Starting phenix.real_space_refine on Wed Sep 17 11:33:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zl1_60215/09_2025/8zl1_60215.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zl1_60215/09_2025/8zl1_60215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zl1_60215/09_2025/8zl1_60215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zl1_60215/09_2025/8zl1_60215.map" model { file = "/net/cci-nas-00/data/ceres_data/8zl1_60215/09_2025/8zl1_60215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zl1_60215/09_2025/8zl1_60215.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.017 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 2 5.49 5 S 88 5.16 5 C 5624 2.51 5 N 1328 2.21 5 O 1424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8466 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4183 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 505} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 4183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4183 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 505} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.71, per 1000 atoms: 0.32 Number of scatterers: 8466 At special positions: 0 Unit cell: (86.7825, 97.527, 105.792, 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 88 16.00 P 2 15.00 O 1424 8.00 N 1328 7.00 C 5624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.01 Conformation dependent library (CDL) restraints added in 406.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 0 sheets defined 80.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 33 through 60 removed outlier: 3.629A pdb=" N PHE A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LYS A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) Proline residue: A 50 - end of helix Proline residue: A 55 - end of helix removed outlier: 3.654A pdb=" N ASN A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 81 Processing helix chain 'A' and resid 84 through 100 removed outlier: 3.757A pdb=" N ILE A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Proline residue: A 92 - end of helix Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.659A pdb=" N TYR A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 132 removed outlier: 3.554A pdb=" N CYS A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 147 removed outlier: 3.624A pdb=" N ARG A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 166 Processing helix chain 'A' and resid 169 through 191 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 220 through 238 Processing helix chain 'A' and resid 245 through 259 removed outlier: 3.643A pdb=" N LEU A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 295 Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 301 through 313 removed outlier: 3.789A pdb=" N GLU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 Processing helix chain 'A' and resid 333 through 352 Processing helix chain 'A' and resid 372 through 386 removed outlier: 4.398A pdb=" N THR A 376 " --> pdb=" O ASN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 423 through 442 removed outlier: 4.238A pdb=" N PHE A 427 " --> pdb=" O TRP A 423 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 452 Processing helix chain 'A' and resid 453 through 458 removed outlier: 4.081A pdb=" N VAL A 457 " --> pdb=" O GLY A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 476 Processing helix chain 'A' and resid 479 through 498 Proline residue: A 489 - end of helix Processing helix chain 'A' and resid 501 through 513 removed outlier: 3.865A pdb=" N LEU A 505 " --> pdb=" O HIS A 501 " (cutoff:3.500A) Proline residue: A 508 - end of helix Processing helix chain 'A' and resid 523 through 533 Processing helix chain 'A' and resid 536 through 544 Processing helix chain 'A' and resid 544 through 567 removed outlier: 4.926A pdb=" N LEU A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'B' and resid 34 through 40 Processing helix chain 'B' and resid 40 through 59 Proline residue: B 50 - end of helix Proline residue: B 55 - end of helix Processing helix chain 'B' and resid 62 through 81 removed outlier: 3.649A pdb=" N ARG B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 90 through 100 removed outlier: 4.095A pdb=" N VAL B 94 " --> pdb=" O MET B 90 " (cutoff:3.500A) Proline residue: B 97 - end of helix Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.592A pdb=" N TYR B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 132 removed outlier: 3.501A pdb=" N CYS B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 147 removed outlier: 3.609A pdb=" N ARG B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 166 Processing helix chain 'B' and resid 169 through 191 Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 220 through 238 Processing helix chain 'B' and resid 239 through 240 No H-bonds generated for 'chain 'B' and resid 239 through 240' Processing helix chain 'B' and resid 241 through 244 Processing helix chain 'B' and resid 245 through 259 removed outlier: 3.661A pdb=" N LEU B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 296 Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 304 through 314 Processing helix chain 'B' and resid 316 through 329 Processing helix chain 'B' and resid 333 through 352 Processing helix chain 'B' and resid 372 through 386 removed outlier: 3.960A pdb=" N THR B 376 " --> pdb=" O ASN B 372 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 413 through 421 Processing helix chain 'B' and resid 423 through 442 removed outlier: 4.222A pdb=" N PHE B 427 " --> pdb=" O TRP B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 454 removed outlier: 4.224A pdb=" N GLY B 454 " --> pdb=" O ASN B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 458 Processing helix chain 'B' and resid 459 through 476 Processing helix chain 'B' and resid 479 through 498 Proline residue: B 489 - end of helix Processing helix chain 'B' and resid 501 through 513 removed outlier: 3.970A pdb=" N LEU B 505 " --> pdb=" O HIS B 501 " (cutoff:3.500A) Proline residue: B 508 - end of helix Processing helix chain 'B' and resid 523 through 533 Processing helix chain 'B' and resid 536 through 567 removed outlier: 3.507A pdb=" N MET B 540 " --> pdb=" O ARG B 536 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY B 546 " --> pdb=" O ILE B 542 " (cutoff:3.500A) Proline residue: B 547 - end of helix removed outlier: 4.757A pdb=" N LEU B 564 " --> pdb=" O GLN B 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 565 " --> pdb=" O THR B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 584 562 hydrogen bonds defined for protein. 1674 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1297 1.32 - 1.44: 2274 1.44 - 1.57: 4967 1.57 - 1.69: 4 1.69 - 1.81: 146 Bond restraints: 8688 Sorted by residual: bond pdb=" N SER B 302 " pdb=" CA SER B 302 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.23e-02 6.61e+03 7.65e+00 bond pdb=" N VAL B 308 " pdb=" CA VAL B 308 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.58e+00 bond pdb=" N MET B 295 " pdb=" CA MET B 295 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.26e-02 6.30e+03 7.31e+00 bond pdb=" N LYS A 260 " pdb=" CA LYS A 260 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.23e-02 6.61e+03 6.41e+00 bond pdb=" N GLU B 307 " pdb=" CA GLU B 307 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 5.87e+00 ... (remaining 8683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 11616 2.33 - 4.66: 168 4.66 - 6.99: 24 6.99 - 9.32: 1 9.32 - 11.65: 1 Bond angle restraints: 11810 Sorted by residual: angle pdb=" N GLU B 304 " pdb=" CA GLU B 304 " pdb=" C GLU B 304 " ideal model delta sigma weight residual 113.30 107.06 6.24 1.34e+00 5.57e-01 2.17e+01 angle pdb=" O11 PTY B 601 " pdb=" P1 PTY B 601 " pdb=" O14 PTY B 601 " ideal model delta sigma weight residual 92.90 104.55 -11.65 3.00e+00 1.11e-01 1.51e+01 angle pdb=" CA SER B 302 " pdb=" C SER B 302 " pdb=" O SER B 302 " ideal model delta sigma weight residual 121.23 117.13 4.10 1.07e+00 8.73e-01 1.47e+01 angle pdb=" N GLN B 309 " pdb=" CA GLN B 309 " pdb=" C GLN B 309 " ideal model delta sigma weight residual 110.97 107.09 3.88 1.09e+00 8.42e-01 1.27e+01 angle pdb=" CA LYS A 260 " pdb=" C LYS A 260 " pdb=" O LYS A 260 " ideal model delta sigma weight residual 121.46 117.34 4.12 1.17e+00 7.31e-01 1.24e+01 ... (remaining 11805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.01: 4971 26.01 - 52.02: 166 52.02 - 78.04: 9 78.04 - 104.05: 0 104.05 - 130.06: 4 Dihedral angle restraints: 5150 sinusoidal: 2026 harmonic: 3124 Sorted by residual: dihedral pdb=" CA ARG A 371 " pdb=" C ARG A 371 " pdb=" N ASN A 372 " pdb=" CA ASN A 372 " ideal model delta harmonic sigma weight residual 180.00 152.55 27.45 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" N1 PTY B 601 " pdb=" C2 PTY B 601 " pdb=" C3 PTY B 601 " pdb=" O11 PTY B 601 " ideal model delta sinusoidal sigma weight residual 65.33 -64.73 130.06 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C3 PTY A 601 " pdb=" O11 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O12 PTY A 601 " ideal model delta sinusoidal sigma weight residual 300.23 176.96 123.27 1 3.00e+01 1.11e-03 1.65e+01 ... (remaining 5147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1072 0.052 - 0.104: 263 0.104 - 0.155: 32 0.155 - 0.207: 8 0.207 - 0.259: 1 Chirality restraints: 1376 Sorted by residual: chirality pdb=" C6 PTY B 601 " pdb=" C1 PTY B 601 " pdb=" C5 PTY B 601 " pdb=" O7 PTY B 601 " both_signs ideal model delta sigma weight residual False 2.49 2.23 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA LYS A 260 " pdb=" N LYS A 260 " pdb=" C LYS A 260 " pdb=" CB LYS A 260 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" CA VAL B 308 " pdb=" N VAL B 308 " pdb=" C VAL B 308 " pdb=" CB VAL B 308 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.01e-01 ... (remaining 1373 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 559 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C CYS A 559 " -0.040 2.00e-02 2.50e+03 pdb=" O CYS A 559 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN A 560 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 559 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.56e+00 pdb=" C CYS B 559 " -0.037 2.00e-02 2.50e+03 pdb=" O CYS B 559 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN B 560 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 54 " 0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO B 55 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 55 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 55 " 0.029 5.00e-02 4.00e+02 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1118 2.75 - 3.29: 8911 3.29 - 3.83: 14599 3.83 - 4.36: 16814 4.36 - 4.90: 29014 Nonbonded interactions: 70456 Sorted by model distance: nonbonded pdb=" O MET B 279 " pdb=" OG1 THR B 283 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR A 350 " pdb=" OG1 THR A 376 " model vdw 2.244 3.040 nonbonded pdb=" O VAL A 348 " pdb=" OG1 THR A 352 " model vdw 2.323 3.040 nonbonded pdb=" OG SER A 373 " pdb=" OG SER B 104 " model vdw 2.329 3.040 nonbonded pdb=" OG1 THR B 475 " pdb=" OD1 ASN B 480 " model vdw 2.340 3.040 ... (remaining 70451 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.620 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.060 Find NCS groups from input model: 0.140 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:9.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 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 : 0.004 0.046 8688 Z= 0.223 Angle : 0.653 11.651 11810 Z= 0.366 Chirality : 0.044 0.259 1376 Planarity : 0.005 0.052 1440 Dihedral : 12.593 130.060 3138 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.22 % Allowed : 0.11 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.25), residues: 1070 helix: 1.41 (0.18), residues: 792 sheet: None (None), residues: 0 loop : -0.71 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 312 TYR 0.027 0.001 TYR B 111 PHE 0.020 0.001 PHE A 251 TRP 0.013 0.001 TRP B 414 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 8688) covalent geometry : angle 0.65317 (11810) hydrogen bonds : bond 0.12131 ( 562) hydrogen bonds : angle 5.67008 ( 1674) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.337 Fit side-chains REVERT: A 323 ASP cc_start: 0.9217 (t70) cc_final: 0.8827 (p0) REVERT: A 340 MET cc_start: 0.9323 (ttm) cc_final: 0.9080 (ttm) REVERT: A 349 MET cc_start: 0.9171 (mmm) cc_final: 0.8869 (mmm) REVERT: B 267 ASP cc_start: 0.8221 (t0) cc_final: 0.7944 (t0) REVERT: B 363 ASP cc_start: 0.9073 (m-30) cc_final: 0.8855 (m-30) outliers start: 2 outliers final: 0 residues processed: 80 average time/residue: 0.6549 time to fit residues: 55.4895 Evaluate side-chains 69 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN B 106 GLN B 189 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.064549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.049270 restraints weight = 27394.461| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.28 r_work: 0.2711 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8688 Z= 0.164 Angle : 0.584 7.139 11810 Z= 0.300 Chirality : 0.042 0.177 1376 Planarity : 0.005 0.047 1440 Dihedral : 8.431 114.927 1226 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.10 % Allowed : 5.51 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.25), residues: 1070 helix: 1.38 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -0.98 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 371 TYR 0.034 0.001 TYR A 282 PHE 0.026 0.001 PHE A 251 TRP 0.014 0.001 TRP B 414 HIS 0.004 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8688) covalent geometry : angle 0.58388 (11810) hydrogen bonds : bond 0.04175 ( 562) hydrogen bonds : angle 4.79188 ( 1674) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.310 Fit side-chains REVERT: A 323 ASP cc_start: 0.9331 (t70) cc_final: 0.8907 (p0) REVERT: A 332 MET cc_start: 0.8169 (ttm) cc_final: 0.7846 (ttp) REVERT: A 340 MET cc_start: 0.9324 (ttm) cc_final: 0.9097 (ttm) REVERT: A 349 MET cc_start: 0.9292 (mmm) cc_final: 0.8985 (mmm) REVERT: B 267 ASP cc_start: 0.8197 (t0) cc_final: 0.7921 (t0) outliers start: 10 outliers final: 3 residues processed: 76 average time/residue: 0.6468 time to fit residues: 52.2886 Evaluate side-chains 75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 494 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 42 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 2 optimal weight: 0.0370 chunk 101 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN A 372 ASN B 106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.064955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.049616 restraints weight = 27041.478| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.27 r_work: 0.2718 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8688 Z= 0.143 Angle : 0.559 7.135 11810 Z= 0.285 Chirality : 0.041 0.170 1376 Planarity : 0.005 0.047 1440 Dihedral : 8.084 129.269 1226 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.21 % Allowed : 8.15 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.25), residues: 1070 helix: 1.47 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -1.10 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 371 TYR 0.027 0.001 TYR A 282 PHE 0.024 0.001 PHE A 251 TRP 0.016 0.001 TRP B 414 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8688) covalent geometry : angle 0.55859 (11810) hydrogen bonds : bond 0.03905 ( 562) hydrogen bonds : angle 4.60199 ( 1674) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.9319 (t70) cc_final: 0.8921 (p0) REVERT: A 349 MET cc_start: 0.9326 (mmm) cc_final: 0.8986 (mmm) REVERT: B 267 ASP cc_start: 0.8174 (t0) cc_final: 0.7878 (t0) outliers start: 11 outliers final: 3 residues processed: 76 average time/residue: 0.6285 time to fit residues: 50.9063 Evaluate side-chains 76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 494 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 83 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 372 ASN B 480 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.066139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.050863 restraints weight = 27288.212| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.31 r_work: 0.2752 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8688 Z= 0.113 Angle : 0.533 6.961 11810 Z= 0.273 Chirality : 0.040 0.160 1376 Planarity : 0.005 0.046 1440 Dihedral : 7.760 125.447 1226 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.99 % Allowed : 10.24 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.25), residues: 1070 helix: 1.55 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -1.10 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 325 TYR 0.026 0.001 TYR A 282 PHE 0.021 0.001 PHE A 251 TRP 0.015 0.001 TRP B 414 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8688) covalent geometry : angle 0.53333 (11810) hydrogen bonds : bond 0.03542 ( 562) hydrogen bonds : angle 4.45293 ( 1674) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.356 Fit side-chains REVERT: A 323 ASP cc_start: 0.9306 (t70) cc_final: 0.8899 (p0) REVERT: A 349 MET cc_start: 0.9357 (mmm) cc_final: 0.8996 (mmm) REVERT: B 267 ASP cc_start: 0.8159 (t0) cc_final: 0.7842 (t0) outliers start: 9 outliers final: 1 residues processed: 76 average time/residue: 0.6204 time to fit residues: 50.2538 Evaluate side-chains 72 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 46 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 389 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.066021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.050714 restraints weight = 27163.632| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.29 r_work: 0.2744 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8688 Z= 0.122 Angle : 0.538 6.647 11810 Z= 0.274 Chirality : 0.040 0.164 1376 Planarity : 0.005 0.045 1440 Dihedral : 7.681 122.535 1226 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.10 % Allowed : 11.23 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.25), residues: 1070 helix: 1.56 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -1.11 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 312 TYR 0.025 0.001 TYR A 282 PHE 0.020 0.001 PHE B 251 TRP 0.015 0.001 TRP B 414 HIS 0.003 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8688) covalent geometry : angle 0.53754 (11810) hydrogen bonds : bond 0.03567 ( 562) hydrogen bonds : angle 4.40046 ( 1674) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.336 Fit side-chains REVERT: A 323 ASP cc_start: 0.9287 (t70) cc_final: 0.8926 (p0) REVERT: A 349 MET cc_start: 0.9368 (mmm) cc_final: 0.8978 (mmm) REVERT: B 110 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8842 (mm) REVERT: B 267 ASP cc_start: 0.8207 (t0) cc_final: 0.7903 (t0) outliers start: 10 outliers final: 4 residues processed: 77 average time/residue: 0.6279 time to fit residues: 51.5072 Evaluate side-chains 75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 220 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 86 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 96 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 389 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.066890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.051711 restraints weight = 26886.978| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.30 r_work: 0.2770 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8688 Z= 0.108 Angle : 0.521 10.596 11810 Z= 0.265 Chirality : 0.039 0.160 1376 Planarity : 0.005 0.045 1440 Dihedral : 7.487 116.663 1226 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.21 % Allowed : 11.45 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.25), residues: 1070 helix: 1.60 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -1.08 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 312 TYR 0.025 0.001 TYR A 282 PHE 0.018 0.001 PHE B 268 TRP 0.014 0.001 TRP B 414 HIS 0.002 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8688) covalent geometry : angle 0.52068 (11810) hydrogen bonds : bond 0.03369 ( 562) hydrogen bonds : angle 4.32581 ( 1674) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 349 MET cc_start: 0.9369 (mmm) cc_final: 0.8959 (mmm) REVERT: A 540 MET cc_start: 0.8705 (ttp) cc_final: 0.8370 (ttm) REVERT: B 110 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8825 (mm) REVERT: B 267 ASP cc_start: 0.8227 (t0) cc_final: 0.7951 (t0) REVERT: B 363 ASP cc_start: 0.8887 (m-30) cc_final: 0.8647 (m-30) outliers start: 11 outliers final: 7 residues processed: 80 average time/residue: 0.6101 time to fit residues: 52.2843 Evaluate side-chains 79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 39 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 64 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.066161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.050841 restraints weight = 27212.427| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.34 r_work: 0.2747 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8688 Z= 0.135 Angle : 0.539 12.956 11810 Z= 0.273 Chirality : 0.040 0.164 1376 Planarity : 0.005 0.045 1440 Dihedral : 7.480 114.077 1226 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.99 % Allowed : 12.33 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.26), residues: 1070 helix: 1.63 (0.18), residues: 814 sheet: None (None), residues: 0 loop : -1.04 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 371 TYR 0.024 0.001 TYR A 282 PHE 0.018 0.001 PHE B 251 TRP 0.013 0.001 TRP B 414 HIS 0.003 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8688) covalent geometry : angle 0.53876 (11810) hydrogen bonds : bond 0.03475 ( 562) hydrogen bonds : angle 4.32929 ( 1674) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.336 Fit side-chains REVERT: A 349 MET cc_start: 0.9372 (mmm) cc_final: 0.8935 (mmm) REVERT: A 540 MET cc_start: 0.8783 (ttp) cc_final: 0.8401 (ttm) REVERT: B 110 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8828 (mm) REVERT: B 267 ASP cc_start: 0.8300 (t0) cc_final: 0.8044 (t0) outliers start: 9 outliers final: 6 residues processed: 76 average time/residue: 0.6399 time to fit residues: 51.8535 Evaluate side-chains 77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 83 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.066528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.050991 restraints weight = 26925.239| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.35 r_work: 0.2749 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8688 Z= 0.124 Angle : 0.537 13.537 11810 Z= 0.273 Chirality : 0.040 0.164 1376 Planarity : 0.005 0.045 1440 Dihedral : 7.448 109.706 1226 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.99 % Allowed : 13.00 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.25), residues: 1070 helix: 1.62 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -1.04 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 312 TYR 0.024 0.001 TYR A 282 PHE 0.016 0.001 PHE A 251 TRP 0.014 0.001 TRP B 414 HIS 0.002 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8688) covalent geometry : angle 0.53678 (11810) hydrogen bonds : bond 0.03409 ( 562) hydrogen bonds : angle 4.29361 ( 1674) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.360 Fit side-chains REVERT: A 241 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8479 (p) REVERT: A 349 MET cc_start: 0.9383 (mmm) cc_final: 0.8951 (mmm) REVERT: A 540 MET cc_start: 0.8762 (ttp) cc_final: 0.8386 (ttm) REVERT: B 110 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8815 (mm) REVERT: B 267 ASP cc_start: 0.8307 (t0) cc_final: 0.8045 (t0) outliers start: 9 outliers final: 6 residues processed: 77 average time/residue: 0.6530 time to fit residues: 53.6520 Evaluate side-chains 77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 21 optimal weight: 0.0270 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.066736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.051446 restraints weight = 27025.166| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.33 r_work: 0.2766 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8688 Z= 0.113 Angle : 0.543 14.356 11810 Z= 0.274 Chirality : 0.040 0.162 1376 Planarity : 0.005 0.045 1440 Dihedral : 7.346 104.463 1226 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.99 % Allowed : 13.22 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.25), residues: 1070 helix: 1.61 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -1.01 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 312 TYR 0.024 0.001 TYR A 282 PHE 0.015 0.001 PHE B 251 TRP 0.014 0.001 TRP B 414 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8688) covalent geometry : angle 0.54275 (11810) hydrogen bonds : bond 0.03333 ( 562) hydrogen bonds : angle 4.26091 ( 1674) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.365 Fit side-chains REVERT: A 99 MET cc_start: 0.9566 (mtm) cc_final: 0.9298 (mtp) REVERT: A 241 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8465 (p) REVERT: A 349 MET cc_start: 0.9370 (mmm) cc_final: 0.8920 (mmm) REVERT: A 540 MET cc_start: 0.8745 (ttp) cc_final: 0.8363 (ttm) REVERT: B 110 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8813 (mm) REVERT: B 267 ASP cc_start: 0.8310 (t0) cc_final: 0.8045 (t0) outliers start: 9 outliers final: 5 residues processed: 75 average time/residue: 0.5927 time to fit residues: 47.4676 Evaluate side-chains 76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 102 optimal weight: 0.3980 chunk 80 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.066520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.050998 restraints weight = 26986.861| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.36 r_work: 0.2750 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8688 Z= 0.125 Angle : 0.545 13.723 11810 Z= 0.275 Chirality : 0.040 0.165 1376 Planarity : 0.005 0.045 1440 Dihedral : 7.311 99.320 1226 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.21 % Allowed : 12.89 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.25), residues: 1070 helix: 1.62 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -0.97 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 371 TYR 0.023 0.001 TYR A 282 PHE 0.016 0.001 PHE A 251 TRP 0.014 0.001 TRP B 414 HIS 0.003 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8688) covalent geometry : angle 0.54499 (11810) hydrogen bonds : bond 0.03394 ( 562) hydrogen bonds : angle 4.26459 ( 1674) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.337 Fit side-chains REVERT: A 99 MET cc_start: 0.9572 (mtm) cc_final: 0.9306 (mtp) REVERT: A 241 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8446 (p) REVERT: A 323 ASP cc_start: 0.9431 (t0) cc_final: 0.8905 (p0) REVERT: A 349 MET cc_start: 0.9384 (mmm) cc_final: 0.8945 (mmm) REVERT: B 110 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8821 (mm) REVERT: B 267 ASP cc_start: 0.8409 (t0) cc_final: 0.8173 (t0) REVERT: B 272 MET cc_start: 0.9446 (ttm) cc_final: 0.9185 (tpp) REVERT: B 363 ASP cc_start: 0.9075 (m-30) cc_final: 0.8840 (m-30) outliers start: 11 outliers final: 3 residues processed: 77 average time/residue: 0.5882 time to fit residues: 48.5273 Evaluate side-chains 74 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.067554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.052211 restraints weight = 26559.330| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.32 r_work: 0.2773 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8688 Z= 0.112 Angle : 0.538 12.563 11810 Z= 0.273 Chirality : 0.039 0.159 1376 Planarity : 0.004 0.045 1440 Dihedral : 7.223 91.204 1226 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.66 % Allowed : 13.33 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.25), residues: 1070 helix: 1.64 (0.18), residues: 822 sheet: None (None), residues: 0 loop : -1.02 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 371 TYR 0.024 0.001 TYR A 282 PHE 0.015 0.001 PHE B 251 TRP 0.015 0.001 TRP B 414 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8688) covalent geometry : angle 0.53806 (11810) hydrogen bonds : bond 0.03307 ( 562) hydrogen bonds : angle 4.23000 ( 1674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2520.39 seconds wall clock time: 43 minutes 54.30 seconds (2634.30 seconds total)