Starting phenix.real_space_refine on Tue Jul 29 02:18:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xhv_38355/07_2025/8xhv_38355.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xhv_38355/07_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_38355/07_2025/8xhv_38355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xhv_38355/07_2025/8xhv_38355.map" model { file = "/net/cci-nas-00/data/ceres_data/8xhv_38355/07_2025/8xhv_38355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xhv_38355/07_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 4.80, per 1000 atoms: 0.77 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: 1.57 Conformation dependent library (CDL) restraints added in 889.7 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: 3.03 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: 2.87 Time building geometry restraints manager: 1.76 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: 65.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.220 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: 0.000 Load rotamer database and sin/cos tables:21.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.830 ------------------------------------------------------------------------------- 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= 0.148 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 Details of bonding type rmsd hydrogen bonds : bond 0.12985 ( 248) hydrogen bonds : angle 6.64448 ( 705) covalent geometry : bond 0.00318 ( 6348) covalent geometry : angle 0.57249 ( 8654) *********************** 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 : 0.689 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: 1.2494 time to fit residues: 163.6330 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 : 0.662 ------------------------------------------------------------------------------- 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 = 0.188571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.143195 restraints weight = 6397.136| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.27 r_work: 0.3329 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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= 0.127 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 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 248) hydrogen bonds : angle 4.99650 ( 705) covalent geometry : bond 0.00284 ( 6348) covalent geometry : angle 0.53691 ( 8654) *********************** 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 : 0.614 Fit side-chains REVERT: A 174 MET cc_start: 0.6998 (ttp) cc_final: 0.6446 (ptm) REVERT: A 183 GLN cc_start: 0.5846 (mm-40) cc_final: 0.5192 (mt0) REVERT: A 322 ASP cc_start: 0.7497 (m-30) cc_final: 0.7008 (m-30) REVERT: A 435 GLN cc_start: 0.6952 (pt0) cc_final: 0.6492 (mp10) REVERT: A 439 GLN cc_start: 0.7619 (pt0) cc_final: 0.6935 (mt0) REVERT: A 600 ARG cc_start: 0.7987 (ptp-110) cc_final: 0.7771 (ptp-170) outliers start: 13 outliers final: 5 residues processed: 107 average time/residue: 1.1524 time to fit residues: 129.6675 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 : 0.615 ------------------------------------------------------------------------------- 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: 10.0000 chunk 69 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.187529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.140721 restraints weight = 6463.125| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.82 r_work: 0.3278 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2178 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= 0.184 Angle : 0.595 8.943 8654 Z= 0.324 Chirality : 0.045 0.154 965 Planarity : 0.004 0.037 1047 Dihedral : 12.436 74.016 943 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.28 % Allowed : 14.06 % Favored : 82.66 % 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: 1.34 (0.34), residues: 252 sheet: 0.60 (0.42), residues: 155 loop : -1.51 (0.32), residues: 308 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 0.023 0.002 TYR A 242 ARG 0.010 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.04981 ( 248) hydrogen bonds : angle 4.95344 ( 705) covalent geometry : bond 0.00436 ( 6348) covalent geometry : angle 0.59526 ( 8654) *********************** 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 107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.606 Fit side-chains REVERT: A 38 HIS cc_start: 0.7130 (OUTLIER) cc_final: 0.6504 (p90) REVERT: A 159 THR cc_start: 0.7405 (m) cc_final: 0.7177 (m) REVERT: A 174 MET cc_start: 0.7007 (ttp) cc_final: 0.6340 (ptm) REVERT: A 183 GLN cc_start: 0.5871 (mm-40) cc_final: 0.5340 (mt0) REVERT: A 270 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8520 (mt) REVERT: A 322 ASP cc_start: 0.7461 (m-30) cc_final: 0.7001 (m-30) REVERT: A 435 GLN cc_start: 0.7214 (pt0) cc_final: 0.6814 (mp10) REVERT: A 600 ARG cc_start: 0.8011 (ptp-110) cc_final: 0.7792 (ptp-170) outliers start: 21 outliers final: 11 residues processed: 97 average time/residue: 1.1846 time to fit residues: 121.2166 Evaluate side-chains 91 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 43 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.187771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141461 restraints weight = 6527.098| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.58 r_work: 0.3307 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6348 Z= 0.159 Angle : 0.567 9.820 8654 Z= 0.309 Chirality : 0.044 0.153 965 Planarity : 0.004 0.036 1047 Dihedral : 12.483 74.997 943 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.44 % Allowed : 16.41 % Favored : 80.16 % 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 (0.31), residues: 715 helix: 1.12 (0.33), residues: 257 sheet: 0.64 (0.42), residues: 155 loop : -1.49 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 282 HIS 0.004 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 Details of bonding type rmsd hydrogen bonds : bond 0.04413 ( 248) hydrogen bonds : angle 4.77005 ( 705) covalent geometry : bond 0.00373 ( 6348) covalent geometry : angle 0.56685 ( 8654) *********************** 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 102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.519 Fit side-chains REVERT: A 12 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: A 38 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6432 (p90) REVERT: A 174 MET cc_start: 0.7105 (ttp) cc_final: 0.6439 (ptm) REVERT: A 183 GLN cc_start: 0.5874 (mm-40) cc_final: 0.5385 (mt0) REVERT: A 270 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8484 (mt) REVERT: A 322 ASP cc_start: 0.7426 (m-30) cc_final: 0.6945 (m-30) REVERT: A 414 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7485 (mp10) REVERT: A 435 GLN cc_start: 0.7283 (pt0) cc_final: 0.6859 (mp10) REVERT: A 509 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7499 (mt) REVERT: A 600 ARG cc_start: 0.8014 (ptp-110) cc_final: 0.7767 (ptp-170) outliers start: 22 outliers final: 10 residues processed: 93 average time/residue: 1.1306 time to fit residues: 110.7892 Evaluate side-chains 90 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 55 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.188782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.133290 restraints weight = 6520.274| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.17 r_work: 0.3300 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6348 Z= 0.131 Angle : 0.541 10.386 8654 Z= 0.295 Chirality : 0.043 0.147 965 Planarity : 0.003 0.036 1047 Dihedral : 12.496 75.613 943 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.59 % Allowed : 17.34 % Favored : 79.06 % 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: -0.04 (0.31), residues: 715 helix: 1.20 (0.33), residues: 253 sheet: 0.66 (0.42), residues: 155 loop : -1.48 (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 602 PHE 0.019 0.001 PHE A 401 TYR 0.017 0.001 TYR A 242 ARG 0.005 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 248) hydrogen bonds : angle 4.63005 ( 705) covalent geometry : bond 0.00300 ( 6348) covalent geometry : angle 0.54053 ( 8654) *********************** 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 109 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.601 Fit side-chains REVERT: A 12 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: A 38 HIS cc_start: 0.7075 (OUTLIER) cc_final: 0.6315 (p90) REVERT: A 183 GLN cc_start: 0.5873 (mm-40) cc_final: 0.5389 (mt0) REVERT: A 270 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8434 (mt) REVERT: A 322 ASP cc_start: 0.7313 (m-30) cc_final: 0.6870 (m-30) REVERT: A 414 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: A 435 GLN cc_start: 0.7265 (pt0) cc_final: 0.6794 (mp10) REVERT: A 600 ARG cc_start: 0.7998 (ptp-110) cc_final: 0.7756 (ptp-170) REVERT: A 734 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6868 (tt) outliers start: 23 outliers final: 14 residues processed: 100 average time/residue: 1.0377 time to fit residues: 109.5789 Evaluate side-chains 100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 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 635 SER Chi-restraints excluded: chain A residue 663 GLN Chi-restraints excluded: chain A residue 734 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.0030 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 40 optimal weight: 0.4980 chunk 3 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.188685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133043 restraints weight = 6479.747| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.23 r_work: 0.3309 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6348 Z= 0.136 Angle : 0.548 11.064 8654 Z= 0.297 Chirality : 0.043 0.147 965 Planarity : 0.003 0.035 1047 Dihedral : 12.501 75.791 943 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.38 % Allowed : 17.97 % Favored : 77.66 % 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: 1.36 (0.33), residues: 246 sheet: 0.60 (0.42), residues: 155 loop : -1.58 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 282 HIS 0.002 0.001 HIS A 696 PHE 0.018 0.001 PHE A 401 TYR 0.016 0.001 TYR A 242 ARG 0.007 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 248) hydrogen bonds : angle 4.58531 ( 705) covalent geometry : bond 0.00313 ( 6348) covalent geometry : angle 0.54771 ( 8654) *********************** 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: 28 poor density : 86 time to evaluate : 0.683 Fit side-chains REVERT: A 12 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: A 38 HIS cc_start: 0.7055 (OUTLIER) cc_final: 0.6343 (p90) REVERT: A 73 MET cc_start: 0.6909 (mpt) cc_final: 0.6519 (OUTLIER) REVERT: A 183 GLN cc_start: 0.5907 (mm-40) cc_final: 0.5433 (mt0) REVERT: A 270 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8458 (mt) REVERT: A 414 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7433 (mp10) REVERT: A 435 GLN cc_start: 0.7291 (pt0) cc_final: 0.6842 (mp10) REVERT: A 600 ARG cc_start: 0.8036 (ptp-110) cc_final: 0.7797 (ptp-170) REVERT: A 734 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.6969 (tt) outliers start: 28 outliers final: 17 residues processed: 105 average time/residue: 1.1054 time to fit residues: 122.2417 Evaluate side-chains 101 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 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 507 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 28 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 60 optimal weight: 0.0980 chunk 53 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.189027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.133366 restraints weight = 6531.901| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.19 r_work: 0.3308 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2795 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= 0.131 Angle : 0.545 11.602 8654 Z= 0.295 Chirality : 0.042 0.146 965 Planarity : 0.003 0.035 1047 Dihedral : 12.508 76.057 943 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.22 % Allowed : 19.69 % Favored : 76.09 % 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: -0.04 (0.31), residues: 715 helix: 1.40 (0.33), residues: 245 sheet: 0.60 (0.42), residues: 155 loop : -1.57 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 282 HIS 0.003 0.001 HIS A 590 PHE 0.012 0.001 PHE A 86 TYR 0.016 0.001 TYR A 242 ARG 0.007 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 248) hydrogen bonds : angle 4.55267 ( 705) covalent geometry : bond 0.00301 ( 6348) covalent geometry : angle 0.54542 ( 8654) *********************** 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 112 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.667 Fit side-chains REVERT: A 12 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: A 38 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6319 (p90) REVERT: A 73 MET cc_start: 0.6918 (mpt) cc_final: 0.6559 (OUTLIER) REVERT: A 183 GLN cc_start: 0.5887 (mm-40) cc_final: 0.5426 (mt0) REVERT: A 270 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8395 (mt) REVERT: A 414 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7377 (mp10) REVERT: A 435 GLN cc_start: 0.7289 (pt0) cc_final: 0.6827 (mp10) REVERT: A 509 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7451 (mt) REVERT: A 600 ARG cc_start: 0.8020 (ptp-110) cc_final: 0.7771 (ptp-170) REVERT: A 734 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.6975 (tt) outliers start: 27 outliers final: 18 residues processed: 103 average time/residue: 1.0712 time to fit residues: 116.4259 Evaluate side-chains 105 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 78 ARG Chi-restraints excluded: chain A residue 134 GLU 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 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 423 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 507 SER 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 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: 7.9990 chunk 10 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 638 ASN A 701 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.184856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.130220 restraints weight = 6513.152| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.01 r_work: 0.3240 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 6348 Z= 0.260 Angle : 0.690 12.188 8654 Z= 0.367 Chirality : 0.048 0.190 965 Planarity : 0.004 0.038 1047 Dihedral : 12.677 75.041 943 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.69 % Allowed : 19.06 % Favored : 76.25 % 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: -0.35 (0.30), residues: 715 helix: 0.87 (0.32), residues: 256 sheet: 0.57 (0.42), residues: 151 loop : -1.63 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 512 HIS 0.007 0.001 HIS A 590 PHE 0.022 0.003 PHE A 86 TYR 0.026 0.002 TYR A 242 ARG 0.006 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.05704 ( 248) hydrogen bonds : angle 4.91782 ( 705) covalent geometry : bond 0.00624 ( 6348) covalent geometry : angle 0.69016 ( 8654) *********************** 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 115 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.615 Fit side-chains REVERT: A 12 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: A 38 HIS cc_start: 0.7301 (OUTLIER) cc_final: 0.6673 (p90) REVERT: A 183 GLN cc_start: 0.6212 (mm-40) cc_final: 0.5800 (mt0) REVERT: A 270 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8595 (mt) REVERT: A 322 ASP cc_start: 0.7619 (m-30) cc_final: 0.7231 (m-30) REVERT: A 435 GLN cc_start: 0.7455 (pt0) cc_final: 0.6992 (mp10) REVERT: A 509 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7593 (mt) REVERT: A 600 ARG cc_start: 0.8086 (ptp-110) cc_final: 0.7855 (ptp-170) REVERT: A 734 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.6998 (tt) outliers start: 30 outliers final: 15 residues processed: 105 average time/residue: 1.0943 time to fit residues: 121.3580 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 : 0.604 ------------------------------------------------------------------------------- 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 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 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 507 SER Chi-restraints excluded: chain A residue 509 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 40 optimal weight: 0.0670 chunk 58 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.190026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.144361 restraints weight = 6553.752| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.38 r_work: 0.3333 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2939 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= 0.118 Angle : 0.552 12.420 8654 Z= 0.297 Chirality : 0.042 0.170 965 Planarity : 0.004 0.051 1047 Dihedral : 12.523 76.367 943 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.91 % Allowed : 21.25 % Favored : 74.84 % 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: -0.10 (0.31), residues: 715 helix: 1.23 (0.33), residues: 252 sheet: 0.56 (0.42), residues: 155 loop : -1.55 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 282 HIS 0.004 0.001 HIS A 590 PHE 0.011 0.001 PHE A 86 TYR 0.014 0.001 TYR A 242 ARG 0.008 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 248) hydrogen bonds : angle 4.58685 ( 705) covalent geometry : bond 0.00264 ( 6348) covalent geometry : angle 0.55240 ( 8654) *********************** 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 114 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.666 Fit side-chains REVERT: A 12 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: A 38 HIS cc_start: 0.7112 (OUTLIER) cc_final: 0.6434 (p90) REVERT: A 73 MET cc_start: 0.6806 (mpt) cc_final: 0.6418 (OUTLIER) REVERT: A 183 GLN cc_start: 0.6018 (mm-40) cc_final: 0.5523 (mt0) REVERT: A 322 ASP cc_start: 0.7465 (m-30) cc_final: 0.6985 (m-30) REVERT: A 414 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7452 (mp10) REVERT: A 435 GLN cc_start: 0.7323 (pt0) cc_final: 0.6856 (mp10) REVERT: A 509 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7480 (mt) REVERT: A 600 ARG cc_start: 0.8020 (ptp-110) cc_final: 0.7782 (ptp-170) REVERT: A 734 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7044 (tt) outliers start: 25 outliers final: 14 residues processed: 105 average time/residue: 1.0436 time to fit residues: 115.8904 Evaluate side-chains 103 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 233 VAL 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 507 SER 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 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: 2.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 638 ASN A 701 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.185012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128766 restraints weight = 6555.706| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.28 r_work: 0.3229 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 6348 Z= 0.264 Angle : 0.700 12.752 8654 Z= 0.372 Chirality : 0.049 0.196 965 Planarity : 0.005 0.052 1047 Dihedral : 12.707 75.284 943 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.44 % Allowed : 21.56 % Favored : 75.00 % 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: -0.43 (0.30), residues: 715 helix: 0.80 (0.32), residues: 256 sheet: 0.52 (0.42), residues: 151 loop : -1.67 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 512 HIS 0.007 0.001 HIS A 590 PHE 0.021 0.003 PHE A 86 TYR 0.024 0.002 TYR A 242 ARG 0.008 0.001 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.05617 ( 248) hydrogen bonds : angle 4.90766 ( 705) covalent geometry : bond 0.00638 ( 6348) covalent geometry : angle 0.70022 ( 8654) ********************** 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 108 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.640 Fit side-chains REVERT: A 12 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: A 38 HIS cc_start: 0.7323 (OUTLIER) cc_final: 0.6688 (p90) REVERT: A 183 GLN cc_start: 0.6224 (mm-40) cc_final: 0.5762 (mt0) REVERT: A 322 ASP cc_start: 0.7679 (m-30) cc_final: 0.7246 (m-30) REVERT: A 414 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7532 (mp10) REVERT: A 435 GLN cc_start: 0.7396 (pt0) cc_final: 0.6903 (mp10) REVERT: A 509 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7641 (mt) REVERT: A 600 ARG cc_start: 0.8080 (ptp-110) cc_final: 0.7844 (ptp-170) REVERT: A 734 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.6974 (tt) outliers start: 22 outliers final: 13 residues processed: 99 average time/residue: 1.1164 time to fit residues: 116.5226 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 : 0.614 ------------------------------------------------------------------------------- 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 233 VAL 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 507 SER 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 642 THR 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 72 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.188873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.134444 restraints weight = 6569.792| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.10 r_work: 0.3314 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6348 Z= 0.132 Angle : 0.577 12.713 8654 Z= 0.308 Chirality : 0.043 0.152 965 Planarity : 0.004 0.047 1047 Dihedral : 12.564 75.885 943 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.12 % Allowed : 22.19 % Favored : 74.69 % 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: -0.18 (0.30), residues: 715 helix: 1.14 (0.33), residues: 252 sheet: 0.65 (0.42), residues: 151 loop : -1.61 (0.31), residues: 312 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 0.014 0.001 PHE A 86 TYR 0.016 0.001 TYR A 242 ARG 0.009 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 248) hydrogen bonds : angle 4.62439 ( 705) covalent geometry : bond 0.00303 ( 6348) covalent geometry : angle 0.57736 ( 8654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5772.02 seconds wall clock time: 99 minutes 12.84 seconds (5952.84 seconds total)