Starting phenix.real_space_refine on Tue Feb 3 16:00:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n4k_48883/02_2026/9n4k_48883_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n4k_48883/02_2026/9n4k_48883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n4k_48883/02_2026/9n4k_48883_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n4k_48883/02_2026/9n4k_48883_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n4k_48883/02_2026/9n4k_48883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n4k_48883/02_2026/9n4k_48883.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 2834 2.51 5 N 774 2.21 5 O 906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4578 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 772 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "B" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 822 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 97} Chain: "C" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 603 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: F, E, D, H Time building chain proxies: 1.02, per 1000 atoms: 0.22 Number of scatterers: 4578 At special positions: 0 Unit cell: (119.138, 76.349, 69.637, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 906 8.00 N 774 7.00 C 2834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 59 " distance=2.03 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 412 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 510 " distance=2.03 Simple disulfide: pdb=" SG CYS B 445 " - pdb=" SG CYS B 512 " distance=2.03 Simple disulfide: pdb=" N PRO E 470 " - pdb=" CD PRO E 470 " distance=1.47 Simple disulfide: pdb=" SG CYS F 29 " - pdb=" SG CYS F 59 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 103 " distance=2.03 Simple disulfide: pdb=" SG CYS F 90 " - pdb=" SG CYS F 102 " distance=2.03 Simple disulfide: pdb=" SG CYS F 104 " - pdb=" SG CYS F 109 " distance=2.03 Simple disulfide: pdb=" SG CYS E 412 " - pdb=" SG CYS E 478 " distance=2.03 Simple disulfide: pdb=" SG CYS E 441 " - pdb=" SG CYS E 510 " distance=2.03 Simple disulfide: pdb=" SG CYS E 445 " - pdb=" SG CYS E 512 " distance=2.03 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 Links applied BETA1-4 " NAG B 601 " - " NAG B 602 " " NAG B 602 " - " BMA B 603 " " NAG E 601 " - " NAG E 602 " " NAG E 602 " - " BMA E 603 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " NAG-ASN " NAG A 201 " - " ASN A 42 " " NAG B 601 " - " ASN B 454 " " NAG E 601 " - " ASN E 454 " " NAG F 201 " - " ASN F 42 " " NAG G 1 " - " ASN A 65 " " NAG H 1 " - " ASN F 65 " Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 153.3 milliseconds 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1036 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 14 sheets defined 10.5% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 456 through 469 Processing helix chain 'E' and resid 456 through 469 Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 73 through 82 Processing helix chain 'D' and resid 59 through 63 Processing helix chain 'D' and resid 73 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 33 removed outlier: 5.383A pdb=" N LEU A 72 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ARG A 64 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 413 through 414 removed outlier: 3.514A pdb=" N ASP B 442 " --> pdb=" O ARG B 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 419 through 420 Processing sheet with id=AA5, first strand: chain 'B' and resid 430 through 432 removed outlier: 6.029A pdb=" N ILE B 430 " --> pdb=" O PHE B 491 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE B 491 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ARG B 508 " --> pdb=" O PRO B 480 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS B 482 " --> pdb=" O VAL B 506 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 506 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASN B 484 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 413 through 414 removed outlier: 3.514A pdb=" N ASP E 442 " --> pdb=" O ARG E 413 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 419 through 420 Processing sheet with id=AA8, first strand: chain 'E' and resid 430 through 432 removed outlier: 6.029A pdb=" N ILE E 430 " --> pdb=" O PHE E 491 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE E 491 " --> pdb=" O ILE E 430 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N ARG E 508 " --> pdb=" O PRO E 480 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS E 482 " --> pdb=" O VAL E 506 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL E 506 " --> pdb=" O LYS E 482 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASN E 484 " --> pdb=" O ASN E 504 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 28 through 30 Processing sheet with id=AB1, first strand: chain 'F' and resid 32 through 33 removed outlier: 5.383A pdb=" N LEU F 72 " --> pdb=" O ARG F 64 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ARG F 64 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AB3, first strand: chain 'C' and resid 66 through 71 Processing sheet with id=AB4, first strand: chain 'D' and resid 33 through 35 Processing sheet with id=AB5, first strand: chain 'D' and resid 66 through 71 120 hydrogen bonds defined for protein. 294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.58 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1485 1.35 - 1.47: 1203 1.47 - 1.59: 1923 1.59 - 1.72: 0 1.72 - 1.84: 74 Bond restraints: 4685 Sorted by residual: bond pdb=" CB VAL B 473 " pdb=" CG1 VAL B 473 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.15e+00 bond pdb=" CB VAL E 473 " pdb=" CG1 VAL E 473 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.15e+00 bond pdb=" CB CYS D 48 " pdb=" SG CYS D 48 " ideal model delta sigma weight residual 1.808 1.842 -0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" CB CYS C 48 " pdb=" SG CYS C 48 " ideal model delta sigma weight residual 1.808 1.842 -0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" CG PRO E 480 " pdb=" CD PRO E 480 " ideal model delta sigma weight residual 1.503 1.473 0.030 3.40e-02 8.65e+02 7.69e-01 ... (remaining 4680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 6121 1.94 - 3.89: 209 3.89 - 5.83: 16 5.83 - 7.77: 0 7.77 - 9.71: 2 Bond angle restraints: 6348 Sorted by residual: angle pdb=" CA LEU B 464 " pdb=" CB LEU B 464 " pdb=" CG LEU B 464 " ideal model delta sigma weight residual 116.30 106.59 9.71 3.50e+00 8.16e-02 7.70e+00 angle pdb=" CA LEU E 464 " pdb=" CB LEU E 464 " pdb=" CG LEU E 464 " ideal model delta sigma weight residual 116.30 106.61 9.69 3.50e+00 8.16e-02 7.66e+00 angle pdb=" C ASN E 469 " pdb=" CA ASN E 469 " pdb=" CB ASN E 469 " ideal model delta sigma weight residual 110.17 115.03 -4.86 1.97e+00 2.58e-01 6.09e+00 angle pdb=" C ASN B 469 " pdb=" CA ASN B 469 " pdb=" CB ASN B 469 " ideal model delta sigma weight residual 110.17 114.99 -4.82 1.97e+00 2.58e-01 5.98e+00 angle pdb=" CG1 VAL B 473 " pdb=" CB VAL B 473 " pdb=" CG2 VAL B 473 " ideal model delta sigma weight residual 110.80 105.49 5.31 2.20e+00 2.07e-01 5.82e+00 ... (remaining 6343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 2726 17.20 - 34.40: 237 34.40 - 51.60: 42 51.60 - 68.80: 4 68.80 - 86.00: 2 Dihedral angle restraints: 3011 sinusoidal: 1401 harmonic: 1610 Sorted by residual: dihedral pdb=" CB PRO E 470 " pdb=" N PRO E 470 " pdb=" CD PRO E 470 " pdb=" CB PRO E 470 " ideal model delta sinusoidal sigma weight residual -86.00 0.00 -86.00 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CA PHE E 447 " pdb=" C PHE E 447 " pdb=" N PRO E 448 " pdb=" CA PRO E 448 " ideal model delta harmonic sigma weight residual 0.00 -29.48 29.48 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA PHE B 447 " pdb=" C PHE B 447 " pdb=" N PRO B 448 " pdb=" CA PRO B 448 " ideal model delta harmonic sigma weight residual 0.00 -29.43 29.43 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 3008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 421 0.035 - 0.070: 182 0.070 - 0.105: 61 0.105 - 0.140: 21 0.140 - 0.175: 13 Chirality restraints: 698 Sorted by residual: chirality pdb=" CA LYS E 475 " pdb=" N LYS E 475 " pdb=" C LYS E 475 " pdb=" CB LYS E 475 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CB VAL E 465 " pdb=" CA VAL E 465 " pdb=" CG1 VAL E 465 " pdb=" CG2 VAL E 465 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CA LYS B 475 " pdb=" N LYS B 475 " pdb=" C LYS B 475 " pdb=" CB LYS B 475 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 695 not shown) Planarity restraints: 824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 447 " -0.022 2.00e-02 2.50e+03 4.41e-02 3.41e+01 pdb=" CG PHE E 447 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE E 447 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE E 447 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE E 447 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 PHE E 447 " 0.042 2.00e-02 2.50e+03 pdb=" CZ PHE E 447 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 447 " 0.022 2.00e-02 2.50e+03 4.40e-02 3.39e+01 pdb=" CG PHE B 447 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE B 447 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 447 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 447 " -0.059 2.00e-02 2.50e+03 pdb=" CE2 PHE B 447 " -0.042 2.00e-02 2.50e+03 pdb=" CZ PHE B 447 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 470 " -0.025 2.00e-02 2.50e+03 5.01e-02 2.51e+01 pdb=" C PRO E 470 " 0.087 2.00e-02 2.50e+03 pdb=" O PRO E 470 " -0.032 2.00e-02 2.50e+03 pdb=" N GLU E 471 " -0.030 2.00e-02 2.50e+03 ... (remaining 821 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 16 2.60 - 3.18: 3769 3.18 - 3.75: 6742 3.75 - 4.33: 9285 4.33 - 4.90: 15083 Nonbonded interactions: 34895 Sorted by model distance: nonbonded pdb=" SG CYS C 35 " pdb=" SG CYS C 53 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS D 35 " pdb=" SG CYS D 53 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS C 94 " pdb=" SG CYS C 99 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS D 94 " pdb=" SG CYS D 99 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS D 81 " pdb=" SG CYS D 93 " model vdw 2.029 3.760 ... (remaining 34890 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.090 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.009 0.559 4716 Z= 0.431 Angle : 0.959 33.834 6424 Z= 0.496 Chirality : 0.050 0.175 698 Planarity : 0.007 0.059 818 Dihedral : 11.857 59.087 1924 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.34), residues: 540 helix: -0.88 (0.68), residues: 58 sheet: -2.54 (0.37), residues: 174 loop : -2.21 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 503 TYR 0.054 0.004 TYR B 472 PHE 0.087 0.004 PHE E 447 TRP 0.035 0.004 TRP E 429 HIS 0.028 0.004 HIS B 466 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4685) covalent geometry : angle 0.75872 ( 6348) SS BOND : bond 0.13558 ( 17) SS BOND : angle 7.91400 ( 34) hydrogen bonds : bond 0.12113 ( 120) hydrogen bonds : angle 7.50094 ( 294) link_BETA1-4 : bond 0.00466 ( 8) link_BETA1-4 : angle 1.32005 ( 24) link_NAG-ASN : bond 0.00305 ( 6) link_NAG-ASN : angle 2.12953 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.9030 (p) cc_final: 0.8749 (p) REVERT: B 446 SER cc_start: 0.8173 (p) cc_final: 0.7972 (m) REVERT: B 493 ASP cc_start: 0.8238 (p0) cc_final: 0.7990 (p0) REVERT: E 446 SER cc_start: 0.8333 (p) cc_final: 0.8045 (m) REVERT: F 54 ASP cc_start: 0.7890 (t0) cc_final: 0.7574 (t0) REVERT: C 60 ASN cc_start: 0.8382 (t0) cc_final: 0.7866 (t0) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.0876 time to fit residues: 22.6039 Evaluate side-chains 136 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.0000 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.0970 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 95 GLN ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.065361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.052719 restraints weight = 18607.036| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.95 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.195 4716 Z= 0.185 Angle : 0.977 41.212 6424 Z= 0.485 Chirality : 0.044 0.167 698 Planarity : 0.005 0.037 818 Dihedral : 5.214 38.527 882 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.51 % Allowed : 14.75 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.33), residues: 540 helix: -0.18 (0.67), residues: 60 sheet: -1.97 (0.38), residues: 150 loop : -1.79 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 40 TYR 0.018 0.001 TYR B 436 PHE 0.020 0.002 PHE B 447 TRP 0.021 0.002 TRP A 36 HIS 0.004 0.001 HIS E 458 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 4685) covalent geometry : angle 0.71325 ( 6348) SS BOND : bond 0.02579 ( 17) SS BOND : angle 9.04561 ( 34) hydrogen bonds : bond 0.04041 ( 120) hydrogen bonds : angle 6.06642 ( 294) link_BETA1-4 : bond 0.00387 ( 8) link_BETA1-4 : angle 1.36519 ( 24) link_NAG-ASN : bond 0.00180 ( 6) link_NAG-ASN : angle 1.96674 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8741 (t0) cc_final: 0.8495 (t0) REVERT: B 446 SER cc_start: 0.8743 (p) cc_final: 0.8277 (m) REVERT: E 436 TYR cc_start: 0.8634 (p90) cc_final: 0.8346 (p90) REVERT: E 444 GLU cc_start: 0.8731 (pt0) cc_final: 0.8380 (pm20) REVERT: E 453 MET cc_start: 0.8478 (mmm) cc_final: 0.8057 (mtt) REVERT: F 81 ASP cc_start: 0.9058 (t0) cc_final: 0.8732 (t0) REVERT: C 47 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.8026 (t70) REVERT: C 60 ASN cc_start: 0.8663 (t0) cc_final: 0.8182 (t0) REVERT: C 63 PHE cc_start: 0.8955 (m-80) cc_final: 0.8620 (m-10) REVERT: C 67 GLN cc_start: 0.6607 (tm-30) cc_final: 0.6393 (tm-30) REVERT: C 71 PHE cc_start: 0.7240 (m-80) cc_final: 0.7005 (m-10) REVERT: C 92 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7268 (mt-10) REVERT: D 60 ASN cc_start: 0.8922 (t0) cc_final: 0.8630 (t0) REVERT: D 63 PHE cc_start: 0.8522 (m-10) cc_final: 0.8195 (m-10) REVERT: D 67 GLN cc_start: 0.6931 (tm-30) cc_final: 0.6294 (tm-30) REVERT: D 71 PHE cc_start: 0.7916 (m-80) cc_final: 0.7662 (m-10) REVERT: D 92 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7410 (mt-10) outliers start: 22 outliers final: 13 residues processed: 163 average time/residue: 0.0856 time to fit residues: 17.1946 Evaluate side-chains 142 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 107 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 27 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 HIS E 415 HIS ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 HIS ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN D 100 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.062718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.050221 restraints weight = 19151.885| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 4.93 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 4716 Z= 0.196 Angle : 0.917 41.402 6424 Z= 0.454 Chirality : 0.042 0.155 698 Planarity : 0.004 0.039 818 Dihedral : 5.179 38.639 882 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.51 % Allowed : 15.78 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.34), residues: 540 helix: 0.08 (0.71), residues: 60 sheet: -2.07 (0.36), residues: 164 loop : -1.54 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 503 TYR 0.020 0.002 TYR B 472 PHE 0.013 0.002 PHE B 447 TRP 0.017 0.001 TRP A 36 HIS 0.005 0.001 HIS D 47 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 4685) covalent geometry : angle 0.63275 ( 6348) SS BOND : bond 0.02660 ( 17) SS BOND : angle 8.98503 ( 34) hydrogen bonds : bond 0.03604 ( 120) hydrogen bonds : angle 5.71580 ( 294) link_BETA1-4 : bond 0.00347 ( 8) link_BETA1-4 : angle 1.43047 ( 24) link_NAG-ASN : bond 0.00182 ( 6) link_NAG-ASN : angle 1.95460 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.9294 (t) cc_final: 0.9066 (m) REVERT: A 81 ASP cc_start: 0.9088 (t0) cc_final: 0.8717 (t0) REVERT: B 444 GLU cc_start: 0.8620 (pt0) cc_final: 0.8290 (pm20) REVERT: B 446 SER cc_start: 0.8857 (p) cc_final: 0.8502 (m) REVERT: B 472 TYR cc_start: 0.8934 (m-80) cc_final: 0.8720 (m-80) REVERT: E 444 GLU cc_start: 0.8703 (pt0) cc_final: 0.8296 (pm20) REVERT: E 453 MET cc_start: 0.8507 (mmm) cc_final: 0.8174 (mtt) REVERT: F 31 TYR cc_start: 0.9470 (t80) cc_final: 0.9172 (t80) REVERT: F 54 ASP cc_start: 0.8777 (t0) cc_final: 0.8382 (t0) REVERT: F 55 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8759 (mmmt) REVERT: F 81 ASP cc_start: 0.9222 (t0) cc_final: 0.8771 (t0) REVERT: F 93 THR cc_start: 0.9363 (OUTLIER) cc_final: 0.9034 (t) REVERT: C 60 ASN cc_start: 0.8778 (t0) cc_final: 0.8269 (t0) REVERT: C 63 PHE cc_start: 0.9015 (m-80) cc_final: 0.8578 (m-10) REVERT: C 92 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7555 (mt-10) REVERT: D 48 CYS cc_start: 0.7065 (t) cc_final: 0.6289 (t) REVERT: D 60 ASN cc_start: 0.8771 (t0) cc_final: 0.8547 (t0) REVERT: D 61 ASP cc_start: 0.8522 (p0) cc_final: 0.8291 (p0) REVERT: D 67 GLN cc_start: 0.7099 (tm-30) cc_final: 0.6536 (tm-30) REVERT: D 92 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7587 (mt-10) outliers start: 22 outliers final: 16 residues processed: 152 average time/residue: 0.0779 time to fit residues: 14.8552 Evaluate side-chains 138 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 85 TYR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 107 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 HIS ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 100 ASN D 47 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.060880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.048311 restraints weight = 18935.707| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 4.88 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.193 4716 Z= 0.230 Angle : 0.940 41.468 6424 Z= 0.462 Chirality : 0.042 0.164 698 Planarity : 0.004 0.030 818 Dihedral : 5.350 39.313 882 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.30 % Allowed : 17.42 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.35), residues: 540 helix: 0.33 (0.74), residues: 60 sheet: -2.15 (0.35), residues: 170 loop : -1.36 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 503 TYR 0.020 0.002 TYR C 66 PHE 0.011 0.002 PHE F 82 TRP 0.007 0.001 TRP F 78 HIS 0.004 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 4685) covalent geometry : angle 0.65735 ( 6348) SS BOND : bond 0.02725 ( 17) SS BOND : angle 9.07675 ( 34) hydrogen bonds : bond 0.03605 ( 120) hydrogen bonds : angle 5.71248 ( 294) link_BETA1-4 : bond 0.00355 ( 8) link_BETA1-4 : angle 1.48197 ( 24) link_NAG-ASN : bond 0.00326 ( 6) link_NAG-ASN : angle 2.07362 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9201 (t0) cc_final: 0.8731 (t0) REVERT: B 444 GLU cc_start: 0.8614 (pt0) cc_final: 0.8228 (pm20) REVERT: B 446 SER cc_start: 0.8915 (p) cc_final: 0.8584 (m) REVERT: E 444 GLU cc_start: 0.8727 (pt0) cc_final: 0.8296 (pm20) REVERT: E 453 MET cc_start: 0.8479 (mmm) cc_final: 0.8252 (mtt) REVERT: F 53 GLN cc_start: 0.9165 (tm-30) cc_final: 0.8737 (tm-30) REVERT: F 54 ASP cc_start: 0.8854 (t0) cc_final: 0.8369 (t0) REVERT: F 55 LYS cc_start: 0.9107 (mmmt) cc_final: 0.8271 (mmmt) REVERT: F 81 ASP cc_start: 0.9297 (t0) cc_final: 0.8819 (t0) REVERT: F 93 THR cc_start: 0.9389 (OUTLIER) cc_final: 0.9076 (t) REVERT: C 60 ASN cc_start: 0.8777 (t0) cc_final: 0.8255 (t0) REVERT: C 63 PHE cc_start: 0.9003 (m-80) cc_final: 0.8571 (m-10) REVERT: C 78 LYS cc_start: 0.9323 (tppp) cc_final: 0.9025 (ttmt) REVERT: C 92 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7541 (mt-10) REVERT: D 48 CYS cc_start: 0.7407 (t) cc_final: 0.6729 (t) REVERT: D 60 ASN cc_start: 0.8979 (t0) cc_final: 0.8618 (t0) REVERT: D 67 GLN cc_start: 0.7110 (tm-30) cc_final: 0.6661 (tm-30) REVERT: D 92 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7488 (mt-10) outliers start: 21 outliers final: 17 residues processed: 142 average time/residue: 0.0776 time to fit residues: 13.8688 Evaluate side-chains 136 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 85 TYR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 57 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.061242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.048484 restraints weight = 19141.908| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 4.96 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.195 4716 Z= 0.187 Angle : 0.913 41.512 6424 Z= 0.450 Chirality : 0.042 0.160 698 Planarity : 0.004 0.030 818 Dihedral : 5.320 38.456 882 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.71 % Allowed : 18.65 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.36), residues: 540 helix: 0.33 (0.73), residues: 60 sheet: -2.12 (0.35), residues: 170 loop : -1.19 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 503 TYR 0.021 0.002 TYR B 472 PHE 0.014 0.002 PHE C 71 TRP 0.007 0.001 TRP F 78 HIS 0.003 0.001 HIS B 458 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 4685) covalent geometry : angle 0.62547 ( 6348) SS BOND : bond 0.02683 ( 17) SS BOND : angle 8.99835 ( 34) hydrogen bonds : bond 0.03333 ( 120) hydrogen bonds : angle 5.52349 ( 294) link_BETA1-4 : bond 0.00319 ( 8) link_BETA1-4 : angle 1.38509 ( 24) link_NAG-ASN : bond 0.00152 ( 6) link_NAG-ASN : angle 1.97882 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9239 (t0) cc_final: 0.8736 (t0) REVERT: B 444 GLU cc_start: 0.8616 (pt0) cc_final: 0.8200 (pm20) REVERT: B 446 SER cc_start: 0.8934 (p) cc_final: 0.8630 (m) REVERT: B 472 TYR cc_start: 0.8855 (m-80) cc_final: 0.8637 (m-80) REVERT: E 444 GLU cc_start: 0.8658 (pt0) cc_final: 0.8228 (pm20) REVERT: F 54 ASP cc_start: 0.8957 (t0) cc_final: 0.8717 (t0) REVERT: F 81 ASP cc_start: 0.9329 (t0) cc_final: 0.8835 (t0) REVERT: F 93 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9079 (t) REVERT: C 48 CYS cc_start: 0.6687 (OUTLIER) cc_final: 0.6071 (t) REVERT: C 60 ASN cc_start: 0.8772 (t0) cc_final: 0.8233 (t0) REVERT: C 63 PHE cc_start: 0.9004 (m-80) cc_final: 0.8564 (m-10) REVERT: C 92 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7924 (mt-10) REVERT: D 48 CYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6839 (t) REVERT: D 67 GLN cc_start: 0.7062 (tm-30) cc_final: 0.6669 (tm-30) REVERT: D 92 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7618 (mt-10) outliers start: 23 outliers final: 15 residues processed: 140 average time/residue: 0.0719 time to fit residues: 12.8323 Evaluate side-chains 134 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 469 ASN Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 85 TYR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 57 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 0.0050 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 106 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.062149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.049636 restraints weight = 19223.673| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 4.92 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.197 4716 Z= 0.164 Angle : 0.901 41.568 6424 Z= 0.445 Chirality : 0.042 0.157 698 Planarity : 0.003 0.029 818 Dihedral : 5.220 37.630 882 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.07 % Allowed : 21.11 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.36), residues: 540 helix: 0.35 (0.74), residues: 60 sheet: -1.89 (0.38), residues: 154 loop : -1.27 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 503 TYR 0.013 0.001 TYR A 32 PHE 0.016 0.001 PHE F 82 TRP 0.006 0.001 TRP F 78 HIS 0.005 0.001 HIS D 47 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 4685) covalent geometry : angle 0.61008 ( 6348) SS BOND : bond 0.02654 ( 17) SS BOND : angle 8.98514 ( 34) hydrogen bonds : bond 0.03168 ( 120) hydrogen bonds : angle 5.39372 ( 294) link_BETA1-4 : bond 0.00373 ( 8) link_BETA1-4 : angle 1.34562 ( 24) link_NAG-ASN : bond 0.00044 ( 6) link_NAG-ASN : angle 1.91234 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9219 (t0) cc_final: 0.8720 (t0) REVERT: A 98 GLN cc_start: 0.8658 (tp40) cc_final: 0.8384 (tp-100) REVERT: B 444 GLU cc_start: 0.8613 (pt0) cc_final: 0.8216 (pm20) REVERT: B 446 SER cc_start: 0.8958 (p) cc_final: 0.8616 (m) REVERT: B 488 VAL cc_start: 0.9727 (t) cc_final: 0.9332 (p) REVERT: E 444 GLU cc_start: 0.8723 (pt0) cc_final: 0.8207 (pm20) REVERT: F 46 LEU cc_start: 0.9151 (mp) cc_final: 0.8943 (mp) REVERT: F 54 ASP cc_start: 0.8923 (t0) cc_final: 0.8688 (t0) REVERT: F 81 ASP cc_start: 0.9318 (t0) cc_final: 0.8806 (t0) REVERT: F 93 THR cc_start: 0.9393 (p) cc_final: 0.9095 (t) REVERT: C 48 CYS cc_start: 0.6797 (OUTLIER) cc_final: 0.6232 (t) REVERT: C 60 ASN cc_start: 0.8768 (t0) cc_final: 0.8225 (t0) REVERT: C 63 PHE cc_start: 0.8988 (m-80) cc_final: 0.8531 (m-10) REVERT: C 92 GLU cc_start: 0.8503 (mt-10) cc_final: 0.7955 (mt-10) REVERT: D 48 CYS cc_start: 0.7581 (OUTLIER) cc_final: 0.6877 (t) REVERT: D 63 PHE cc_start: 0.8768 (m-80) cc_final: 0.8502 (m-80) REVERT: D 92 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7685 (mt-10) outliers start: 15 outliers final: 12 residues processed: 136 average time/residue: 0.0795 time to fit residues: 13.5819 Evaluate side-chains 132 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 85 TYR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 57 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 0.0010 chunk 48 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 7 optimal weight: 0.0570 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.4304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN D 72 GLN D 106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.062005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.049484 restraints weight = 18840.367| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 4.89 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.198 4716 Z= 0.157 Angle : 0.900 41.588 6424 Z= 0.445 Chirality : 0.042 0.163 698 Planarity : 0.003 0.029 818 Dihedral : 5.140 37.467 882 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.69 % Allowed : 20.90 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.36), residues: 540 helix: 0.19 (0.72), residues: 60 sheet: -1.78 (0.38), residues: 154 loop : -1.20 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 503 TYR 0.016 0.001 TYR B 472 PHE 0.016 0.001 PHE A 82 TRP 0.006 0.001 TRP F 78 HIS 0.002 0.001 HIS E 458 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 4685) covalent geometry : angle 0.61003 ( 6348) SS BOND : bond 0.02642 ( 17) SS BOND : angle 8.97756 ( 34) hydrogen bonds : bond 0.03045 ( 120) hydrogen bonds : angle 5.34866 ( 294) link_BETA1-4 : bond 0.00378 ( 8) link_BETA1-4 : angle 1.32851 ( 24) link_NAG-ASN : bond 0.00064 ( 6) link_NAG-ASN : angle 1.86930 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9253 (t0) cc_final: 0.8795 (t0) REVERT: A 98 GLN cc_start: 0.8679 (tp40) cc_final: 0.8391 (tp-100) REVERT: B 444 GLU cc_start: 0.8581 (pt0) cc_final: 0.8216 (pm20) REVERT: B 446 SER cc_start: 0.8941 (p) cc_final: 0.8597 (m) REVERT: B 488 VAL cc_start: 0.9724 (t) cc_final: 0.9331 (p) REVERT: E 444 GLU cc_start: 0.8654 (pt0) cc_final: 0.8141 (pm20) REVERT: F 46 LEU cc_start: 0.9150 (mp) cc_final: 0.8938 (mp) REVERT: F 55 LYS cc_start: 0.9105 (mmmt) cc_final: 0.8880 (mtmt) REVERT: F 81 ASP cc_start: 0.9335 (t0) cc_final: 0.8819 (t0) REVERT: F 93 THR cc_start: 0.9385 (p) cc_final: 0.9091 (t) REVERT: C 48 CYS cc_start: 0.6663 (OUTLIER) cc_final: 0.6064 (t) REVERT: C 60 ASN cc_start: 0.8749 (t0) cc_final: 0.8239 (t0) REVERT: C 63 PHE cc_start: 0.8991 (m-80) cc_final: 0.8531 (m-10) REVERT: C 78 LYS cc_start: 0.9363 (tppp) cc_final: 0.9163 (tppp) REVERT: D 48 CYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6794 (t) REVERT: D 63 PHE cc_start: 0.8842 (m-80) cc_final: 0.8617 (m-80) REVERT: D 67 GLN cc_start: 0.7205 (tm-30) cc_final: 0.6836 (tm-30) REVERT: D 92 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7496 (mt-10) outliers start: 18 outliers final: 12 residues processed: 140 average time/residue: 0.0758 time to fit residues: 13.4779 Evaluate side-chains 135 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 85 TYR Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 57 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 106 GLN D 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.060664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.048097 restraints weight = 19586.687| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 4.96 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 4716 Z= 0.220 Angle : 0.945 41.577 6424 Z= 0.473 Chirality : 0.043 0.177 698 Planarity : 0.004 0.033 818 Dihedral : 5.334 40.351 882 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.10 % Allowed : 22.34 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.36), residues: 540 helix: 0.35 (0.73), residues: 58 sheet: -1.84 (0.36), residues: 174 loop : -1.00 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 503 TYR 0.017 0.002 TYR B 436 PHE 0.020 0.002 PHE F 82 TRP 0.007 0.001 TRP F 36 HIS 0.004 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 4685) covalent geometry : angle 0.67295 ( 6348) SS BOND : bond 0.02718 ( 17) SS BOND : angle 8.97184 ( 34) hydrogen bonds : bond 0.03121 ( 120) hydrogen bonds : angle 5.63530 ( 294) link_BETA1-4 : bond 0.00343 ( 8) link_BETA1-4 : angle 1.50928 ( 24) link_NAG-ASN : bond 0.00371 ( 6) link_NAG-ASN : angle 2.01571 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9303 (t0) cc_final: 0.8838 (t0) REVERT: A 93 THR cc_start: 0.9640 (OUTLIER) cc_final: 0.9350 (t) REVERT: A 98 GLN cc_start: 0.8738 (tp40) cc_final: 0.8471 (tp-100) REVERT: B 444 GLU cc_start: 0.8590 (pt0) cc_final: 0.8176 (pm20) REVERT: B 446 SER cc_start: 0.8913 (p) cc_final: 0.8603 (m) REVERT: B 453 MET cc_start: 0.8571 (mmm) cc_final: 0.8217 (mtt) REVERT: B 488 VAL cc_start: 0.9744 (t) cc_final: 0.9371 (p) REVERT: E 444 GLU cc_start: 0.8622 (pt0) cc_final: 0.8097 (pm20) REVERT: F 46 LEU cc_start: 0.9204 (mp) cc_final: 0.8974 (mp) REVERT: F 81 ASP cc_start: 0.9345 (t0) cc_final: 0.8816 (t0) REVERT: F 93 THR cc_start: 0.9428 (p) cc_final: 0.9144 (t) REVERT: C 45 GLU cc_start: 0.8916 (tp30) cc_final: 0.7954 (tm-30) REVERT: C 48 CYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6911 (t) REVERT: C 60 ASN cc_start: 0.8801 (t0) cc_final: 0.8333 (t0) REVERT: C 63 PHE cc_start: 0.8982 (m-80) cc_final: 0.8514 (m-10) REVERT: C 92 GLU cc_start: 0.8486 (mt-10) cc_final: 0.7731 (mt-10) REVERT: D 48 CYS cc_start: 0.7621 (OUTLIER) cc_final: 0.6895 (t) REVERT: D 63 PHE cc_start: 0.8874 (m-80) cc_final: 0.8638 (m-80) REVERT: D 92 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7531 (mt-10) outliers start: 20 outliers final: 15 residues processed: 132 average time/residue: 0.0745 time to fit residues: 12.5345 Evaluate side-chains 133 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 469 ASN Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 85 TYR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 57 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 106 GLN D 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.061381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.048994 restraints weight = 18867.639| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.91 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 4716 Z= 0.178 Angle : 0.935 41.543 6424 Z= 0.466 Chirality : 0.042 0.164 698 Planarity : 0.003 0.031 818 Dihedral : 5.292 38.837 882 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.28 % Allowed : 23.16 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.36), residues: 540 helix: 0.33 (0.74), residues: 58 sheet: -1.75 (0.36), residues: 174 loop : -0.97 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 503 TYR 0.016 0.001 TYR B 436 PHE 0.019 0.002 PHE A 82 TRP 0.006 0.001 TRP D 98 HIS 0.003 0.001 HIS B 458 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 4685) covalent geometry : angle 0.66130 ( 6348) SS BOND : bond 0.02737 ( 17) SS BOND : angle 8.96249 ( 34) hydrogen bonds : bond 0.03020 ( 120) hydrogen bonds : angle 5.48583 ( 294) link_BETA1-4 : bond 0.00349 ( 8) link_BETA1-4 : angle 1.34171 ( 24) link_NAG-ASN : bond 0.00052 ( 6) link_NAG-ASN : angle 1.90240 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9277 (t0) cc_final: 0.8801 (t0) REVERT: A 98 GLN cc_start: 0.8738 (tp40) cc_final: 0.8472 (tp-100) REVERT: B 444 GLU cc_start: 0.8572 (pt0) cc_final: 0.8160 (pm20) REVERT: B 446 SER cc_start: 0.8989 (p) cc_final: 0.8682 (m) REVERT: B 488 VAL cc_start: 0.9750 (t) cc_final: 0.9400 (p) REVERT: E 444 GLU cc_start: 0.8560 (pt0) cc_final: 0.8063 (pm20) REVERT: F 46 LEU cc_start: 0.9169 (mp) cc_final: 0.8944 (mp) REVERT: F 81 ASP cc_start: 0.9348 (t0) cc_final: 0.8824 (t0) REVERT: F 93 THR cc_start: 0.9432 (p) cc_final: 0.9193 (t) REVERT: C 45 GLU cc_start: 0.8854 (tp30) cc_final: 0.7894 (tm-30) REVERT: C 48 CYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6782 (t) REVERT: C 60 ASN cc_start: 0.8789 (t0) cc_final: 0.8324 (t0) REVERT: C 63 PHE cc_start: 0.8983 (m-80) cc_final: 0.8521 (m-10) REVERT: C 92 GLU cc_start: 0.8497 (mt-10) cc_final: 0.7703 (mt-10) REVERT: D 48 CYS cc_start: 0.7638 (OUTLIER) cc_final: 0.6915 (t) REVERT: D 63 PHE cc_start: 0.8841 (m-80) cc_final: 0.8603 (m-80) REVERT: D 92 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7574 (mt-10) outliers start: 16 outliers final: 14 residues processed: 133 average time/residue: 0.0721 time to fit residues: 12.3160 Evaluate side-chains 135 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 469 ASN Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 85 TYR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 40 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 0.0060 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.061008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.048630 restraints weight = 18878.754| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 4.81 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 4716 Z= 0.174 Angle : 0.940 41.630 6424 Z= 0.470 Chirality : 0.042 0.172 698 Planarity : 0.003 0.031 818 Dihedral : 5.266 38.590 882 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.07 % Allowed : 23.36 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.36), residues: 540 helix: 0.19 (0.72), residues: 58 sheet: -1.73 (0.36), residues: 174 loop : -0.93 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 503 TYR 0.017 0.002 TYR B 436 PHE 0.024 0.002 PHE D 71 TRP 0.007 0.001 TRP F 78 HIS 0.002 0.001 HIS E 458 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 4685) covalent geometry : angle 0.66756 ( 6348) SS BOND : bond 0.02704 ( 17) SS BOND : angle 8.96552 ( 34) hydrogen bonds : bond 0.03085 ( 120) hydrogen bonds : angle 5.47612 ( 294) link_BETA1-4 : bond 0.00360 ( 8) link_BETA1-4 : angle 1.36347 ( 24) link_NAG-ASN : bond 0.00060 ( 6) link_NAG-ASN : angle 1.88964 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9283 (t0) cc_final: 0.8812 (t0) REVERT: A 98 GLN cc_start: 0.8735 (tp40) cc_final: 0.8474 (tp-100) REVERT: B 444 GLU cc_start: 0.8572 (pt0) cc_final: 0.8320 (pm20) REVERT: B 446 SER cc_start: 0.8969 (p) cc_final: 0.8696 (m) REVERT: B 453 MET cc_start: 0.8467 (mmm) cc_final: 0.8143 (mtt) REVERT: B 488 VAL cc_start: 0.9775 (t) cc_final: 0.9431 (p) REVERT: B 505 MET cc_start: 0.9462 (mmm) cc_final: 0.9239 (mmm) REVERT: F 81 ASP cc_start: 0.9332 (t0) cc_final: 0.8811 (t0) REVERT: F 93 THR cc_start: 0.9443 (p) cc_final: 0.9202 (t) REVERT: C 45 GLU cc_start: 0.8907 (tp30) cc_final: 0.8069 (tm-30) REVERT: C 48 CYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6873 (t) REVERT: C 60 ASN cc_start: 0.8740 (t0) cc_final: 0.8312 (t0) REVERT: C 63 PHE cc_start: 0.8982 (m-80) cc_final: 0.8689 (m-80) REVERT: C 92 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7722 (mt-10) REVERT: D 38 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8605 (pp20) REVERT: D 48 CYS cc_start: 0.7741 (OUTLIER) cc_final: 0.6978 (t) REVERT: D 63 PHE cc_start: 0.8881 (m-80) cc_final: 0.8643 (m-80) REVERT: D 92 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7591 (mt-10) outliers start: 15 outliers final: 12 residues processed: 138 average time/residue: 0.0808 time to fit residues: 14.0454 Evaluate side-chains 133 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 85 TYR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.0010 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.060916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.048440 restraints weight = 18842.847| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 4.82 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.197 4716 Z= 0.165 Angle : 0.934 41.688 6424 Z= 0.466 Chirality : 0.042 0.172 698 Planarity : 0.004 0.027 818 Dihedral : 5.258 38.384 882 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.48 % Allowed : 22.54 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.36), residues: 540 helix: 0.20 (0.72), residues: 58 sheet: -1.76 (0.36), residues: 174 loop : -0.93 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 503 TYR 0.016 0.001 TYR B 436 PHE 0.021 0.002 PHE A 82 TRP 0.006 0.001 TRP F 78 HIS 0.002 0.001 HIS E 458 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 4685) covalent geometry : angle 0.65913 ( 6348) SS BOND : bond 0.02644 ( 17) SS BOND : angle 8.97525 ( 34) hydrogen bonds : bond 0.03027 ( 120) hydrogen bonds : angle 5.45889 ( 294) link_BETA1-4 : bond 0.00363 ( 8) link_BETA1-4 : angle 1.34161 ( 24) link_NAG-ASN : bond 0.00071 ( 6) link_NAG-ASN : angle 1.85343 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1202.76 seconds wall clock time: 21 minutes 29.78 seconds (1289.78 seconds total)