Starting phenix.real_space_refine on Fri Jan 17 14:03:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xhv_38355/01_2025/8xhv_38355.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xhv_38355/01_2025/8xhv_38355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xhv_38355/01_2025/8xhv_38355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xhv_38355/01_2025/8xhv_38355.map" model { file = "/net/cci-nas-00/data/ceres_data/8xhv_38355/01_2025/8xhv_38355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xhv_38355/01_2025/8xhv_38355.cif" } resolution = 2.81 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= -0.001 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5813 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 14 5.49 5 S 29 5.16 5 C 3907 2.51 5 N 1092 2.21 5 O 1156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6199 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5879 Classifications: {'peptide': 721} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 23, 'TRANS': 697} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 295 Classifications: {'DNA': 14} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 13} Chain breaks: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1, 'water': 19} Link IDs: {None: 19} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 4.21, per 1000 atoms: 0.68 Number of scatterers: 6199 At special positions: 0 Unit cell: (73.186, 92.759, 106.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 29 16.00 P 14 15.00 O 1156 8.00 N 1092 7.00 C 3907 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: 1.43 Conformation dependent library (CDL) restraints added in 799.5 milliseconds 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1378 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 7 sheets defined 38.4% alpha, 19.6% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 removed outlier: 3.854A pdb=" N LEU A 17 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 48 Processing helix chain 'A' and resid 84 through 108 removed outlier: 3.664A pdb=" N HIS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 257 through 268 Processing helix chain 'A' and resid 271 through 288 Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 325 through 332 Processing helix chain 'A' and resid 349 through 356 Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.922A pdb=" N ALA A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 400 removed outlier: 3.736A pdb=" N PHE A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 394 through 400' Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 409 removed outlier: 3.519A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 409' Processing helix chain 'A' and resid 422 through 428 Processing helix chain 'A' and resid 432 through 445 removed outlier: 3.797A pdb=" N GLY A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 467 Processing helix chain 'A' and resid 476 through 489 removed outlier: 3.845A pdb=" N CYS A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 507 removed outlier: 4.133A pdb=" N THR A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 585 Processing helix chain 'A' and resid 602 through 613 removed outlier: 4.147A pdb=" N VAL A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 693 through 695 No H-bonds generated for 'chain 'A' and resid 693 through 695' Processing helix chain 'A' and resid 706 through 721 removed outlier: 3.912A pdb=" N ALA A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 9 removed outlier: 6.810A pdb=" N VAL A 127 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLN A 122 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE A 129 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLN A 120 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU A 131 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 53 removed outlier: 3.926A pdb=" N GLU A 74 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 241 through 243 removed outlier: 4.116A pdb=" N VAL A 230 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN A 191 " --> pdb=" O HIS A 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.576A pdb=" N THR A 646 " --> pdb=" O CYS A 657 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 591 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL A 620 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE A 593 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE A 622 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG A 595 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 524 " --> pdb=" O HIS A 594 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ASP A 596 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE A 526 " --> pdb=" O ASP A 596 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET A 539 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 378 through 382 removed outlier: 6.583A pdb=" N GLY A 339 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N THR A 381 " --> pdb=" O GLY A 339 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 341 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N THR A 416 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS A 342 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU A 418 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER A 344 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N PHE A 420 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU A 346 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL A 417 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE A 452 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA A 419 " --> pdb=" O ILE A 452 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 248 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1714 1.33 - 1.45: 1150 1.45 - 1.57: 3407 1.57 - 1.69: 27 1.69 - 1.81: 50 Bond restraints: 6348 Sorted by residual: bond pdb=" P DT B 1 " pdb=" OP3 DT B 1 " ideal model delta sigma weight residual 1.480 1.600 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" C1' DT B 1 " pdb=" N1 DT B 1 " ideal model delta sigma weight residual 1.490 1.459 0.031 3.00e-02 1.11e+03 1.10e+00 bond pdb=" C3' G B 11 " pdb=" C2' G B 11 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.00e-02 2.50e+03 8.99e-01 bond pdb=" O4' G B 11 " pdb=" C1' G B 11 " ideal model delta sigma weight residual 1.414 1.397 0.017 2.00e-02 2.50e+03 7.63e-01 bond pdb=" C4' A B 17 " pdb=" O4' A B 17 " ideal model delta sigma weight residual 1.450 1.434 0.016 2.00e-02 2.50e+03 6.26e-01 ... (remaining 6343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 8480 1.73 - 3.46: 155 3.46 - 5.20: 13 5.20 - 6.93: 3 6.93 - 8.66: 3 Bond angle restraints: 8654 Sorted by residual: angle pdb=" OP2 DT B 1 " pdb=" P DT B 1 " pdb=" OP3 DT B 1 " ideal model delta sigma weight residual 109.47 118.13 -8.66 3.00e+00 1.11e-01 8.33e+00 angle pdb=" N ILE A 709 " pdb=" CA ILE A 709 " pdb=" C ILE A 709 " ideal model delta sigma weight residual 112.96 110.09 2.87 1.00e+00 1.00e+00 8.21e+00 angle pdb=" O5' DT B 1 " pdb=" P DT B 1 " pdb=" OP3 DT B 1 " ideal model delta sigma weight residual 109.47 101.27 8.20 3.00e+00 1.11e-01 7.47e+00 angle pdb=" C4 DT B 1 " pdb=" C5 DT B 1 " pdb=" C7 DT B 1 " ideal model delta sigma weight residual 122.40 118.89 3.51 1.50e+00 4.44e-01 5.49e+00 angle pdb=" OP1 DT B 1 " pdb=" P DT B 1 " pdb=" OP2 DT B 1 " ideal model delta sigma weight residual 120.00 113.16 6.84 3.00e+00 1.11e-01 5.20e+00 ... (remaining 8649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 3262 16.49 - 32.98: 356 32.98 - 49.47: 86 49.47 - 65.96: 30 65.96 - 82.44: 10 Dihedral angle restraints: 3744 sinusoidal: 1611 harmonic: 2133 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 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA GLY A 544 " pdb=" C GLY A 544 " pdb=" N SER A 545 " pdb=" CA SER A 545 " ideal model delta harmonic sigma weight residual 180.00 158.70 21.30 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA TYR A 242 " pdb=" C TYR A 242 " pdb=" N ALA A 243 " pdb=" CA ALA A 243 " ideal model delta harmonic sigma weight residual 180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 3741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 884 0.080 - 0.159: 80 0.159 - 0.239: 0 0.239 - 0.319: 0 0.319 - 0.399: 1 Chirality restraints: 965 Sorted by residual: chirality pdb=" P DT B 1 " pdb=" OP1 DT B 1 " pdb=" OP2 DT B 1 " pdb=" O5' DT B 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.74 -0.40 2.00e-01 2.50e+01 3.97e+00 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 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CG LEU A 734 " pdb=" CB LEU A 734 " pdb=" CD1 LEU A 734 " pdb=" CD2 LEU A 734 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 962 not shown) Planarity restraints: 1047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT B 1 " 0.020 2.00e-02 2.50e+03 9.11e-03 2.08e+00 pdb=" N1 DT B 1 " -0.015 2.00e-02 2.50e+03 pdb=" C2 DT B 1 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT B 1 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT B 1 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT B 1 " 0.000 2.00e-02 2.50e+03 pdb=" O4 DT B 1 " 0.011 2.00e-02 2.50e+03 pdb=" C5 DT B 1 " -0.005 2.00e-02 2.50e+03 pdb=" C7 DT B 1 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT B 1 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 510 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO A 511 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 734 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.51e+00 pdb=" C LEU A 734 " 0.021 2.00e-02 2.50e+03 pdb=" O LEU A 734 " -0.008 2.00e-02 2.50e+03 pdb=" N PRO A 735 " -0.007 2.00e-02 2.50e+03 ... (remaining 1044 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 14 2.35 - 2.99: 2948 2.99 - 3.63: 8869 3.63 - 4.26: 14177 4.26 - 4.90: 24028 Nonbonded interactions: 50036 Sorted by model distance: nonbonded pdb=" O VAL A 737 " pdb="MN MN A 801 " model vdw 1.715 2.320 nonbonded pdb=" OP1 A B 3 " pdb="MN MN A 801 " model vdw 1.857 2.320 nonbonded pdb=" C VAL A 737 " pdb="MN MN A 801 " model vdw 1.982 2.550 nonbonded pdb=" OXT VAL A 737 " pdb="MN MN A 801 " model vdw 2.066 2.320 nonbonded pdb=" OH TYR A 37 " pdb=" NH2 ARG A 41 " model vdw 2.230 3.120 ... (remaining 50031 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.230 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 0.003 0.120 6348 Z= 0.210 Angle : 0.572 8.661 8654 Z= 0.309 Chirality : 0.044 0.399 965 Planarity : 0.003 0.032 1047 Dihedral : 15.522 82.445 2366 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -0.01 (0.31), residues: 715 helix: 1.39 (0.33), residues: 248 sheet: 0.71 (0.46), residues: 123 loop : -1.39 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 282 HIS 0.006 0.001 HIS A 602 PHE 0.020 0.001 PHE A 351 TYR 0.019 0.001 TYR A 242 ARG 0.003 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 159 THR cc_start: 0.7198 (p) cc_final: 0.6996 (t) REVERT: A 322 ASP cc_start: 0.7756 (m-30) cc_final: 0.7534 (m-30) REVERT: A 439 GLN cc_start: 0.7565 (pt0) cc_final: 0.7033 (mt0) REVERT: A 600 ARG cc_start: 0.7349 (ptp-110) cc_final: 0.7135 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 1.3217 time to fit residues: 172.8523 Evaluate side-chains 87 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 18 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 259 GLN A 541 ASN A 571 ASN A 663 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.188572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.143196 restraints weight = 6397.118| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.27 r_work: 0.3331 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6348 Z= 0.185 Angle : 0.537 6.329 8654 Z= 0.297 Chirality : 0.043 0.146 965 Planarity : 0.004 0.034 1047 Dihedral : 12.358 74.751 943 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.03 % Allowed : 11.41 % Favored : 86.56 % 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: 0.09 (0.31), residues: 715 helix: 1.48 (0.34), residues: 254 sheet: 0.63 (0.42), residues: 160 loop : -1.55 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 282 HIS 0.006 0.001 HIS A 56 PHE 0.023 0.002 PHE A 401 TYR 0.017 0.001 TYR A 242 ARG 0.009 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.714 Fit side-chains REVERT: A 174 MET cc_start: 0.7018 (ttp) cc_final: 0.6473 (ptm) REVERT: A 183 GLN cc_start: 0.5857 (mm-40) cc_final: 0.5202 (mt0) REVERT: A 322 ASP cc_start: 0.7497 (m-30) cc_final: 0.7006 (m-30) REVERT: A 435 GLN cc_start: 0.7003 (pt0) cc_final: 0.6548 (mp10) REVERT: A 439 GLN cc_start: 0.7656 (pt0) cc_final: 0.6975 (mt0) REVERT: A 600 ARG cc_start: 0.7992 (ptp-110) cc_final: 0.7775 (ptp-170) outliers start: 13 outliers final: 5 residues processed: 107 average time/residue: 1.2388 time to fit residues: 139.2765 Evaluate side-chains 81 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 573 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 6 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 548 HIS A 571 ASN A 638 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.186970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.131304 restraints weight = 6460.155| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.16 r_work: 0.3283 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6348 Z= 0.305 Angle : 0.608 8.868 8654 Z= 0.330 Chirality : 0.046 0.155 965 Planarity : 0.004 0.038 1047 Dihedral : 12.457 73.814 943 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.28 % Allowed : 13.91 % Favored : 82.81 % 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: -0.07 (0.31), residues: 715 helix: 1.19 (0.33), residues: 257 sheet: 0.60 (0.42), residues: 155 loop : -1.51 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 282 HIS 0.005 0.001 HIS A 602 PHE 0.018 0.002 PHE A 401 TYR 0.024 0.002 TYR A 242 ARG 0.009 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.627 Fit side-chains REVERT: A 38 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6481 (p90) REVERT: A 61 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7980 (m-10) REVERT: A 159 THR cc_start: 0.7429 (m) cc_final: 0.7201 (m) REVERT: A 174 MET cc_start: 0.7042 (ttp) cc_final: 0.6371 (ptm) REVERT: A 183 GLN cc_start: 0.5915 (mm-40) cc_final: 0.5391 (mt0) REVERT: A 270 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8543 (mt) REVERT: A 322 ASP cc_start: 0.7467 (m-30) cc_final: 0.7030 (m-30) REVERT: A 414 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7500 (mp10) REVERT: A 435 GLN cc_start: 0.7208 (pt0) cc_final: 0.6835 (mp10) REVERT: A 600 ARG cc_start: 0.8011 (ptp-110) cc_final: 0.7787 (ptp-170) outliers start: 21 outliers final: 11 residues processed: 96 average time/residue: 1.1867 time to fit residues: 119.8120 Evaluate side-chains 93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 662 GLN Chi-restraints excluded: chain A residue 663 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 1 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.187417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.140881 restraints weight = 6531.242| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.58 r_work: 0.3303 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6348 Z= 0.253 Angle : 0.575 9.975 8654 Z= 0.313 Chirality : 0.044 0.153 965 Planarity : 0.004 0.037 1047 Dihedral : 12.511 74.910 943 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.06 % Allowed : 16.41 % Favored : 79.53 % 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: -0.13 (0.31), residues: 715 helix: 1.07 (0.33), residues: 257 sheet: 0.62 (0.42), residues: 155 loop : -1.51 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 282 HIS 0.003 0.001 HIS A 602 PHE 0.019 0.002 PHE A 401 TYR 0.020 0.002 TYR A 242 ARG 0.006 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.714 Fit side-chains REVERT: A 12 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: A 38 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6448 (p90) REVERT: A 183 GLN cc_start: 0.5882 (mm-40) cc_final: 0.5393 (mt0) REVERT: A 270 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8509 (mt) REVERT: A 322 ASP cc_start: 0.7443 (m-30) cc_final: 0.6953 (m-30) REVERT: A 414 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7464 (mp10) REVERT: A 435 GLN cc_start: 0.7290 (pt0) cc_final: 0.6863 (mp10) REVERT: A 509 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7511 (mt) REVERT: A 600 ARG cc_start: 0.8019 (ptp-110) cc_final: 0.7773 (ptp-170) outliers start: 26 outliers final: 12 residues processed: 94 average time/residue: 1.1990 time to fit residues: 118.5776 Evaluate side-chains 91 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 662 GLN Chi-restraints excluded: chain A residue 663 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 59 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 364 GLN A 571 ASN A 638 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.186242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.139109 restraints weight = 6525.678| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.77 r_work: 0.3245 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6348 Z= 0.290 Angle : 0.602 10.659 8654 Z= 0.326 Chirality : 0.045 0.151 965 Planarity : 0.004 0.039 1047 Dihedral : 12.583 74.432 943 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.38 % Allowed : 16.88 % Favored : 78.75 % 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: -0.22 (0.31), residues: 715 helix: 0.96 (0.33), residues: 257 sheet: 0.56 (0.42), residues: 155 loop : -1.52 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 282 HIS 0.003 0.001 HIS A 696 PHE 0.017 0.002 PHE A 401 TYR 0.022 0.002 TYR A 242 ARG 0.004 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.690 Fit side-chains REVERT: A 12 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: A 38 HIS cc_start: 0.7106 (OUTLIER) cc_final: 0.6432 (p90) REVERT: A 183 GLN cc_start: 0.5936 (mm-40) cc_final: 0.5478 (mt0) REVERT: A 270 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8507 (mt) REVERT: A 322 ASP cc_start: 0.7426 (m-30) cc_final: 0.7030 (m-30) REVERT: A 435 GLN cc_start: 0.7250 (pt0) cc_final: 0.6824 (mp10) REVERT: A 509 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7485 (mt) REVERT: A 600 ARG cc_start: 0.7965 (ptp-110) cc_final: 0.7702 (ptp-170) outliers start: 28 outliers final: 16 residues processed: 101 average time/residue: 1.1417 time to fit residues: 121.5070 Evaluate side-chains 99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 662 GLN Chi-restraints excluded: chain A residue 663 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 571 ASN A 701 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.186600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.130907 restraints weight = 6474.421| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.19 r_work: 0.3250 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6348 Z= 0.272 Angle : 0.595 11.994 8654 Z= 0.321 Chirality : 0.044 0.164 965 Planarity : 0.004 0.039 1047 Dihedral : 12.569 74.666 943 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.53 % Allowed : 18.59 % Favored : 76.88 % 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: -0.26 (0.30), residues: 715 helix: 1.11 (0.33), residues: 250 sheet: 0.50 (0.42), residues: 155 loop : -1.64 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 282 HIS 0.003 0.001 HIS A 696 PHE 0.019 0.002 PHE A 401 TYR 0.020 0.002 TYR A 242 ARG 0.008 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.608 Fit side-chains REVERT: A 12 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: A 38 HIS cc_start: 0.7161 (OUTLIER) cc_final: 0.6499 (p90) REVERT: A 183 GLN cc_start: 0.6006 (mm-40) cc_final: 0.5554 (mt0) REVERT: A 270 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8533 (mt) REVERT: A 322 ASP cc_start: 0.7457 (m-30) cc_final: 0.7021 (m-30) REVERT: A 435 GLN cc_start: 0.7363 (pt0) cc_final: 0.6885 (mp10) REVERT: A 509 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7499 (mt) REVERT: A 600 ARG cc_start: 0.8061 (ptp-110) cc_final: 0.7799 (ptp-170) REVERT: A 734 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.6943 (tt) outliers start: 29 outliers final: 16 residues processed: 104 average time/residue: 1.1643 time to fit residues: 127.3797 Evaluate side-chains 102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 662 GLN Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 571 ASN A 638 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.188126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.132339 restraints weight = 6533.469| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.23 r_work: 0.3280 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6348 Z= 0.214 Angle : 0.568 12.012 8654 Z= 0.306 Chirality : 0.043 0.149 965 Planarity : 0.003 0.038 1047 Dihedral : 12.524 75.687 943 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.22 % Allowed : 19.84 % Favored : 75.94 % 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: -0.15 (0.31), residues: 715 helix: 1.27 (0.33), residues: 250 sheet: 0.52 (0.42), residues: 155 loop : -1.62 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 282 HIS 0.002 0.001 HIS A 696 PHE 0.012 0.001 PHE A 86 TYR 0.017 0.001 TYR A 242 ARG 0.007 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.677 Fit side-chains REVERT: A 12 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: A 38 HIS cc_start: 0.7116 (OUTLIER) cc_final: 0.6449 (p90) REVERT: A 78 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7219 (mtm180) REVERT: A 183 GLN cc_start: 0.5980 (mm-40) cc_final: 0.5491 (mt0) REVERT: A 270 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8480 (mt) REVERT: A 435 GLN cc_start: 0.7362 (pt0) cc_final: 0.6879 (mp10) REVERT: A 600 ARG cc_start: 0.8023 (ptp-110) cc_final: 0.7790 (ptp-170) REVERT: A 734 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.6943 (tt) outliers start: 27 outliers final: 15 residues processed: 105 average time/residue: 1.1657 time to fit residues: 129.3717 Evaluate side-chains 102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 47 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 461 GLN A 571 ASN A 701 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.183556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129260 restraints weight = 6515.964| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.02 r_work: 0.3202 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 6348 Z= 0.518 Angle : 0.751 12.557 8654 Z= 0.400 Chirality : 0.051 0.209 965 Planarity : 0.005 0.042 1047 Dihedral : 12.834 75.581 943 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.00 % Allowed : 19.53 % Favored : 75.47 % 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: -0.60 (0.30), residues: 715 helix: 0.65 (0.32), residues: 255 sheet: 0.45 (0.42), residues: 151 loop : -1.76 (0.31), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 512 HIS 0.009 0.001 HIS A 590 PHE 0.025 0.003 PHE A 86 TYR 0.031 0.003 TYR A 242 ARG 0.006 0.001 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.693 Fit side-chains REVERT: A 12 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: A 38 HIS cc_start: 0.7352 (OUTLIER) cc_final: 0.6713 (p90) REVERT: A 183 GLN cc_start: 0.6292 (mm-40) cc_final: 0.5848 (mt0) REVERT: A 270 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8593 (mt) REVERT: A 414 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7553 (mp10) REVERT: A 600 ARG cc_start: 0.8106 (ptp-110) cc_final: 0.7862 (ptp-170) REVERT: A 734 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7025 (tt) outliers start: 32 outliers final: 17 residues processed: 103 average time/residue: 1.0844 time to fit residues: 118.1247 Evaluate side-chains 102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 662 GLN Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 259 GLN A 435 GLN A 571 ASN A 638 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.188505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.142563 restraints weight = 6576.387| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.62 r_work: 0.3310 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6348 Z= 0.185 Angle : 0.565 12.713 8654 Z= 0.305 Chirality : 0.043 0.153 965 Planarity : 0.004 0.054 1047 Dihedral : 12.607 75.692 943 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.44 % Allowed : 22.19 % Favored : 74.38 % 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: -0.23 (0.30), residues: 715 helix: 1.13 (0.33), residues: 252 sheet: 0.62 (0.42), residues: 151 loop : -1.67 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 282 HIS 0.002 0.001 HIS A 178 PHE 0.010 0.001 PHE A 86 TYR 0.017 0.001 TYR A 242 ARG 0.008 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.635 Fit side-chains REVERT: A 12 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: A 38 HIS cc_start: 0.7191 (OUTLIER) cc_final: 0.6539 (p90) REVERT: A 183 GLN cc_start: 0.6027 (mm-40) cc_final: 0.5511 (mt0) REVERT: A 270 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8446 (mt) REVERT: A 414 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7505 (mp10) REVERT: A 600 ARG cc_start: 0.8039 (ptp-110) cc_final: 0.7789 (ptp-170) REVERT: A 734 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6950 (tt) outliers start: 22 outliers final: 12 residues processed: 103 average time/residue: 1.1641 time to fit residues: 126.0806 Evaluate side-chains 102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 26 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 435 GLN A 571 ASN A 701 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.186910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.132328 restraints weight = 6568.162| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.03 r_work: 0.3267 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6348 Z= 0.264 Angle : 0.612 12.638 8654 Z= 0.327 Chirality : 0.044 0.171 965 Planarity : 0.004 0.053 1047 Dihedral : 12.647 75.269 943 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.44 % Allowed : 22.03 % Favored : 74.53 % 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: -0.30 (0.30), residues: 715 helix: 0.97 (0.32), residues: 256 sheet: 0.54 (0.42), residues: 151 loop : -1.63 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 282 HIS 0.003 0.001 HIS A 696 PHE 0.019 0.002 PHE A 401 TYR 0.020 0.002 TYR A 242 ARG 0.009 0.000 ARG A 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.624 Fit side-chains REVERT: A 12 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7626 (mp0) REVERT: A 38 HIS cc_start: 0.7191 (OUTLIER) cc_final: 0.6615 (p90) REVERT: A 183 GLN cc_start: 0.6115 (mm-40) cc_final: 0.5617 (mt0) REVERT: A 270 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8495 (mt) REVERT: A 322 ASP cc_start: 0.7742 (m-30) cc_final: 0.7404 (m-30) REVERT: A 414 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7247 (mp10) REVERT: A 509 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7482 (mt) REVERT: A 600 ARG cc_start: 0.8054 (ptp-110) cc_final: 0.7805 (ptp-170) REVERT: A 734 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.6915 (tt) outliers start: 22 outliers final: 12 residues processed: 99 average time/residue: 1.0921 time to fit residues: 114.1188 Evaluate side-chains 102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 72 optimal weight: 2.9990 chunk 3 optimal weight: 0.0000 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 571 ASN A 638 ASN A 701 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.188017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130870 restraints weight = 6602.587| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.27 r_work: 0.3289 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6348 Z= 0.220 Angle : 0.586 12.543 8654 Z= 0.313 Chirality : 0.043 0.158 965 Planarity : 0.004 0.049 1047 Dihedral : 12.597 76.080 943 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.75 % Allowed : 21.88 % Favored : 74.38 % 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: -0.23 (0.30), residues: 715 helix: 1.01 (0.33), residues: 257 sheet: 0.59 (0.42), residues: 151 loop : -1.58 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 282 HIS 0.003 0.001 HIS A 590 PHE 0.012 0.001 PHE A 86 TYR 0.017 0.001 TYR A 242 ARG 0.008 0.000 ARG A 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5393.15 seconds wall clock time: 95 minutes 50.79 seconds (5750.79 seconds total)