Starting phenix.real_space_refine on Sat May 10 15:12:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pm4_17757/05_2025/8pm4_17757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pm4_17757/05_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_17757/05_2025/8pm4_17757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pm4_17757/05_2025/8pm4_17757.map" model { file = "/net/cci-nas-00/data/ceres_data/8pm4_17757/05_2025/8pm4_17757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pm4_17757/05_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-5687/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: 4.82, per 1000 atoms: 0.73 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: 2.15 Conformation dependent library (CDL) restraints added in 625.9 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: 2.78 Creating SS restraints... Processing helix chain 'A' and resid 18 through 53 removed outlier: 3.593A pdb=" N ALA A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 84 Processing helix chain 'A' and resid 91 through 119 removed outlier: 4.112A pdb=" N ALA A 95 " --> pdb=" O HIS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 145 Processing helix chain 'A' and resid 151 through 175 Processing helix chain 'A' and resid 206 through 212 Processing helix chain 'A' and resid 228 through 235 removed outlier: 3.935A pdb=" N THR A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 368 through 404 removed outlier: 4.020A pdb=" N GLU A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 425 through 439 removed outlier: 4.208A pdb=" N PHE A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR A 439 " --> pdb=" O GLN A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 491 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 508 through 511 Processing helix chain 'A' and resid 514 through 529 Processing helix chain 'A' and resid 529 through 544 Processing helix chain 'A' and resid 588 through 604 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 195 removed outlier: 5.704A pdb=" N ILE A 283 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS A 306 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 285 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ALA A 299 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 3 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N THR A 263 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER A 254 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU A 265 " --> pdb=" O CYS A 252 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 353 through 355 removed outlier: 3.673A pdb=" N ALA A 335 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A 334 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 319 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ASP A 497 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N VAL A 321 " --> pdb=" O ASP A 497 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 578 through 579 310 hydrogen bonds defined for protein. 912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 174 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 2.46 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: 0.430 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.950 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.030 ------------------------------------------------------------------------------- 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 : 0.551 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: 1.0728 time to fit residues: 63.8374 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 : 0.622 ------------------------------------------------------------------------------- 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: 2.9990 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: 1.2982 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.150905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.117454 restraints weight = 8130.247| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.53 r_work: 0.3406 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6964 Z= 0.178 Angle : 0.530 5.301 9915 Z= 0.295 Chirality : 0.037 0.196 1172 Planarity : 0.004 0.037 929 Dihedral : 22.319 140.785 1979 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 : 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: 1.71 (0.34), residues: 602 helix: 2.34 (0.27), residues: 322 sheet: -0.52 (0.53), residues: 91 loop : -0.04 (0.45), residues: 189 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 0.019 0.001 TYR A 587 ARG 0.006 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.04618 ( 399) hydrogen bonds : angle 3.76378 ( 1086) SS BOND : bond 0.00059 ( 1) SS BOND : angle 1.89346 ( 2) covalent geometry : bond 0.00379 ( 6963) covalent geometry : angle 0.52900 ( 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 61 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 276 MET cc_start: 0.9131 (mmt) cc_final: 0.8904 (mmt) REVERT: A 400 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6633 (mp) REVERT: A 494 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8134 (tt) REVERT: A 560 HIS cc_start: 0.7811 (t-170) cc_final: 0.7409 (t-170) outliers start: 15 outliers final: 3 residues processed: 56 average time/residue: 1.0286 time to fit residues: 61.4170 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 : 0.590 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 66 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.0000 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.150430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.117009 restraints weight = 8197.737| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.53 r_work: 0.3402 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6964 Z= 0.196 Angle : 0.528 5.069 9915 Z= 0.293 Chirality : 0.037 0.193 1172 Planarity : 0.004 0.035 929 Dihedral : 22.202 139.804 1979 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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 (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: -0.15 (0.58), residues: 79 loop : -0.11 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 454 HIS 0.007 0.001 HIS A 565 PHE 0.005 0.001 PHE A 155 TYR 0.022 0.002 TYR A 587 ARG 0.006 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.04478 ( 399) hydrogen bonds : angle 3.68827 ( 1086) SS BOND : bond 0.00076 ( 1) SS BOND : angle 1.69258 ( 2) covalent geometry : bond 0.00427 ( 6963) covalent geometry : angle 0.52712 ( 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 59 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 400 LEU cc_start: 0.7193 (mp) cc_final: 0.6803 (mp) REVERT: A 494 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8132 (tt) REVERT: A 560 HIS cc_start: 0.7790 (t-170) cc_final: 0.7465 (t-170) outliers start: 10 outliers final: 3 residues processed: 54 average time/residue: 1.0087 time to fit residues: 58.2447 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 : 0.622 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 35 optimal weight: 0.0040 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.153587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.120525 restraints weight = 8321.170| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.55 r_work: 0.3448 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1450 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= 0.134 Angle : 0.487 4.728 9915 Z= 0.271 Chirality : 0.035 0.177 1172 Planarity : 0.004 0.034 929 Dihedral : 22.081 139.496 1977 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.98 % Allowed : 16.04 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.17 (0.34), residues: 602 helix: 2.73 (0.28), residues: 321 sheet: 0.07 (0.59), residues: 79 loop : -0.09 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 587 ARG 0.009 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 399) hydrogen bonds : angle 3.46204 ( 1086) SS BOND : bond 0.00074 ( 1) SS BOND : angle 1.25658 ( 2) covalent geometry : bond 0.00279 ( 6963) covalent geometry : angle 0.48660 ( 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 57 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 16 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7759 (tp40) REVERT: A 125 ARG cc_start: 0.7300 (mtp85) cc_final: 0.7083 (mtp180) REVERT: A 276 MET cc_start: 0.9095 (mmt) cc_final: 0.8890 (mmt) REVERT: A 560 HIS cc_start: 0.7700 (t-170) cc_final: 0.7347 (t-170) outliers start: 9 outliers final: 2 residues processed: 54 average time/residue: 1.2083 time to fit residues: 68.9954 Evaluate side-chains 48 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.148233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.114267 restraints weight = 8264.802| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.58 r_work: 0.3365 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 6964 Z= 0.300 Angle : 0.593 5.101 9915 Z= 0.324 Chirality : 0.042 0.205 1172 Planarity : 0.005 0.052 929 Dihedral : 22.108 138.133 1977 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.86 % Allowed : 16.04 % Favored : 81.10 % 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: 1.64 (0.34), residues: 602 helix: 2.21 (0.28), residues: 322 sheet: -0.30 (0.57), residues: 80 loop : -0.11 (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 0.008 0.002 PHE A 487 TYR 0.020 0.002 TYR A 587 ARG 0.007 0.001 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.04855 ( 399) hydrogen bonds : angle 3.78966 ( 1086) SS BOND : bond 0.00189 ( 1) SS BOND : angle 1.73511 ( 2) covalent geometry : bond 0.00662 ( 6963) covalent geometry : angle 0.59219 ( 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 56 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 330 HIS cc_start: 0.7804 (m-70) cc_final: 0.7555 (m-70) REVERT: A 494 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8162 (tt) REVERT: A 560 HIS cc_start: 0.7770 (t-170) cc_final: 0.7333 (t-170) outliers start: 13 outliers final: 3 residues processed: 52 average time/residue: 1.1672 time to fit residues: 64.3081 Evaluate side-chains 46 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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=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: 3.9990 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.0870 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.9760 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.151965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.118850 restraints weight = 8130.630| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.52 r_work: 0.3428 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1478 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= 0.149 Angle : 0.501 4.902 9915 Z= 0.278 Chirality : 0.036 0.182 1172 Planarity : 0.004 0.033 929 Dihedral : 22.082 139.303 1977 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.42 % Allowed : 16.92 % Favored : 80.66 % 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: 2.04 (0.34), residues: 602 helix: 2.58 (0.28), residues: 322 sheet: -0.08 (0.58), residues: 79 loop : -0.04 (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 0.022 0.002 TYR A 486 ARG 0.007 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 399) hydrogen bonds : angle 3.52357 ( 1086) SS BOND : bond 0.00092 ( 1) SS BOND : angle 1.43170 ( 2) covalent geometry : bond 0.00316 ( 6963) covalent geometry : angle 0.50039 ( 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 59 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6419 (mtm-85) REVERT: A 125 ARG cc_start: 0.7315 (mtp85) cc_final: 0.7093 (mtp180) REVERT: A 276 MET cc_start: 0.9104 (mmt) cc_final: 0.8901 (mmt) REVERT: A 560 HIS cc_start: 0.7756 (t-170) cc_final: 0.7391 (t-170) outliers start: 11 outliers final: 3 residues processed: 54 average time/residue: 1.2157 time to fit residues: 69.6400 Evaluate side-chains 46 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 400 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.151582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.117901 restraints weight = 8148.866| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.54 r_work: 0.3413 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6964 Z= 0.172 Angle : 0.514 4.939 9915 Z= 0.284 Chirality : 0.037 0.186 1172 Planarity : 0.004 0.033 929 Dihedral : 22.041 138.328 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 : 1.76 % Allowed : 17.80 % 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: 2.07 (0.34), residues: 602 helix: 2.60 (0.28), residues: 322 sheet: -0.01 (0.59), 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 0.028 0.002 TYR A 587 ARG 0.007 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 399) hydrogen bonds : angle 3.53415 ( 1086) SS BOND : bond 0.00167 ( 1) SS BOND : angle 1.48990 ( 2) covalent geometry : bond 0.00368 ( 6963) covalent geometry : angle 0.51364 ( 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 56 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6412 (mtm-85) REVERT: A 125 ARG cc_start: 0.7322 (mtp85) cc_final: 0.7097 (mtp180) REVERT: A 235 MET cc_start: 0.9048 (ptm) cc_final: 0.8731 (ptm) REVERT: A 560 HIS cc_start: 0.7797 (t-170) cc_final: 0.7343 (t-170) outliers start: 8 outliers final: 4 residues processed: 54 average time/residue: 1.1194 time to fit residues: 64.2678 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 : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 556 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 18 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 0.0870 chunk 7 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.150823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.117185 restraints weight = 8189.278| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.54 r_work: 0.3400 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6964 Z= 0.195 Angle : 0.538 8.443 9915 Z= 0.292 Chirality : 0.038 0.191 1172 Planarity : 0.004 0.032 929 Dihedral : 22.036 138.124 1977 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.42 % Allowed : 18.46 % 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 (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: 1.98 (0.34), residues: 602 helix: 2.54 (0.28), residues: 321 sheet: -0.03 (0.59), residues: 79 loop : -0.12 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 454 HIS 0.011 0.001 HIS A 565 PHE 0.005 0.002 PHE A 155 TYR 0.031 0.003 TYR A 486 ARG 0.004 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 399) hydrogen bonds : angle 3.59636 ( 1086) SS BOND : bond 0.00184 ( 1) SS BOND : angle 1.55086 ( 2) covalent geometry : bond 0.00423 ( 6963) covalent geometry : angle 0.53746 ( 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 56 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 83 ARG cc_start: 0.6365 (mtp-110) cc_final: 0.6155 (mmm-85) REVERT: A 85 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6434 (mtm-85) REVERT: A 125 ARG cc_start: 0.7315 (mtp85) cc_final: 0.7088 (mtp180) REVERT: A 235 MET cc_start: 0.9024 (ptm) cc_final: 0.8662 (ptm) REVERT: A 276 MET cc_start: 0.9133 (mmt) cc_final: 0.8922 (mmt) REVERT: A 301 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8418 (mt) REVERT: A 494 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8112 (tt) REVERT: A 560 HIS cc_start: 0.7774 (t-170) cc_final: 0.7281 (t-170) outliers start: 11 outliers final: 3 residues processed: 53 average time/residue: 1.1571 time to fit residues: 65.0050 Evaluate side-chains 50 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 494 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 34 optimal weight: 0.0030 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.149443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115631 restraints weight = 8301.973| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.55 r_work: 0.3388 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6964 Z= 0.231 Angle : 0.566 8.520 9915 Z= 0.307 Chirality : 0.039 0.200 1172 Planarity : 0.004 0.032 929 Dihedral : 22.057 138.027 1977 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.76 % Allowed : 19.34 % Favored : 78.90 % 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: 1.77 (0.34), residues: 602 helix: 2.33 (0.28), residues: 322 sheet: -0.11 (0.59), residues: 79 loop : -0.16 (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 0.006 0.002 PHE A 487 TYR 0.035 0.003 TYR A 486 ARG 0.003 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.04537 ( 399) hydrogen bonds : angle 3.71496 ( 1086) SS BOND : bond 0.00246 ( 1) SS BOND : angle 1.70508 ( 2) covalent geometry : bond 0.00505 ( 6963) covalent geometry : angle 0.56583 ( 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 : 0.555 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6492 (mtm-85) REVERT: A 125 ARG cc_start: 0.7334 (mtp85) cc_final: 0.7102 (mtp180) REVERT: A 235 MET cc_start: 0.9010 (ptm) cc_final: 0.8702 (ptm) REVERT: A 301 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8473 (mt) REVERT: A 330 HIS cc_start: 0.7784 (m-70) cc_final: 0.7577 (m-70) REVERT: A 469 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8156 (ttp-110) REVERT: A 494 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8136 (tt) REVERT: A 560 HIS cc_start: 0.7812 (t-170) cc_final: 0.7266 (t-170) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 1.2933 time to fit residues: 70.8347 Evaluate side-chains 49 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 494 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.149772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.115830 restraints weight = 8360.844| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.56 r_work: 0.3391 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6964 Z= 0.224 Angle : 0.571 8.861 9915 Z= 0.308 Chirality : 0.039 0.223 1172 Planarity : 0.004 0.032 929 Dihedral : 22.071 138.468 1977 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.54 % Allowed : 19.78 % Favored : 78.68 % 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: 1.71 (0.34), residues: 602 helix: 2.28 (0.28), residues: 322 sheet: -0.13 (0.59), residues: 79 loop : -0.18 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 454 HIS 0.013 0.001 HIS A 565 PHE 0.007 0.002 PHE A 487 TYR 0.038 0.003 TYR A 486 ARG 0.004 0.000 ARG A 534 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 399) hydrogen bonds : angle 3.73549 ( 1086) SS BOND : bond 0.00192 ( 1) SS BOND : angle 1.69566 ( 2) covalent geometry : bond 0.00490 ( 6963) covalent geometry : angle 0.57076 ( 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 50 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6529 (mtm-85) REVERT: A 125 ARG cc_start: 0.7334 (mtp85) cc_final: 0.7103 (mtp180) REVERT: A 235 MET cc_start: 0.8991 (ptm) cc_final: 0.8706 (ptm) REVERT: A 330 HIS cc_start: 0.7892 (m-70) cc_final: 0.7687 (m-70) REVERT: A 494 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8125 (tt) REVERT: A 560 HIS cc_start: 0.7808 (t-170) cc_final: 0.7271 (t-170) outliers start: 7 outliers final: 3 residues processed: 50 average time/residue: 1.3706 time to fit residues: 72.2961 Evaluate side-chains 46 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 494 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.148388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.114533 restraints weight = 8320.333| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.57 r_work: 0.3363 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 6964 Z= 0.265 Angle : 0.603 9.307 9915 Z= 0.324 Chirality : 0.041 0.290 1172 Planarity : 0.005 0.036 929 Dihedral : 22.115 138.392 1977 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.76 % Allowed : 20.00 % Favored : 78.24 % 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: 1.48 (0.34), residues: 602 helix: 2.10 (0.28), residues: 322 sheet: -0.46 (0.55), residues: 89 loop : -0.15 (0.46), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 454 HIS 0.012 0.001 HIS A 565 PHE 0.009 0.002 PHE A 487 TYR 0.035 0.003 TYR A 486 ARG 0.005 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.04792 ( 399) hydrogen bonds : angle 3.83622 ( 1086) SS BOND : bond 0.00200 ( 1) SS BOND : angle 1.86402 ( 2) covalent geometry : bond 0.00584 ( 6963) covalent geometry : angle 0.60247 ( 9913) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4360.54 seconds wall clock time: 75 minutes 54.76 seconds (4554.76 seconds total)