 Chirality : 0.037 0.185 1172 Planarity : 0.004 0.032 929 Dihedral : 22.058 138.365 1977 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.10 % Allowed : 18.90 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (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 TRP 0.012 0.001 TRP A 454 HIS 0.011 0.001 HIS A 565 PHE 0.005 0.001 PHE A 155 TYR 0.031 0.003 TYR A 587 ARG 0.007 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 399) hydrogen bonds : angle 3.51637 ( 1086) SS BOND : bond 0.00285 ( 1) SS BOND : angle 1.35236 ( 2) covalent geometry : bond 0.00364 ( 6963) covalent geometry : angle 0.51521 ( 9913) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6373 (mtm-85) REVERT: A 125 ARG cc_start: 0.7321 (mtp85) cc_final: 0.7096 (mtp180) REVERT: A 235 MET cc_start: 0.9038 (ptm) cc_final: 0.8733 (ptm) outliers start: 5 outliers final: 2 residues processed: 51 average time/residue: 1.1870 time to fit residues: 64.1700 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 : 0.553 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 18 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 0.0870 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.152245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.118891 restraints weight = 8170.342| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.53 r_work: 0.3427 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1600 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= 0.156 Angle : 0.509 4.684 9915 Z= 0.279 Chirality : 0.036 0.182 1172 Planarity : 0.004 0.032 929 Dihedral : 22.032 138.145 1977 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.54 % Allowed : 18.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.34), residues: 602 helix: 2.64 (0.28), residues: 322 sheet: 0.15 (0.64), residues: 68 loop : -0.14 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 454 HIS 0.011 0.001 HIS A 565 PHE 0.005 0.001 PHE A 155 TYR 0.031 0.002 TYR A 486 ARG 0.007 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 399) hydrogen bonds : angle 3.50916 ( 1086) SS BOND : bond 0.00268 ( 1) SS BOND : angle 1.40335 ( 2) covalent geometry : bond 0.00331 ( 6963) covalent geometry : angle 0.50844 ( 9913) *********************** 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 55 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6421 (mtm-85) REVERT: A 125 ARG cc_start: 0.7316 (mtp85) cc_final: 0.7093 (mtp180) REVERT: A 235 MET cc_start: 0.9041 (ptm) cc_final: 0.8703 (ptm) REVERT: A 560 HIS cc_start: 0.7538 (t-170) cc_final: 0.7290 (t70) outliers start: 7 outliers final: 2 residues processed: 53 average time/residue: 1.2695 time to fit residues: 70.9375 Evaluate side-chains 51 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 31 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 34 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.149334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115462 restraints weight = 8302.245| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.56 r_work: 0.3375 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.005 0.049 6964 Z= 0.250 Angle : 0.570 5.386 9915 Z= 0.310 Chirality : 0.040 0.201 1172 Planarity : 0.005 0.032 929 Dihedral : 22.058 137.484 1977 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.76 % Allowed : 18.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.34), residues: 602 helix: 2.30 (0.28), residues: 322 sheet: -0.04 (0.59), residues: 79 loop : -0.15 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 454 HIS 0.011 0.001 HIS A 565 PHE 0.007 0.002 PHE A 487 TYR 0.035 0.003 TYR A 486 ARG 0.004 0.000 ARG A 471 Details of bonding type rmsd hydrogen bonds : bond 0.04593 ( 399) hydrogen bonds : angle 3.73018 ( 1086) SS BOND : bond 0.00296 ( 1) SS BOND : angle 1.71317 ( 2) covalent geometry : bond 0.00546 ( 6963) covalent geometry : angle 0.56974 ( 9913) *********************** 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 52 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6414 (mtm-85) REVERT: A 125 ARG cc_start: 0.7345 (mtp85) cc_final: 0.7112 (mtp180) REVERT: A 235 MET cc_start: 0.9015 (ptm) cc_final: 0.8634 (ptm) REVERT: A 301 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8511 (mt) REVERT: A 330 HIS cc_start: 0.7914 (m-70) cc_final: 0.7701 (m-70) REVERT: A 469 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8163 (ttp-110) outliers start: 8 outliers final: 3 residues processed: 51 average time/residue: 1.7184 time to fit residues: 92.3441 Evaluate side-chains 47 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 301 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 469 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.151483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.117957 restraints weight = 8322.991| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.55 r_work: 0.3413 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6964 Z= 0.172 Angle : 0.538 7.335 9915 Z= 0.292 Chirality : 0.038 0.219 1172 Planarity : 0.004 0.032 929 Dihedral : 22.057 138.458 1977 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.76 % Allowed : 18.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.34), residues: 602 helix: 2.46 (0.28), residues: 322 sheet: 0.09 (0.60), residues: 79 loop : -0.16 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 454 HIS 0.012 0.001 HIS A 565 PHE 0.005 0.002 PHE A 155 TYR 0.036 0.003 TYR A 486 ARG 0.007 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 399) hydrogen bonds : angle 3.64657 ( 1086) SS BOND : bond 0.00265 ( 1) SS BOND : angle 1.52897 ( 2) covalent geometry : bond 0.00370 ( 6963) covalent geometry : angle 0.53797 ( 9913) ********************** 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 53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6438 (mtm-85) REVERT: A 125 ARG cc_start: 0.7313 (mtp85) cc_final: 0.7088 (mtp180) REVERT: A 235 MET cc_start: 0.9022 (ptm) cc_final: 0.8640 (ptm) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 1.2299 time to fit residues: 67.5898 Evaluate side-chains 44 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 22 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.147789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114021 restraints weight = 8332.554| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.57 r_work: 0.3363 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 6964 Z= 0.288 Angle : 0.613 9.361 9915 Z= 0.330 Chirality : 0.042 0.288 1172 Planarity : 0.005 0.032 929 Dihedral : 22.096 137.625 1977 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.32 % Allowed : 19.12 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.34), residues: 602 helix: 2.11 (0.28), residues: 322 sheet: -0.53 (0.54), residues: 93 loop : -0.13 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 454 HIS 0.011 0.001 HIS A 565 PHE 0.010 0.002 PHE A 487 TYR 0.036 0.003 TYR A 486 ARG 0.004 0.001 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 399) hydrogen bonds : angle 3.87844 ( 1086) SS BOND : bond 0.00304 ( 1) SS BOND : angle 1.86548 ( 2) covalent geometry : bond 0.00634 ( 6963) covalent geometry : angle 0.61207 ( 9913) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5118.33 seconds wall clock time: 90 minutes 56.51 seconds (5456.51 seconds total)