Starting phenix.real_space_refine on Tue Feb 11 09:21:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xhs_38354/02_2025/8xhs_38354.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xhs_38354/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xhs_38354/02_2025/8xhs_38354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xhs_38354/02_2025/8xhs_38354.map" model { file = "/net/cci-nas-00/data/ceres_data/8xhs_38354/02_2025/8xhs_38354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xhs_38354/02_2025/8xhs_38354.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.87, per 1000 atoms: 0.76 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: 1.19 Conformation dependent library (CDL) restraints added in 583.8 milliseconds 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: 0.62 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: 1.50 Time building geometry restraints manager: 1.40 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: 1.690 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: 0.390 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 16.140 Find NCS groups from input model: 0.070 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:14.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.840 ------------------------------------------------------------------------------- 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= 0.158 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.007 0.001 TRP A 512 HIS 0.002 0.000 HIS A 696 PHE 0.024 0.001 PHE A 682 TYR 0.009 0.001 TYR A 53 ARG 0.002 0.000 ARG A 704 *********************** 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 : 0.534 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: 1.3506 time to fit residues: 122.0821 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 : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 0.0000 chunk 25 optimal weight: 0.0670 chunk 15 optimal weight: 0.0040 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.1734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 120 GLN A 289 GLN A 439 GLN A 461 GLN A 546 GLN A 674 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.202924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.159219 restraints weight = 5362.682| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.51 r_work: 0.3496 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5164 Z= 0.119 Angle : 0.459 5.763 6981 Z= 0.246 Chirality : 0.041 0.152 774 Planarity : 0.003 0.039 882 Dihedral : 3.961 19.490 673 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.92 % Allowed : 11.58 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.34), residues: 608 helix: 1.47 (0.38), residues: 209 sheet: 0.83 (0.49), residues: 120 loop : -0.82 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 512 HIS 0.003 0.000 HIS A 467 PHE 0.014 0.001 PHE A 682 TYR 0.006 0.001 TYR A 53 ARG 0.003 0.000 ARG A 600 *********************** 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 73 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.672 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 531 GLU cc_start: 0.6782 (tt0) cc_final: 0.6482 (tt0) outliers start: 5 outliers final: 1 residues processed: 72 average time/residue: 1.2825 time to fit residues: 96.9975 Evaluate side-chains 60 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 chunk 60 optimal weight: 0.0020 chunk 38 optimal weight: 3.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 = 0.4265 r_free = 0.4265 target = 0.200066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.155542 restraints weight = 5388.743| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.78 r_work: 0.3438 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1387 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= 0.152 Angle : 0.468 4.922 6981 Z= 0.253 Chirality : 0.041 0.146 774 Planarity : 0.003 0.043 882 Dihedral : 4.016 19.590 673 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.29 % Allowed : 14.15 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.35), residues: 608 helix: 1.61 (0.38), residues: 209 sheet: 0.79 (0.47), residues: 132 loop : -0.80 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 512 HIS 0.003 0.000 HIS A 467 PHE 0.012 0.001 PHE A 682 TYR 0.008 0.001 TYR A 158 ARG 0.007 0.000 ARG A 45 *********************** 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 70 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.624 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 531 GLU cc_start: 0.6944 (tt0) cc_final: 0.6625 (tt0) outliers start: 7 outliers final: 3 residues processed: 66 average time/residue: 1.2261 time to fit residues: 84.7235 Evaluate side-chains 64 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 678 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 2 optimal weight: 0.4980 chunk 54 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 674 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.193245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.147896 restraints weight = 5470.231| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 3.13 r_work: 0.3333 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5164 Z= 0.353 Angle : 0.593 6.728 6981 Z= 0.320 Chirality : 0.046 0.166 774 Planarity : 0.004 0.045 882 Dihedral : 4.713 22.576 673 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.21 % Allowed : 16.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.33), residues: 608 helix: 1.21 (0.37), residues: 208 sheet: 1.03 (0.52), residues: 98 loop : -1.14 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 512 HIS 0.004 0.001 HIS A 548 PHE 0.015 0.002 PHE A 420 TYR 0.014 0.001 TYR A 158 ARG 0.007 0.001 ARG A 45 *********************** 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 79 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.509 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 531 GLU cc_start: 0.7305 (tt0) cc_final: 0.6868 (tt0) REVERT: A 548 HIS cc_start: 0.7780 (OUTLIER) cc_final: 0.7285 (p90) REVERT: A 700 MET cc_start: 0.8926 (tpt) cc_final: 0.8668 (tpt) outliers start: 12 outliers final: 5 residues processed: 71 average time/residue: 1.1800 time to fit residues: 87.7884 Evaluate side-chains 71 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 548 HIS Chi-restraints excluded: chain A residue 582 THR 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 37 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.0030 chunk 54 optimal weight: 4.9990 chunk 58 optimal weight: 0.0570 chunk 56 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.4108 ------------------------------------------------------------------------------- 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 = 0.4243 r_free = 0.4243 target = 0.198047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.154280 restraints weight = 5383.969| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.63 r_work: 0.3439 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5164 Z= 0.133 Angle : 0.458 5.444 6981 Z= 0.248 Chirality : 0.041 0.147 774 Planarity : 0.003 0.043 882 Dihedral : 4.170 21.209 673 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.29 % Allowed : 17.65 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.34), residues: 608 helix: 1.54 (0.38), residues: 209 sheet: 0.83 (0.48), residues: 120 loop : -0.92 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 512 HIS 0.003 0.000 HIS A 467 PHE 0.008 0.001 PHE A 412 TYR 0.009 0.001 TYR A 37 ARG 0.008 0.000 ARG A 45 *********************** 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 73 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.578 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 13 ARG cc_start: 0.8018 (mpt90) cc_final: 0.7612 (mmm160) REVERT: A 470 LYS cc_start: 0.8322 (mttm) cc_final: 0.8084 (mmtm) REVERT: A 531 GLU cc_start: 0.7137 (tt0) cc_final: 0.6702 (tt0) outliers start: 7 outliers final: 3 residues processed: 69 average time/residue: 1.2526 time to fit residues: 90.3187 Evaluate side-chains 65 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 678 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 0.4980 chunk 6 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4226 r_free = 0.4226 target = 0.196183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.153041 restraints weight = 5410.041| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.83 r_work: 0.3381 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1705 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= 0.218 Angle : 0.505 5.606 6981 Z= 0.274 Chirality : 0.043 0.157 774 Planarity : 0.003 0.045 882 Dihedral : 4.347 20.458 673 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.65 % Allowed : 18.38 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.33), residues: 608 helix: 1.44 (0.38), residues: 209 sheet: 1.14 (0.52), residues: 98 loop : -1.08 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 512 HIS 0.003 0.001 HIS A 467 PHE 0.011 0.001 PHE A 420 TYR 0.010 0.001 TYR A 158 ARG 0.008 0.000 ARG A 45 *********************** 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 74 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.563 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 470 LYS cc_start: 0.8367 (mttm) cc_final: 0.8029 (mmtm) REVERT: A 531 GLU cc_start: 0.7212 (tt0) cc_final: 0.6799 (tt0) outliers start: 9 outliers final: 3 residues processed: 69 average time/residue: 1.2686 time to fit residues: 91.4232 Evaluate side-chains 66 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 678 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 25 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 0.0270 chunk 37 optimal weight: 3.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.196021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.153392 restraints weight = 5323.627| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.68 r_work: 0.3429 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1714 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= 0.166 Angle : 0.478 5.906 6981 Z= 0.258 Chirality : 0.042 0.152 774 Planarity : 0.003 0.045 882 Dihedral : 4.224 20.280 673 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.47 % Allowed : 19.12 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.34), residues: 608 helix: 1.53 (0.38), residues: 209 sheet: 0.91 (0.49), residues: 120 loop : -1.00 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 512 HIS 0.003 0.001 HIS A 467 PHE 0.008 0.001 PHE A 420 TYR 0.010 0.001 TYR A 37 ARG 0.010 0.000 ARG A 45 *********************** 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 71 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.596 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 470 LYS cc_start: 0.8350 (mttm) cc_final: 0.8140 (mttm) REVERT: A 531 GLU cc_start: 0.7238 (tt0) cc_final: 0.6775 (tt0) outliers start: 8 outliers final: 5 residues processed: 67 average time/residue: 1.2788 time to fit residues: 90.0284 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 : 0.823 ------------------------------------------------------------------------------- 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 284 GLN Chi-restraints excluded: chain A residue 678 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 42 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.0370 chunk 60 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.196257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.153756 restraints weight = 5357.354| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.74 r_work: 0.3389 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5164 Z= 0.159 Angle : 0.475 6.298 6981 Z= 0.256 Chirality : 0.042 0.149 774 Planarity : 0.003 0.045 882 Dihedral : 4.122 20.014 673 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.29 % Allowed : 19.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.34), residues: 608 helix: 1.55 (0.38), residues: 209 sheet: 0.98 (0.49), residues: 120 loop : -1.00 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 512 HIS 0.003 0.000 HIS A 467 PHE 0.008 0.001 PHE A 420 TYR 0.008 0.001 TYR A 158 ARG 0.011 0.000 ARG A 45 *********************** 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 73 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.608 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 470 LYS cc_start: 0.8390 (mttm) cc_final: 0.8162 (mttm) REVERT: A 531 GLU cc_start: 0.7275 (tt0) cc_final: 0.6785 (tt0) outliers start: 7 outliers final: 5 residues processed: 69 average time/residue: 1.2061 time to fit residues: 87.2610 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 : 0.561 ------------------------------------------------------------------------------- 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 284 GLN 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 1 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4226 r_free = 0.4226 target = 0.196325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.151297 restraints weight = 5324.011| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.81 r_work: 0.3401 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5164 Z= 0.174 Angle : 0.493 6.826 6981 Z= 0.266 Chirality : 0.042 0.151 774 Planarity : 0.003 0.045 882 Dihedral : 4.156 19.677 673 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.65 % Allowed : 19.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.34), residues: 608 helix: 1.53 (0.38), residues: 209 sheet: 1.17 (0.52), residues: 104 loop : -1.04 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 512 HIS 0.003 0.001 HIS A 467 PHE 0.009 0.001 PHE A 420 TYR 0.016 0.001 TYR A 37 ARG 0.011 0.000 ARG A 45 *********************** 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 69 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.571 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 470 LYS cc_start: 0.8403 (mttm) cc_final: 0.8173 (mttm) REVERT: A 531 GLU cc_start: 0.7278 (tt0) cc_final: 0.6802 (tt0) outliers start: 9 outliers final: 6 residues processed: 63 average time/residue: 1.1846 time to fit residues: 78.1620 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 : 0.592 ------------------------------------------------------------------------------- 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 284 GLN Chi-restraints excluded: chain A residue 582 THR 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 12 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.195678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.152461 restraints weight = 5344.933| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.54 r_work: 0.3428 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5164 Z= 0.190 Angle : 0.511 7.520 6981 Z= 0.275 Chirality : 0.043 0.159 774 Planarity : 0.004 0.051 882 Dihedral : 4.217 20.269 673 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.47 % Allowed : 20.04 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.34), residues: 608 helix: 1.50 (0.38), residues: 209 sheet: 1.21 (0.52), residues: 104 loop : -1.05 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 512 HIS 0.003 0.000 HIS A 467 PHE 0.009 0.001 PHE A 420 TYR 0.010 0.001 TYR A 53 ARG 0.011 0.000 ARG A 45 ********************** 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 69 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.573 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. REVERT: A 470 LYS cc_start: 0.8412 (mttm) cc_final: 0.8186 (mttm) REVERT: A 531 GLU cc_start: 0.7359 (tt0) cc_final: 0.6811 (tt0) outliers start: 8 outliers final: 7 residues processed: 64 average time/residue: 1.1295 time to fit residues: 75.8459 Evaluate side-chains 67 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 81 ASN 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 582 THR 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 10 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 37 optimal weight: 0.0470 chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.195795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.152589 restraints weight = 5378.052| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.57 r_work: 0.3415 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5164 Z= 0.173 Angle : 0.506 8.150 6981 Z= 0.271 Chirality : 0.042 0.165 774 Planarity : 0.004 0.052 882 Dihedral : 4.168 19.781 673 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.47 % Allowed : 20.04 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.34), residues: 608 helix: 1.50 (0.38), residues: 209 sheet: 1.20 (0.52), residues: 104 loop : -1.02 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 512 HIS 0.003 0.001 HIS A 467 PHE 0.008 0.001 PHE A 420 TYR 0.021 0.001 TYR A 37 ARG 0.013 0.000 ARG A 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3819.28 seconds wall clock time: 68 minutes 46.13 seconds (4126.13 seconds total)