Starting phenix.real_space_refine on Wed Sep 17 05:21:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xhs_38354/09_2025/8xhs_38354.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xhs_38354/09_2025/8xhs_38354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xhs_38354/09_2025/8xhs_38354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xhs_38354/09_2025/8xhs_38354.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xhs_38354/09_2025/8xhs_38354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xhs_38354/09_2025/8xhs_38354.map" } resolution = 2.85 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= -0.002 sd= 0.072 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3244 2.51 5 N 887 2.21 5 O 910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s 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: 5067 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5044 Classifications: {'peptide': 618} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 20, 'TRANS': 597} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Time building chain proxies: 1.59, per 1000 atoms: 0.31 Number of scatterers: 5067 At special positions: 0 Unit cell: (73.186, 83.398, 108.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 910 8.00 N 887 7.00 C 3244 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: 0.40 Conformation dependent library (CDL) restraints added in 208.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1180 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 7 sheets defined 36.6% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 37 through 46 Processing helix chain 'A' and resid 84 through 107 removed outlier: 3.713A pdb=" N ALA A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 269 removed outlier: 4.643A pdb=" N LEU A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 287 removed outlier: 3.879A pdb=" N TYR A 280 " --> pdb=" O MET A 276 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 325 through 333 Processing helix chain 'A' and resid 349 through 354 removed outlier: 3.538A pdb=" N LYS A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 377 removed outlier: 4.170A pdb=" N ILE A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 428 removed outlier: 3.518A pdb=" N ASN A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 446 through 450 removed outlier: 3.503A pdb=" N SER A 449 " --> pdb=" O ASP A 446 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN A 450 " --> pdb=" O ILE A 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 446 through 450' Processing helix chain 'A' and resid 453 through 467 Processing helix chain 'A' and resid 476 through 489 removed outlier: 4.223A pdb=" N ASN A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 506 removed outlier: 4.438A pdb=" N THR A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY A 502 " --> pdb=" O ASN A 498 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 585 Processing helix chain 'A' and resid 602 through 614 removed outlier: 3.663A pdb=" N VAL A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 693 removed outlier: 3.551A pdb=" N SER A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 removed outlier: 3.640A pdb=" N ALA A 631 " --> pdb=" O TYR A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 13 removed outlier: 5.257A pdb=" N ILE A 144 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN A 122 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU A 131 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLN A 120 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ILE A 133 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU A 118 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LEU A 135 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N LEU A 116 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.537A pdb=" N GLU A 74 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 311 removed outlier: 6.418A pdb=" N ILE A 591 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A 620 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE A 593 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE A 622 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG A 595 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL A 528 " --> pdb=" O ASP A 596 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER A 529 " --> pdb=" O ALA A 537 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA A 537 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY A 538 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N MET A 540 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN A 552 " --> pdb=" O MET A 540 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 542 " --> pdb=" O ILE A 550 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA6, first strand: chain 'A' and resid 339 through 343 removed outlier: 6.619A pdb=" N GLY A 339 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N THR A 381 " --> pdb=" O GLY A 339 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE A 341 " --> pdb=" O THR A 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 346 through 347 removed outlier: 6.372A pdb=" N LEU A 346 " --> pdb=" O PHE A 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 214 hydrogen bonds defined for protein. 591 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: 1.21 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1627 1.34 - 1.46: 1067 1.46 - 1.58: 2425 1.58 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 5164 Sorted by residual: bond pdb=" CA GLU A 141 " pdb=" CB GLU A 141 " ideal model delta sigma weight residual 1.527 1.547 -0.019 1.70e-02 3.46e+03 1.31e+00 bond pdb=" CB GLU A 141 " pdb=" CG GLU A 141 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.17e+00 bond pdb=" CA HIS A 696 " pdb=" C HIS A 696 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.12e-02 7.97e+03 9.44e-01 bond pdb=" CA GLU A 403 " pdb=" C GLU A 403 " ideal model delta sigma weight residual 1.523 1.536 -0.013 1.41e-02 5.03e+03 8.75e-01 bond pdb=" N LEU A 408 " pdb=" CA LEU A 408 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.29e-02 6.01e+03 5.93e-01 ... (remaining 5159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 6810 1.39 - 2.78: 141 2.78 - 4.17: 23 4.17 - 5.56: 4 5.56 - 6.95: 3 Bond angle restraints: 6981 Sorted by residual: angle pdb=" CA GLU A 141 " pdb=" CB GLU A 141 " pdb=" CG GLU A 141 " ideal model delta sigma weight residual 114.10 121.05 -6.95 2.00e+00 2.50e-01 1.21e+01 angle pdb=" CA GLU A 403 " pdb=" C GLU A 403 " pdb=" N GLU A 404 " ideal model delta sigma weight residual 118.44 122.90 -4.46 1.41e+00 5.03e-01 1.00e+01 angle pdb=" C LEU A 408 " pdb=" CA LEU A 408 " pdb=" CB LEU A 408 " ideal model delta sigma weight residual 110.42 115.96 -5.54 1.99e+00 2.53e-01 7.75e+00 angle pdb=" N HIS A 320 " pdb=" CA HIS A 320 " pdb=" C HIS A 320 " ideal model delta sigma weight residual 114.09 110.47 3.62 1.55e+00 4.16e-01 5.47e+00 angle pdb=" C ALA A 46 " pdb=" N ASN A 47 " pdb=" CA ASN A 47 " ideal model delta sigma weight residual 121.54 125.44 -3.90 1.91e+00 2.74e-01 4.16e+00 ... (remaining 6976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 2705 16.62 - 33.23: 290 33.23 - 49.85: 63 49.85 - 66.46: 10 66.46 - 83.08: 3 Dihedral angle restraints: 3071 sinusoidal: 1247 harmonic: 1824 Sorted by residual: dihedral pdb=" CA PHE A 319 " pdb=" C PHE A 319 " pdb=" N HIS A 320 " pdb=" CA HIS A 320 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ARG A 78 " pdb=" C ARG A 78 " pdb=" N HIS A 79 " pdb=" CA HIS A 79 " ideal model delta harmonic sigma weight residual 180.00 162.27 17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA GLN A 284 " pdb=" C GLN A 284 " pdb=" N GLN A 285 " pdb=" CA GLN A 285 " ideal model delta harmonic sigma weight residual 180.00 164.77 15.23 0 5.00e+00 4.00e-02 9.28e+00 ... (remaining 3068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 491 0.032 - 0.063: 187 0.063 - 0.095: 55 0.095 - 0.127: 38 0.127 - 0.158: 3 Chirality restraints: 774 Sorted by residual: chirality pdb=" CA ILE A 671 " pdb=" N ILE A 671 " pdb=" C ILE A 671 " pdb=" CB ILE A 671 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ILE A 128 " pdb=" N ILE A 128 " pdb=" C ILE A 128 " pdb=" CB ILE A 128 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA GLU A 141 " pdb=" N GLU A 141 " pdb=" C GLU A 141 " pdb=" CB GLU A 141 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 771 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 682 " 0.010 2.00e-02 2.50e+03 1.07e-02 2.00e+00 pdb=" CG PHE A 682 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 682 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 682 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 682 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 682 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 682 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 510 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO A 511 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 680 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO A 681 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 681 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 681 " 0.018 5.00e-02 4.00e+02 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 453 2.75 - 3.29: 4697 3.29 - 3.82: 7870 3.82 - 4.36: 9631 4.36 - 4.90: 17008 Nonbonded interactions: 39659 Sorted by model distance: nonbonded pdb=" OG1 THR A 402 " pdb=" OE1 GLU A 404 " model vdw 2.210 3.040 nonbonded pdb=" O ALA A 668 " pdb=" O HOH A 801 " model vdw 2.278 3.040 nonbonded pdb=" N GLY A 645 " pdb=" O CYS A 657 " model vdw 2.293 3.120 nonbonded pdb=" NZ LYS A 334 " pdb=" O ALA A 375 " model vdw 2.325 3.120 nonbonded pdb=" OG SER A 423 " pdb=" OE2 GLU A 454 " model vdw 2.328 3.040 ... (remaining 39654 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.430 Set stop_for_unknowns flag: 0.010 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.930 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 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 : 0.002 0.032 5164 Z= 0.114 Angle : 0.510 6.948 6981 Z= 0.281 Chirality : 0.042 0.158 774 Planarity : 0.003 0.034 882 Dihedral : 14.235 83.079 1891 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 0.16 (0.34), residues: 608 helix: 1.22 (0.38), residues: 201 sheet: 0.67 (0.48), residues: 120 loop : -0.96 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 704 TYR 0.009 0.001 TYR A 53 PHE 0.024 0.001 PHE A 682 TRP 0.007 0.001 TRP A 512 HIS 0.002 0.000 HIS A 696 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 5164) covalent geometry : angle 0.51032 ( 6981) hydrogen bonds : bond 0.14438 ( 214) hydrogen bonds : angle 5.70729 ( 591) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.272 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 531 GLU cc_start: 0.6748 (tt0) cc_final: 0.6534 (tt0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.7054 time to fit residues: 63.4699 Evaluate side-chains 61 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN A 439 GLN A 461 GLN A 546 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.194438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149725 restraints weight = 5451.420| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.82 r_work: 0.3377 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5164 Z= 0.187 Angle : 0.575 5.875 6981 Z= 0.310 Chirality : 0.045 0.173 774 Planarity : 0.004 0.045 882 Dihedral : 4.580 21.031 673 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.84 % Allowed : 12.32 % Favored : 85.85 % 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: -0.00 (0.34), residues: 608 helix: 1.11 (0.37), residues: 209 sheet: 0.76 (0.50), residues: 113 loop : -1.19 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 13 TYR 0.012 0.001 TYR A 158 PHE 0.020 0.002 PHE A 682 TRP 0.008 0.002 TRP A 512 HIS 0.003 0.001 HIS A 612 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 5164) covalent geometry : angle 0.57520 ( 6981) hydrogen bonds : bond 0.05160 ( 214) hydrogen bonds : angle 5.03008 ( 591) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.197 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 531 GLU cc_start: 0.7153 (tt0) cc_final: 0.6777 (tt0) REVERT: A 548 HIS cc_start: 0.7724 (OUTLIER) cc_final: 0.7355 (p90) REVERT: A 700 MET cc_start: 0.8860 (tpt) cc_final: 0.8555 (tpt) outliers start: 10 outliers final: 4 residues processed: 70 average time/residue: 0.5500 time to fit residues: 40.2443 Evaluate side-chains 65 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 678 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.193981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.150434 restraints weight = 5328.329| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.83 r_work: 0.3380 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5164 Z= 0.128 Angle : 0.506 5.168 6981 Z= 0.274 Chirality : 0.042 0.163 774 Planarity : 0.003 0.046 882 Dihedral : 4.372 21.191 673 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.84 % Allowed : 14.34 % Favored : 83.82 % 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: 0.19 (0.34), residues: 608 helix: 1.30 (0.38), residues: 209 sheet: 0.76 (0.50), residues: 114 loop : -1.05 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 45 TYR 0.009 0.001 TYR A 158 PHE 0.011 0.001 PHE A 682 TRP 0.008 0.001 TRP A 512 HIS 0.003 0.001 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 5164) covalent geometry : angle 0.50576 ( 6981) hydrogen bonds : bond 0.04156 ( 214) hydrogen bonds : angle 4.70215 ( 591) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.214 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 548 HIS cc_start: 0.7770 (OUTLIER) cc_final: 0.7349 (p90) outliers start: 10 outliers final: 4 residues processed: 69 average time/residue: 0.5628 time to fit residues: 40.5138 Evaluate side-chains 64 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 678 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 0.0870 chunk 15 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN A 585 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.197160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.155204 restraints weight = 5322.413| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.34 r_work: 0.3410 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5164 Z= 0.105 Angle : 0.471 5.124 6981 Z= 0.256 Chirality : 0.042 0.157 774 Planarity : 0.003 0.046 882 Dihedral : 4.220 20.888 673 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.47 % Allowed : 17.28 % Favored : 81.25 % 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: 0.35 (0.34), residues: 608 helix: 1.46 (0.38), residues: 209 sheet: 0.85 (0.50), residues: 114 loop : -0.97 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 45 TYR 0.007 0.001 TYR A 158 PHE 0.008 0.001 PHE A 412 TRP 0.007 0.001 TRP A 512 HIS 0.003 0.000 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 5164) covalent geometry : angle 0.47107 ( 6981) hydrogen bonds : bond 0.03681 ( 214) hydrogen bonds : angle 4.51077 ( 591) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.184 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 13 ARG cc_start: 0.8038 (mpt90) cc_final: 0.7607 (mmm160) REVERT: A 548 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.7324 (p90) outliers start: 8 outliers final: 4 residues processed: 68 average time/residue: 0.5623 time to fit residues: 39.9661 Evaluate side-chains 68 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 678 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 60 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4208 r_free = 0.4208 target = 0.194628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.139259 restraints weight = 5385.104| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.08 r_work: 0.3442 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5164 Z= 0.129 Angle : 0.495 5.453 6981 Z= 0.268 Chirality : 0.042 0.161 774 Planarity : 0.003 0.047 882 Dihedral : 4.317 20.643 673 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.02 % Allowed : 17.65 % Favored : 80.33 % 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: 0.33 (0.34), residues: 608 helix: 1.43 (0.38), residues: 209 sheet: 0.91 (0.50), residues: 114 loop : -1.03 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 45 TYR 0.010 0.001 TYR A 158 PHE 0.010 0.001 PHE A 420 TRP 0.008 0.001 TRP A 512 HIS 0.003 0.001 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 5164) covalent geometry : angle 0.49465 ( 6981) hydrogen bonds : bond 0.04124 ( 214) hydrogen bonds : angle 4.59204 ( 591) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.156 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 18 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: A 531 GLU cc_start: 0.7305 (tt0) cc_final: 0.6814 (tt0) REVERT: A 548 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.7404 (p90) REVERT: A 700 MET cc_start: 0.8743 (tpt) cc_final: 0.8296 (mmm) outliers start: 11 outliers final: 5 residues processed: 65 average time/residue: 0.5379 time to fit residues: 36.4932 Evaluate side-chains 65 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 678 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.193659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138256 restraints weight = 5415.802| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.08 r_work: 0.3389 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5164 Z= 0.175 Angle : 0.540 5.626 6981 Z= 0.293 Chirality : 0.044 0.170 774 Planarity : 0.004 0.047 882 Dihedral : 4.566 21.639 673 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.94 % Allowed : 17.83 % Favored : 79.23 % 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: 0.13 (0.33), residues: 608 helix: 1.27 (0.37), residues: 209 sheet: 1.15 (0.53), residues: 98 loop : -1.17 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 45 TYR 0.012 0.001 TYR A 158 PHE 0.013 0.001 PHE A 420 TRP 0.008 0.002 TRP A 512 HIS 0.004 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 5164) covalent geometry : angle 0.54007 ( 6981) hydrogen bonds : bond 0.04734 ( 214) hydrogen bonds : angle 4.79546 ( 591) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.120 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 531 GLU cc_start: 0.7326 (tt0) cc_final: 0.6794 (tt0) REVERT: A 548 HIS cc_start: 0.7878 (OUTLIER) cc_final: 0.7434 (p90) outliers start: 16 outliers final: 8 residues processed: 71 average time/residue: 0.5466 time to fit residues: 40.4862 Evaluate side-chains 68 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 678 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 0.0570 chunk 49 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 60 optimal weight: 0.0970 chunk 50 optimal weight: 0.7980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.198618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.156058 restraints weight = 5458.148| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.54 r_work: 0.3429 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5164 Z= 0.095 Angle : 0.467 5.630 6981 Z= 0.253 Chirality : 0.042 0.153 774 Planarity : 0.003 0.045 882 Dihedral : 4.153 21.245 673 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.47 % Allowed : 19.85 % Favored : 78.68 % 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: 0.47 (0.34), residues: 608 helix: 1.53 (0.38), residues: 209 sheet: 1.00 (0.49), residues: 120 loop : -0.96 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 45 TYR 0.011 0.001 TYR A 37 PHE 0.008 0.001 PHE A 412 TRP 0.009 0.001 TRP A 512 HIS 0.003 0.000 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 5164) covalent geometry : angle 0.46655 ( 6981) hydrogen bonds : bond 0.03438 ( 214) hydrogen bonds : angle 4.42446 ( 591) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.197 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 41 ARG cc_start: 0.7423 (mmm-85) cc_final: 0.5814 (ttp80) REVERT: A 548 HIS cc_start: 0.7714 (OUTLIER) cc_final: 0.7344 (p90) REVERT: A 700 MET cc_start: 0.8755 (tpt) cc_final: 0.8327 (mmm) outliers start: 8 outliers final: 4 residues processed: 67 average time/residue: 0.5579 time to fit residues: 39.0987 Evaluate side-chains 66 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 548 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 0.0070 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.195111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.150182 restraints weight = 5380.859| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.87 r_work: 0.3385 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5164 Z= 0.128 Angle : 0.502 6.265 6981 Z= 0.271 Chirality : 0.043 0.161 774 Planarity : 0.003 0.046 882 Dihedral : 4.285 20.861 673 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.84 % Allowed : 19.30 % Favored : 78.86 % 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: 0.35 (0.34), residues: 608 helix: 1.48 (0.38), residues: 209 sheet: 1.19 (0.52), residues: 104 loop : -1.07 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 45 TYR 0.010 0.001 TYR A 158 PHE 0.010 0.001 PHE A 420 TRP 0.008 0.001 TRP A 512 HIS 0.003 0.001 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5164) covalent geometry : angle 0.50157 ( 6981) hydrogen bonds : bond 0.04004 ( 214) hydrogen bonds : angle 4.54747 ( 591) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.192 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 531 GLU cc_start: 0.7277 (tt0) cc_final: 0.6754 (tt0) REVERT: A 548 HIS cc_start: 0.7726 (OUTLIER) cc_final: 0.7296 (p90) outliers start: 10 outliers final: 5 residues processed: 65 average time/residue: 0.5717 time to fit residues: 38.8773 Evaluate side-chains 66 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 678 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 60 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.197716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.153251 restraints weight = 5411.516| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.98 r_work: 0.3417 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5164 Z= 0.111 Angle : 0.491 6.336 6981 Z= 0.265 Chirality : 0.042 0.154 774 Planarity : 0.003 0.046 882 Dihedral : 4.165 20.839 673 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.65 % Allowed : 20.04 % Favored : 78.31 % 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: 0.46 (0.34), residues: 608 helix: 1.51 (0.38), residues: 209 sheet: 1.08 (0.50), residues: 120 loop : -1.01 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 45 TYR 0.014 0.001 TYR A 37 PHE 0.008 0.001 PHE A 420 TRP 0.008 0.001 TRP A 512 HIS 0.003 0.001 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 5164) covalent geometry : angle 0.49142 ( 6981) hydrogen bonds : bond 0.03677 ( 214) hydrogen bonds : angle 4.45644 ( 591) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.201 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 531 GLU cc_start: 0.7196 (tt0) cc_final: 0.6714 (tt0) REVERT: A 548 HIS cc_start: 0.7763 (OUTLIER) cc_final: 0.7388 (p90) REVERT: A 700 MET cc_start: 0.8741 (tpt) cc_final: 0.8315 (mmm) outliers start: 9 outliers final: 5 residues processed: 67 average time/residue: 0.5656 time to fit residues: 39.6009 Evaluate side-chains 67 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 678 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.194910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.150964 restraints weight = 5468.619| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.97 r_work: 0.3341 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5164 Z= 0.169 Angle : 0.560 8.985 6981 Z= 0.300 Chirality : 0.044 0.167 774 Planarity : 0.004 0.047 882 Dihedral : 4.476 21.362 673 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.47 % Allowed : 20.22 % Favored : 78.31 % 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: 0.20 (0.34), residues: 608 helix: 1.32 (0.37), residues: 209 sheet: 1.35 (0.54), residues: 98 loop : -1.19 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 45 TYR 0.012 0.001 TYR A 158 PHE 0.012 0.001 PHE A 420 TRP 0.007 0.001 TRP A 512 HIS 0.003 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 5164) covalent geometry : angle 0.56029 ( 6981) hydrogen bonds : bond 0.04556 ( 214) hydrogen bonds : angle 4.71755 ( 591) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1216 Ramachandran restraints generated. 608 Oldfield, 0 Emsley, 608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.200 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 531 GLU cc_start: 0.7299 (tt0) cc_final: 0.6773 (tt0) REVERT: A 548 HIS cc_start: 0.7803 (OUTLIER) cc_final: 0.7347 (p90) outliers start: 8 outliers final: 5 residues processed: 65 average time/residue: 0.5587 time to fit residues: 37.9924 Evaluate side-chains 67 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 678 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 0.0370 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 overall best weight: 0.6262 ------------------------------------------------------------------------------- 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 = 0.4218 r_free = 0.4218 target = 0.195785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.153733 restraints weight = 5498.260| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.64 r_work: 0.3412 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5164 Z= 0.109 Angle : 0.501 7.670 6981 Z= 0.270 Chirality : 0.042 0.158 774 Planarity : 0.003 0.047 882 Dihedral : 4.220 21.028 673 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.84 % Allowed : 19.85 % Favored : 78.31 % 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: 0.41 (0.34), residues: 608 helix: 1.47 (0.38), residues: 209 sheet: 1.04 (0.50), residues: 120 loop : -1.04 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 45 TYR 0.026 0.001 TYR A 37 PHE 0.007 0.001 PHE A 420 TRP 0.008 0.001 TRP A 512 HIS 0.003 0.000 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 5164) covalent geometry : angle 0.50124 ( 6981) hydrogen bonds : bond 0.03685 ( 214) hydrogen bonds : angle 4.48911 ( 591) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2020.22 seconds wall clock time: 35 minutes 17.26 seconds (2117.26 seconds total)