Starting phenix.real_space_refine on Fri Jan 17 14:07:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xk0_38412/01_2025/8xk0_38412.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xk0_38412/01_2025/8xk0_38412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xk0_38412/01_2025/8xk0_38412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xk0_38412/01_2025/8xk0_38412.map" model { file = "/net/cci-nas-00/data/ceres_data/8xk0_38412/01_2025/8xk0_38412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xk0_38412/01_2025/8xk0_38412.cif" } resolution = 2.96 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= -0.000 sd= 0.072 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 5720 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 2 7.51 5 P 32 5.49 5 S 29 5.16 5 C 3910 2.51 5 N 1116 2.21 5 O 1213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6302 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5621 Classifications: {'peptide': 692} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 668} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "C" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 298 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2, 'water': 17} Link IDs: {None: 18} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.44, per 1000 atoms: 0.70 Number of scatterers: 6302 At special positions: 0 Unit cell: (74.888, 91.057, 111.481, 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 2 24.99 S 29 16.00 P 32 15.00 O 1213 8.00 N 1116 7.00 C 3910 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: 1.58 Conformation dependent library (CDL) restraints added in 891.0 milliseconds 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1320 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 36.6% alpha, 19.9% beta 7 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 84 through 105 Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.748A pdb=" N GLU A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 271 through 290 removed outlier: 3.777A pdb=" N TRP A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN A 289 " --> pdb=" O GLN A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 332 Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.508A pdb=" N VAL A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 394 through 400 Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 412 removed outlier: 3.807A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Proline residue: A 410 - end of helix No H-bonds generated for 'chain 'A' and resid 406 through 412' Processing helix chain 'A' and resid 422 through 428 Processing helix chain 'A' and resid 432 through 442 Processing helix chain 'A' and resid 453 through 467 removed outlier: 3.916A pdb=" N ILE A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 477 removed outlier: 3.516A pdb=" N GLU A 477 " --> pdb=" O PRO A 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 474 through 477' Processing helix chain 'A' and resid 478 through 488 removed outlier: 3.841A pdb=" N ARG A 482 " --> pdb=" O GLN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 Processing helix chain 'A' and resid 565 through 583 removed outlier: 3.544A pdb=" N GLN A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 613 removed outlier: 3.920A 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 706 through 721 removed outlier: 3.839A pdb=" N ALA A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 715 " --> pdb=" O TYR A 711 " (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 13 removed outlier: 5.251A pdb=" N ILE A 144 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 127 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN A 122 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE A 129 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLN A 120 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 131 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 234 removed outlier: 3.653A pdb=" N ILE A 231 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR A 242 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.700A pdb=" N THR A 646 " --> pdb=" O CYS A 657 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A 591 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL A 620 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE A 593 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE A 622 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG A 595 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL A 528 " --> pdb=" O ASP A 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA8, first strand: chain 'A' and resid 378 through 382 removed outlier: 8.748A pdb=" N THR A 416 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS A 342 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU A 418 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER A 344 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N PHE A 420 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU A 346 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL A 417 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE A 452 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA A 419 " --> pdb=" O ILE A 452 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1568 1.33 - 1.45: 1391 1.45 - 1.57: 3414 1.57 - 1.69: 63 1.69 - 1.81: 51 Bond restraints: 6487 Sorted by residual: bond pdb=" P DT B 1 " pdb=" OP3 DT B 1 " ideal model delta sigma weight residual 1.480 1.592 -0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" O3' DT B 1 " pdb=" P DG B 2 " ideal model delta sigma weight residual 1.607 1.574 0.033 1.50e-02 4.44e+03 4.71e+00 bond pdb=" P DA B 17 " pdb=" OP2 DA B 17 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" P DT B 16 " pdb=" OP1 DT B 16 " ideal model delta sigma weight residual 1.480 1.515 -0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" P DA B 17 " pdb=" OP1 DA B 17 " ideal model delta sigma weight residual 1.480 1.515 -0.035 2.00e-02 2.50e+03 3.00e+00 ... (remaining 6482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 8663 1.54 - 3.08: 206 3.08 - 4.61: 29 4.61 - 6.15: 8 6.15 - 7.69: 5 Bond angle restraints: 8911 Sorted by residual: angle pdb=" N PRO A 474 " pdb=" CA PRO A 474 " pdb=" CB PRO A 474 " ideal model delta sigma weight residual 103.25 110.94 -7.69 1.05e+00 9.07e-01 5.37e+01 angle pdb=" N VAL A 542 " pdb=" CA VAL A 542 " pdb=" C VAL A 542 " ideal model delta sigma weight residual 109.34 103.16 6.18 2.08e+00 2.31e-01 8.84e+00 angle pdb=" C TYR A 473 " pdb=" N PRO A 474 " pdb=" CA PRO A 474 " ideal model delta sigma weight residual 119.84 123.27 -3.43 1.25e+00 6.40e-01 7.51e+00 angle pdb=" C GLN A 731 " pdb=" N THR A 732 " pdb=" CA THR A 732 " ideal model delta sigma weight residual 121.54 126.60 -5.06 1.91e+00 2.74e-01 7.01e+00 angle pdb=" C4 DT B 16 " pdb=" C5 DT B 16 " pdb=" C7 DT B 16 " ideal model delta sigma weight residual 122.40 118.49 3.91 1.50e+00 4.44e-01 6.79e+00 ... (remaining 8906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.50: 3625 32.50 - 65.00: 155 65.00 - 97.50: 11 97.50 - 130.00: 0 130.00 - 162.50: 1 Dihedral angle restraints: 3792 sinusoidal: 1750 harmonic: 2042 Sorted by residual: dihedral pdb=" C4' DT B 16 " pdb=" C3' DT B 16 " pdb=" O3' DT B 16 " pdb=" P DA B 17 " ideal model delta sinusoidal sigma weight residual 220.00 57.50 162.50 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" N PRO A 474 " pdb=" C PRO A 474 " pdb=" CA PRO A 474 " pdb=" CB PRO A 474 " ideal model delta harmonic sigma weight residual 115.10 123.91 -8.81 0 2.50e+00 1.60e-01 1.24e+01 dihedral pdb=" CA ASN A 541 " pdb=" C ASN A 541 " pdb=" N VAL A 542 " pdb=" CA VAL A 542 " ideal model delta harmonic sigma weight residual 180.00 164.29 15.71 0 5.00e+00 4.00e-02 9.88e+00 ... (remaining 3789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 977 0.116 - 0.232: 14 0.232 - 0.348: 1 0.348 - 0.465: 0 0.465 - 0.581: 2 Chirality restraints: 994 Sorted by residual: chirality pdb=" P DA B 17 " pdb=" OP1 DA B 17 " pdb=" OP2 DA B 17 " pdb=" O5' DA B 17 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.58 2.00e-01 2.50e+01 8.43e+00 chirality pdb=" P DT B 16 " pdb=" OP1 DT B 16 " pdb=" OP2 DT B 16 " pdb=" O5' DT B 16 " both_signs ideal model delta sigma weight residual True 2.35 -2.85 -0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA PRO A 474 " pdb=" N PRO A 474 " pdb=" C PRO A 474 " pdb=" CB PRO A 474 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 991 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 553 " -0.043 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO A 554 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 554 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 554 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 583 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.92e+00 pdb=" C GLN A 583 " -0.024 2.00e-02 2.50e+03 pdb=" O GLN A 583 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE A 584 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT B 1 " 0.017 2.00e-02 2.50e+03 8.52e-03 1.82e+00 pdb=" N1 DT B 1 " -0.018 2.00e-02 2.50e+03 pdb=" C2 DT B 1 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DT B 1 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DT B 1 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DT B 1 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT B 1 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DT B 1 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT B 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT B 1 " -0.003 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 43 2.60 - 3.17: 4972 3.17 - 3.75: 9288 3.75 - 4.32: 13839 4.32 - 4.90: 22613 Nonbonded interactions: 50755 Sorted by model distance: nonbonded pdb=" OP1 DT C 7 " pdb="MN MN A 802 " model vdw 2.023 2.320 nonbonded pdb=" OP1 DA B 3 " pdb="MN MN A 801 " model vdw 2.128 2.320 nonbonded pdb=" O GLN A 669 " pdb=" O HOH A 901 " model vdw 2.208 3.040 nonbonded pdb=" OP3 DT B 1 " pdb="MN MN A 801 " model vdw 2.238 2.320 nonbonded pdb=" OD1 ASP A 48 " pdb=" NH2 ARG A 105 " model vdw 2.273 3.120 ... (remaining 50750 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: 0.810 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: 20.740 Find NCS groups from input model: 0.070 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:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 0.112 6487 Z= 0.212 Angle : 0.595 7.691 8911 Z= 0.327 Chirality : 0.049 0.581 994 Planarity : 0.004 0.065 1020 Dihedral : 16.436 162.500 2472 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.27 % Favored : 93.44 % Rotamer: Outliers : 0.16 % Allowed : 0.00 % 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: -0.69 (0.32), residues: 686 helix: 0.65 (0.35), residues: 234 sheet: -0.11 (0.41), residues: 162 loop : -1.56 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 445 HIS 0.007 0.001 HIS A 465 PHE 0.019 0.001 PHE A 682 TYR 0.020 0.001 TYR A 719 ARG 0.002 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.629 Fit side-chains REVERT: A 108 HIS cc_start: 0.6966 (m-70) cc_final: 0.6764 (m90) outliers start: 1 outliers final: 1 residues processed: 104 average time/residue: 1.2211 time to fit residues: 133.7105 Evaluate side-chains 90 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN A 259 GLN A 465 HIS A 467 HIS A 701 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.157392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119886 restraints weight = 7255.897| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.92 r_work: 0.3125 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6487 Z= 0.338 Angle : 0.650 9.704 8911 Z= 0.352 Chirality : 0.045 0.165 994 Planarity : 0.004 0.042 1020 Dihedral : 15.861 148.618 1111 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.41 % Favored : 93.29 % Rotamer: Outliers : 1.48 % Allowed : 10.67 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.86 (0.32), residues: 686 helix: 0.51 (0.35), residues: 237 sheet: -0.16 (0.41), residues: 161 loop : -1.70 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 512 HIS 0.007 0.001 HIS A 320 PHE 0.024 0.002 PHE A 319 TYR 0.014 0.002 TYR A 130 ARG 0.008 0.001 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.698 Fit side-chains REVERT: A 108 HIS cc_start: 0.7630 (m-70) cc_final: 0.7394 (m90) REVERT: A 435 GLN cc_start: 0.8218 (tt0) cc_final: 0.7856 (tp-100) outliers start: 9 outliers final: 2 residues processed: 100 average time/residue: 1.0385 time to fit residues: 110.3316 Evaluate side-chains 85 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 128 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.157886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.120947 restraints weight = 7265.663| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.91 r_work: 0.3154 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6487 Z= 0.246 Angle : 0.591 8.315 8911 Z= 0.323 Chirality : 0.043 0.174 994 Planarity : 0.004 0.038 1020 Dihedral : 15.642 145.682 1109 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.98 % Favored : 93.73 % Rotamer: Outliers : 1.64 % Allowed : 13.79 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.32), residues: 686 helix: 0.62 (0.35), residues: 237 sheet: 0.26 (0.44), residues: 140 loop : -1.82 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 599 HIS 0.008 0.001 HIS A 320 PHE 0.023 0.002 PHE A 319 TYR 0.011 0.001 TYR A 130 ARG 0.005 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.7546 (m-70) cc_final: 0.7315 (m90) REVERT: A 435 GLN cc_start: 0.8225 (tt0) cc_final: 0.7841 (tp-100) outliers start: 10 outliers final: 3 residues processed: 94 average time/residue: 1.0390 time to fit residues: 103.8370 Evaluate side-chains 85 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 128 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 0.0570 chunk 11 optimal weight: 5.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS A 467 HIS A 552 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.157384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.119998 restraints weight = 7162.801| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.92 r_work: 0.3154 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 6487 Z= 0.457 Angle : 0.698 9.269 8911 Z= 0.379 Chirality : 0.048 0.169 994 Planarity : 0.004 0.042 1020 Dihedral : 16.057 145.919 1109 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.12 % Favored : 93.44 % Rotamer: Outliers : 2.46 % Allowed : 16.09 % Favored : 81.44 % 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: -1.02 (0.32), residues: 686 helix: 0.25 (0.34), residues: 239 sheet: 0.02 (0.41), residues: 161 loop : -1.88 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 512 HIS 0.008 0.001 HIS A 320 PHE 0.026 0.003 PHE A 319 TYR 0.016 0.002 TYR A 130 ARG 0.007 0.001 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.7788 (m-70) cc_final: 0.7584 (m90) REVERT: A 427 SER cc_start: 0.7848 (t) cc_final: 0.7529 (p) REVERT: A 428 ASN cc_start: 0.7259 (t0) cc_final: 0.6975 (t0) REVERT: A 435 GLN cc_start: 0.8343 (tt0) cc_final: 0.7908 (tp-100) REVERT: A 576 MET cc_start: 0.8362 (mmp) cc_final: 0.8037 (mmp) outliers start: 15 outliers final: 7 residues processed: 98 average time/residue: 0.9223 time to fit residues: 96.4269 Evaluate side-chains 90 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain A residue 737 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.160472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123545 restraints weight = 7114.304| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.93 r_work: 0.3189 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6487 Z= 0.266 Angle : 0.597 8.084 8911 Z= 0.326 Chirality : 0.044 0.171 994 Planarity : 0.004 0.041 1020 Dihedral : 15.695 144.401 1109 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.54 % Favored : 94.02 % Rotamer: Outliers : 2.46 % Allowed : 17.24 % Favored : 80.30 % 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: -0.76 (0.32), residues: 686 helix: 0.64 (0.35), residues: 234 sheet: 0.34 (0.44), residues: 145 loop : -1.87 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 599 HIS 0.008 0.001 HIS A 320 PHE 0.023 0.002 PHE A 319 TYR 0.011 0.001 TYR A 130 ARG 0.007 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 427 SER cc_start: 0.7739 (t) cc_final: 0.7413 (p) REVERT: A 435 GLN cc_start: 0.8290 (tt0) cc_final: 0.7872 (tp-100) outliers start: 15 outliers final: 9 residues processed: 99 average time/residue: 0.9219 time to fit residues: 97.3346 Evaluate side-chains 90 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 737 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 52 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.162359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.124016 restraints weight = 7066.998| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.99 r_work: 0.3210 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6487 Z= 0.235 Angle : 0.587 8.053 8911 Z= 0.322 Chirality : 0.043 0.168 994 Planarity : 0.004 0.041 1020 Dihedral : 15.614 143.302 1109 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.98 % Favored : 93.59 % Rotamer: Outliers : 2.63 % Allowed : 17.90 % Favored : 79.47 % 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: -0.65 (0.32), residues: 686 helix: 0.73 (0.35), residues: 234 sheet: 0.41 (0.44), residues: 145 loop : -1.82 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 599 HIS 0.008 0.001 HIS A 320 PHE 0.022 0.002 PHE A 319 TYR 0.011 0.001 TYR A 719 ARG 0.006 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.603 Fit side-chains REVERT: A 427 SER cc_start: 0.7752 (t) cc_final: 0.7385 (p) REVERT: A 435 GLN cc_start: 0.8260 (tt0) cc_final: 0.7847 (tp-100) REVERT: A 562 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6449 (mm-30) REVERT: A 576 MET cc_start: 0.8219 (mmp) cc_final: 0.7978 (mmp) outliers start: 16 outliers final: 7 residues processed: 93 average time/residue: 0.9908 time to fit residues: 97.9503 Evaluate side-chains 86 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 701 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.164628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.128852 restraints weight = 7123.086| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.62 r_work: 0.3282 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6487 Z= 0.186 Angle : 0.563 9.749 8911 Z= 0.305 Chirality : 0.042 0.170 994 Planarity : 0.003 0.039 1020 Dihedral : 15.396 140.858 1109 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.96 % Favored : 94.61 % Rotamer: Outliers : 2.96 % Allowed : 17.90 % Favored : 79.15 % 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: -0.51 (0.32), residues: 686 helix: 0.91 (0.35), residues: 234 sheet: 0.32 (0.43), residues: 146 loop : -1.70 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 445 HIS 0.008 0.001 HIS A 320 PHE 0.020 0.001 PHE A 319 TYR 0.012 0.001 TYR A 719 ARG 0.007 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 427 SER cc_start: 0.7702 (t) cc_final: 0.7348 (p) REVERT: A 435 GLN cc_start: 0.8152 (tt0) cc_final: 0.7799 (tp-100) outliers start: 18 outliers final: 9 residues processed: 98 average time/residue: 0.9979 time to fit residues: 104.1478 Evaluate side-chains 94 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 572 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 0.0170 chunk 44 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS A 701 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.164925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.127969 restraints weight = 7110.758| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.71 r_work: 0.3272 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6487 Z= 0.189 Angle : 0.573 10.685 8911 Z= 0.308 Chirality : 0.042 0.162 994 Planarity : 0.003 0.038 1020 Dihedral : 15.347 138.897 1109 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.39 % Favored : 94.17 % Rotamer: Outliers : 2.30 % Allowed : 19.87 % Favored : 77.83 % 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: -0.48 (0.32), residues: 686 helix: 0.92 (0.35), residues: 234 sheet: 0.37 (0.43), residues: 146 loop : -1.70 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 445 HIS 0.008 0.001 HIS A 320 PHE 0.019 0.001 PHE A 319 TYR 0.013 0.001 TYR A 719 ARG 0.007 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 253 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.8863 (m-80) REVERT: A 427 SER cc_start: 0.7640 (t) cc_final: 0.7349 (p) REVERT: A 435 GLN cc_start: 0.8111 (tt0) cc_final: 0.7789 (tp-100) outliers start: 14 outliers final: 7 residues processed: 98 average time/residue: 0.9862 time to fit residues: 102.7597 Evaluate side-chains 94 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 549 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.162104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125259 restraints weight = 7133.439| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.72 r_work: 0.3250 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6487 Z= 0.289 Angle : 0.624 9.960 8911 Z= 0.334 Chirality : 0.044 0.168 994 Planarity : 0.004 0.062 1020 Dihedral : 15.590 138.796 1109 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.83 % Favored : 93.73 % Rotamer: Outliers : 1.81 % Allowed : 20.03 % Favored : 78.16 % 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: -0.70 (0.32), residues: 686 helix: 0.69 (0.35), residues: 239 sheet: 0.43 (0.44), residues: 140 loop : -1.88 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 512 HIS 0.008 0.001 HIS A 320 PHE 0.022 0.002 PHE A 319 TYR 0.016 0.001 TYR A 719 ARG 0.016 0.001 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 427 SER cc_start: 0.7705 (t) cc_final: 0.7386 (p) REVERT: A 435 GLN cc_start: 0.8100 (tt0) cc_final: 0.7765 (tp-100) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 1.0357 time to fit residues: 98.9346 Evaluate side-chains 90 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 549 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.164345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.127047 restraints weight = 7175.472| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.74 r_work: 0.3259 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6487 Z= 0.203 Angle : 0.593 10.125 8911 Z= 0.317 Chirality : 0.043 0.178 994 Planarity : 0.004 0.039 1020 Dihedral : 15.386 137.246 1109 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.39 % Favored : 94.17 % Rotamer: Outliers : 1.64 % Allowed : 20.20 % Favored : 78.16 % 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: -0.59 (0.32), residues: 686 helix: 0.80 (0.35), residues: 236 sheet: 0.50 (0.44), residues: 140 loop : -1.81 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 599 HIS 0.008 0.001 HIS A 320 PHE 0.020 0.001 PHE A 319 TYR 0.015 0.001 TYR A 719 ARG 0.008 0.000 ARG A 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 427 SER cc_start: 0.7759 (t) cc_final: 0.7384 (p) REVERT: A 435 GLN cc_start: 0.8033 (tt0) cc_final: 0.7732 (tp-100) outliers start: 10 outliers final: 8 residues processed: 91 average time/residue: 1.0072 time to fit residues: 97.2932 Evaluate side-chains 93 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 549 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 chunk 65 optimal weight: 5.9990 chunk 28 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.163608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.125800 restraints weight = 7320.853| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.78 r_work: 0.3242 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6487 Z= 0.228 Angle : 0.596 9.952 8911 Z= 0.319 Chirality : 0.043 0.193 994 Planarity : 0.004 0.040 1020 Dihedral : 15.413 136.240 1109 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.83 % Favored : 93.73 % Rotamer: Outliers : 1.64 % Allowed : 20.36 % Favored : 78.00 % 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: -0.60 (0.32), residues: 686 helix: 0.76 (0.35), residues: 236 sheet: 0.51 (0.44), residues: 140 loop : -1.81 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 512 HIS 0.008 0.001 HIS A 320 PHE 0.021 0.002 PHE A 319 TYR 0.016 0.001 TYR A 719 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: 4520.00 seconds wall clock time: 80 minutes 31.83 seconds (4831.83 seconds total)