Starting phenix.real_space_refine on Wed Mar 4 01:36:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2q_27146/03_2026/8d2q_27146.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2q_27146/03_2026/8d2q_27146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d2q_27146/03_2026/8d2q_27146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2q_27146/03_2026/8d2q_27146.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d2q_27146/03_2026/8d2q_27146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2q_27146/03_2026/8d2q_27146.map" } resolution = 2.58 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= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 121 5.49 5 Mg 5 5.21 5 S 17 5.16 5 C 5643 2.51 5 N 1817 2.21 5 O 2118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9721 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7143 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 51, 'TRANS': 849} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1835 Classifications: {'RNA': 86} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 39, 'rna3p_pyr': 36} Link IDs: {'rna2p': 11, 'rna3p': 74} Chain breaks: 2 Chain: "T" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 226 Classifications: {'DNA': 11} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 10} Chain: "X" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 243 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" 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: 2.38, per 1000 atoms: 0.24 Number of scatterers: 9721 At special positions: 0 Unit cell: (96.525, 109.725, 119.625, 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) S 17 16.00 P 121 15.00 Mg 5 11.99 O 2118 8.00 N 1817 7.00 C 5643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 578 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 610 " distance=2.04 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS A 578 " - pdb=" SG CYS A 610 " distance=2.03 Simple disulfide: pdb=" SG CYS A 610 " - pdb=" SG CYS A 613 " 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 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 400.8 milliseconds 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 8 sheets defined 43.6% alpha, 10.7% beta 44 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 59 through 92 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 120 through 138 Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 221 through 237 removed outlier: 3.574A pdb=" N VAL A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 486 through 508 Processing helix chain 'A' and resid 524 through 552 removed outlier: 3.848A pdb=" N ALA A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 572 Processing helix chain 'A' and resid 636 through 643 Processing helix chain 'A' and resid 653 through 669 removed outlier: 3.607A pdb=" N SER A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 703 Processing helix chain 'A' and resid 714 through 721 Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 748 through 758 Processing helix chain 'A' and resid 761 through 782 removed outlier: 4.417A pdb=" N PHE A 780 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TRP A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 807 Processing helix chain 'A' and resid 809 through 820 removed outlier: 3.707A pdb=" N ARG A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 861 Processing helix chain 'A' and resid 864 through 876 Processing helix chain 'A' and resid 957 through 963 Processing helix chain 'A' and resid 981 through 986 Processing helix chain 'A' and resid 988 through 997 Processing helix chain 'A' and resid 1024 through 1033 removed outlier: 3.992A pdb=" N TYR A1032 " --> pdb=" O MET A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1071 Processing helix chain 'A' and resid 1076 through 1086 Processing helix chain 'A' and resid 1094 through 1098 Processing sheet with id=AA1, first strand: chain 'A' and resid 706 through 711 removed outlier: 6.343A pdb=" N ILE A 513 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE A 710 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL A 515 " --> pdb=" O PHE A 710 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TRP A 13 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N VAL A 514 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 15 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N GLU A 516 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL A 17 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 24 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER A 44 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 26 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A 42 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA A 28 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 824 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 590 through 591 removed outlier: 3.726A pdb=" N ASP A 590 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 846 through 849 Processing sheet with id=AA4, first strand: chain 'A' and resid 854 through 855 Processing sheet with id=AA5, first strand: chain 'A' and resid 899 through 900 Processing sheet with id=AA6, first strand: chain 'A' and resid 921 through 924 Processing sheet with id=AA7, first strand: chain 'A' and resid 948 through 956 removed outlier: 3.641A pdb=" N GLY A1004 " --> pdb=" O VAL A 939 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG A 941 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLN A1002 " --> pdb=" O ARG A 941 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 6.527A pdb=" N ARG A1048 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N PHE A1043 " --> pdb=" O ARG A1048 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN A1050 " --> pdb=" O THR A1041 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU A1011 " --> pdb=" O ILE A1106 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 112 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.06 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: 2206 1.33 - 1.46: 2986 1.46 - 1.58: 4720 1.58 - 1.70: 240 1.70 - 1.82: 24 Bond restraints: 10176 Sorted by residual: bond pdb=" CG PRO A 487 " pdb=" CD PRO A 487 " ideal model delta sigma weight residual 1.503 1.315 0.188 3.40e-02 8.65e+02 3.05e+01 bond pdb=" C1' DT T 23 " pdb=" N1 DT T 23 " ideal model delta sigma weight residual 1.490 1.607 -0.117 3.00e-02 1.11e+03 1.53e+01 bond pdb=" CG PRO A 476 " pdb=" CD PRO A 476 " ideal model delta sigma weight residual 1.503 1.391 0.112 3.40e-02 8.65e+02 1.09e+01 bond pdb=" O3' A B 12 " pdb=" P A B 13 " ideal model delta sigma weight residual 1.607 1.656 -0.049 1.50e-02 4.44e+03 1.06e+01 bond pdb=" C3' DT T 22 " pdb=" O3' DT T 22 " ideal model delta sigma weight residual 1.422 1.518 -0.096 3.00e-02 1.11e+03 1.03e+01 ... (remaining 10171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 14060 2.87 - 5.75: 255 5.75 - 8.62: 38 8.62 - 11.50: 8 11.50 - 14.37: 5 Bond angle restraints: 14366 Sorted by residual: angle pdb=" CA PRO A 487 " pdb=" N PRO A 487 " pdb=" CD PRO A 487 " ideal model delta sigma weight residual 112.00 97.63 14.37 1.40e+00 5.10e-01 1.05e+02 angle pdb=" N PRO A 487 " pdb=" CD PRO A 487 " pdb=" CG PRO A 487 " ideal model delta sigma weight residual 103.20 89.19 14.01 1.50e+00 4.44e-01 8.73e+01 angle pdb=" C3' A B 12 " pdb=" O3' A B 12 " pdb=" P A B 13 " ideal model delta sigma weight residual 120.20 133.24 -13.04 1.50e+00 4.44e-01 7.56e+01 angle pdb=" C PRO A 675 " pdb=" N GLU A 676 " pdb=" CA GLU A 676 " ideal model delta sigma weight residual 121.70 134.99 -13.29 1.80e+00 3.09e-01 5.45e+01 angle pdb=" N GLU A1067 " pdb=" CA GLU A1067 " pdb=" CB GLU A1067 " ideal model delta sigma weight residual 110.12 120.81 -10.69 1.47e+00 4.63e-01 5.28e+01 ... (remaining 14361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.09: 5612 31.09 - 62.17: 457 62.17 - 93.26: 103 93.26 - 124.34: 3 124.34 - 155.43: 4 Dihedral angle restraints: 6179 sinusoidal: 3563 harmonic: 2616 Sorted by residual: dihedral pdb=" CB CYS A 575 " pdb=" SG CYS A 575 " pdb=" SG CYS A 610 " pdb=" CB CYS A 610 " ideal model delta sinusoidal sigma weight residual -86.00 -5.03 -80.97 1 1.00e+01 1.00e-02 8.09e+01 dihedral pdb=" CB CYS A 578 " pdb=" SG CYS A 578 " pdb=" SG CYS A 610 " pdb=" CB CYS A 610 " ideal model delta sinusoidal sigma weight residual -86.00 -166.52 80.52 1 1.00e+01 1.00e-02 8.02e+01 dihedral pdb=" CB CYS A 575 " pdb=" SG CYS A 575 " pdb=" SG CYS A 613 " pdb=" CB CYS A 613 " ideal model delta sinusoidal sigma weight residual -86.00 -162.59 76.59 1 1.00e+01 1.00e-02 7.37e+01 ... (remaining 6176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1450 0.076 - 0.151: 177 0.151 - 0.227: 19 0.227 - 0.303: 5 0.303 - 0.378: 2 Chirality restraints: 1653 Sorted by residual: chirality pdb=" CG LEU A 84 " pdb=" CB LEU A 84 " pdb=" CD1 LEU A 84 " pdb=" CD2 LEU A 84 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA GLU A1067 " pdb=" N GLU A1067 " pdb=" C GLU A1067 " pdb=" CB GLU A1067 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C1' A B 12 " pdb=" O4' A B 12 " pdb=" C2' A B 12 " pdb=" N9 A B 12 " both_signs ideal model delta sigma weight residual False 2.46 2.16 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 1650 not shown) Planarity restraints: 1420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 486 " 0.082 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO A 487 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT T 22 " 0.032 2.00e-02 2.50e+03 2.58e-02 1.66e+01 pdb=" N1 DT T 22 " -0.068 2.00e-02 2.50e+03 pdb=" C2 DT T 22 " 0.025 2.00e-02 2.50e+03 pdb=" O2 DT T 22 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DT T 22 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT T 22 " -0.001 2.00e-02 2.50e+03 pdb=" O4 DT T 22 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DT T 22 " -0.003 2.00e-02 2.50e+03 pdb=" C7 DT T 22 " 0.018 2.00e-02 2.50e+03 pdb=" C6 DT T 22 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1063 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.93e+00 pdb=" C VAL A1063 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL A1063 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A1064 " 0.018 2.00e-02 2.50e+03 ... (remaining 1417 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 281 2.67 - 3.23: 8105 3.23 - 3.79: 18047 3.79 - 4.34: 23052 4.34 - 4.90: 34466 Nonbonded interactions: 83951 Sorted by model distance: nonbonded pdb=" OD2 ASP A 18 " pdb="MG MG A1201 " model vdw 2.113 2.170 nonbonded pdb=" ND1 HIS A 750 " pdb="MG MG A1201 " model vdw 2.158 2.250 nonbonded pdb=" OP1 C B 52 " pdb="MG MG B 204 " model vdw 2.241 2.170 nonbonded pdb=" OG SER A 59 " pdb=" OP1 C B 17 " model vdw 2.246 3.040 nonbonded pdb=" OG1 THR A 684 " pdb=" OP1 DT T 23 " model vdw 2.256 3.040 ... (remaining 83946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.350 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:5.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.006 0.188 10181 Z= 0.272 Angle : 0.976 14.373 14376 Z= 0.526 Chirality : 0.052 0.378 1653 Planarity : 0.009 0.115 1420 Dihedral : 20.817 155.427 4468 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.68 (0.25), residues: 898 helix: -1.09 (0.23), residues: 397 sheet: -0.27 (0.54), residues: 85 loop : -1.19 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A1048 TYR 0.023 0.002 TYR A 698 PHE 0.047 0.003 PHE A 76 TRP 0.012 0.002 TRP A 942 HIS 0.007 0.002 HIS A 574 Details of bonding type rmsd covalent geometry : bond 0.00593 (10176) covalent geometry : angle 0.97432 (14366) SS BOND : bond 0.00400 ( 5) SS BOND : angle 2.36256 ( 10) hydrogen bonds : bond 0.08606 ( 432) hydrogen bonds : angle 5.78117 ( 1150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.292 Fit side-chains REVERT: A 487 PRO cc_start: 0.6995 (Cg_exo) cc_final: 0.6628 (Cg_endo) REVERT: A 804 LYS cc_start: 0.8030 (tttp) cc_final: 0.7803 (tppt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.8816 time to fit residues: 66.6139 Evaluate side-chains 57 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.0770 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS A 802 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.206896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.157603 restraints weight = 9573.874| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.64 r_work: 0.3431 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10181 Z= 0.142 Angle : 0.599 7.839 14376 Z= 0.313 Chirality : 0.038 0.300 1653 Planarity : 0.005 0.043 1420 Dihedral : 22.192 155.090 2766 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.54 % Allowed : 5.80 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: -0.36 (0.26), residues: 898 helix: 0.50 (0.26), residues: 395 sheet: -0.32 (0.53), residues: 84 loop : -0.87 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1048 TYR 0.010 0.001 TYR A 986 PHE 0.024 0.001 PHE A 76 TRP 0.007 0.001 TRP A 145 HIS 0.005 0.001 HIS A 749 Details of bonding type rmsd covalent geometry : bond 0.00300 (10176) covalent geometry : angle 0.59784 (14366) SS BOND : bond 0.00231 ( 5) SS BOND : angle 1.76460 ( 10) hydrogen bonds : bond 0.05658 ( 432) hydrogen bonds : angle 4.38378 ( 1150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.290 Fit side-chains REVERT: A 576 MET cc_start: 0.1917 (OUTLIER) cc_final: 0.1544 (mmt) REVERT: A 802 GLN cc_start: 0.7062 (tp40) cc_final: 0.6532 (tt0) REVERT: A 804 LYS cc_start: 0.8102 (tttp) cc_final: 0.7879 (tppt) REVERT: A 805 GLU cc_start: 0.7478 (tp30) cc_final: 0.6846 (tp30) outliers start: 4 outliers final: 0 residues processed: 67 average time/residue: 0.7273 time to fit residues: 51.6553 Evaluate side-chains 59 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 576 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 31 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 0.0010 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.203622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.154237 restraints weight = 9509.684| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.85 r_work: 0.3346 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10181 Z= 0.194 Angle : 0.636 8.174 14376 Z= 0.330 Chirality : 0.041 0.309 1653 Planarity : 0.005 0.042 1420 Dihedral : 22.181 161.846 2766 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.62 % Allowed : 6.87 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: 0.08 (0.27), residues: 898 helix: 1.01 (0.26), residues: 397 sheet: -0.38 (0.53), residues: 84 loop : -0.76 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1048 TYR 0.017 0.002 TYR A 187 PHE 0.028 0.002 PHE A 76 TRP 0.010 0.001 TRP A 145 HIS 0.005 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00414 (10176) covalent geometry : angle 0.63527 (14366) SS BOND : bond 0.00285 ( 5) SS BOND : angle 1.55050 ( 10) hydrogen bonds : bond 0.06248 ( 432) hydrogen bonds : angle 4.12837 ( 1150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8246 (mt0) cc_final: 0.7843 (mt0) REVERT: A 230 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.6305 (mpt90) REVERT: A 804 LYS cc_start: 0.8080 (tttp) cc_final: 0.7867 (tppt) REVERT: A 805 GLU cc_start: 0.7262 (tp30) cc_final: 0.6628 (tp30) outliers start: 12 outliers final: 5 residues processed: 66 average time/residue: 0.7546 time to fit residues: 52.6313 Evaluate side-chains 62 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 905 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS A 802 GLN A 946 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.204274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.157478 restraints weight = 9635.242| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.82 r_work: 0.3338 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10181 Z= 0.167 Angle : 0.591 7.732 14376 Z= 0.308 Chirality : 0.039 0.297 1653 Planarity : 0.005 0.040 1420 Dihedral : 22.128 163.408 2766 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.89 % Allowed : 8.49 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: 0.31 (0.27), residues: 898 helix: 1.20 (0.26), residues: 398 sheet: -0.27 (0.56), residues: 79 loop : -0.62 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1048 TYR 0.018 0.001 TYR A 698 PHE 0.027 0.002 PHE A 76 TRP 0.008 0.001 TRP A 145 HIS 0.004 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00355 (10176) covalent geometry : angle 0.58944 (14366) SS BOND : bond 0.00253 ( 5) SS BOND : angle 1.62294 ( 10) hydrogen bonds : bond 0.05718 ( 432) hydrogen bonds : angle 3.97327 ( 1150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8234 (mt0) cc_final: 0.7831 (mt0) REVERT: A 191 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.6733 (ttm170) REVERT: A 230 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.5917 (mpt90) REVERT: A 804 LYS cc_start: 0.8155 (tttp) cc_final: 0.7940 (tppt) REVERT: A 805 GLU cc_start: 0.7328 (tp30) cc_final: 0.6686 (tp30) REVERT: A 895 GLU cc_start: 0.6666 (mp0) cc_final: 0.6107 (pm20) outliers start: 14 outliers final: 6 residues processed: 70 average time/residue: 0.8101 time to fit residues: 59.9757 Evaluate side-chains 66 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 905 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 41 optimal weight: 0.0370 chunk 39 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS A 802 GLN A 946 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.204484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.155632 restraints weight = 9620.373| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.88 r_work: 0.3351 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10181 Z= 0.156 Angle : 0.575 7.079 14376 Z= 0.300 Chirality : 0.038 0.287 1653 Planarity : 0.005 0.044 1420 Dihedral : 22.028 164.382 2766 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.02 % Allowed : 9.97 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: 0.48 (0.27), residues: 898 helix: 1.37 (0.26), residues: 398 sheet: -0.30 (0.57), residues: 79 loop : -0.53 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 923 TYR 0.019 0.002 TYR A 698 PHE 0.027 0.002 PHE A 76 TRP 0.007 0.001 TRP A 161 HIS 0.004 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00330 (10176) covalent geometry : angle 0.57298 (14366) SS BOND : bond 0.00228 ( 5) SS BOND : angle 1.69316 ( 10) hydrogen bonds : bond 0.05605 ( 432) hydrogen bonds : angle 3.88233 ( 1150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8224 (mt0) cc_final: 0.7806 (mt0) REVERT: A 191 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6759 (ttm170) REVERT: A 804 LYS cc_start: 0.8110 (tttp) cc_final: 0.7896 (tppt) REVERT: A 805 GLU cc_start: 0.7217 (tp30) cc_final: 0.6599 (tp30) REVERT: A 895 GLU cc_start: 0.6578 (mp0) cc_final: 0.6050 (pm20) outliers start: 15 outliers final: 6 residues processed: 69 average time/residue: 0.7626 time to fit residues: 55.8487 Evaluate side-chains 64 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 905 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 79 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS A 802 GLN A 946 HIS A1060 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.201048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.153014 restraints weight = 9589.449| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.88 r_work: 0.3298 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 10181 Z= 0.296 Angle : 0.739 9.486 14376 Z= 0.377 Chirality : 0.046 0.324 1653 Planarity : 0.006 0.057 1420 Dihedral : 22.175 162.191 2766 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.16 % Allowed : 10.92 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: 0.09 (0.27), residues: 898 helix: 0.98 (0.26), residues: 398 sheet: -0.41 (0.58), residues: 79 loop : -0.70 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1048 TYR 0.024 0.002 TYR A 698 PHE 0.031 0.002 PHE A 76 TRP 0.015 0.002 TRP A 145 HIS 0.007 0.002 HIS A 936 Details of bonding type rmsd covalent geometry : bond 0.00641 (10176) covalent geometry : angle 0.73771 (14366) SS BOND : bond 0.00408 ( 5) SS BOND : angle 1.89390 ( 10) hydrogen bonds : bond 0.06954 ( 432) hydrogen bonds : angle 4.17005 ( 1150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8329 (mt0) cc_final: 0.7888 (mt0) REVERT: A 191 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6794 (ttm170) REVERT: A 230 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.5902 (mpt90) REVERT: A 804 LYS cc_start: 0.8165 (tttp) cc_final: 0.7936 (tppt) REVERT: A 805 GLU cc_start: 0.7274 (tp30) cc_final: 0.6642 (tp30) REVERT: A 895 GLU cc_start: 0.6709 (mp0) cc_final: 0.6111 (pm20) outliers start: 16 outliers final: 7 residues processed: 66 average time/residue: 0.8550 time to fit residues: 59.3883 Evaluate side-chains 63 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain A residue 905 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 93 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS A 802 GLN A 946 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.204501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.156658 restraints weight = 9570.802| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.89 r_work: 0.3356 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10181 Z= 0.147 Angle : 0.576 7.198 14376 Z= 0.302 Chirality : 0.038 0.286 1653 Planarity : 0.004 0.042 1420 Dihedral : 21.969 163.531 2766 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.48 % Allowed : 11.73 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: 0.47 (0.28), residues: 898 helix: 1.36 (0.26), residues: 398 sheet: -0.35 (0.60), residues: 79 loop : -0.53 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1048 TYR 0.016 0.001 TYR A 698 PHE 0.028 0.002 PHE A 76 TRP 0.008 0.001 TRP A 184 HIS 0.005 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00310 (10176) covalent geometry : angle 0.57404 (14366) SS BOND : bond 0.00208 ( 5) SS BOND : angle 1.73302 ( 10) hydrogen bonds : bond 0.05490 ( 432) hydrogen bonds : angle 3.87682 ( 1150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8212 (mt0) cc_final: 0.7807 (mt0) REVERT: A 230 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.5940 (mpt90) REVERT: A 804 LYS cc_start: 0.8138 (tttp) cc_final: 0.7926 (tppt) REVERT: A 805 GLU cc_start: 0.7237 (tp30) cc_final: 0.6614 (tp30) REVERT: A 882 LEU cc_start: 0.8267 (tp) cc_final: 0.7995 (tp) REVERT: A 895 GLU cc_start: 0.6537 (mp0) cc_final: 0.5934 (pm20) outliers start: 11 outliers final: 4 residues processed: 67 average time/residue: 0.8453 time to fit residues: 59.6405 Evaluate side-chains 60 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 849 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 4 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 77 optimal weight: 0.0870 chunk 40 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 overall best weight: 1.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS A 802 GLN A 946 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.202734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.154690 restraints weight = 9546.091| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.81 r_work: 0.3333 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10181 Z= 0.194 Angle : 0.622 7.619 14376 Z= 0.322 Chirality : 0.040 0.296 1653 Planarity : 0.005 0.043 1420 Dihedral : 21.942 162.945 2766 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.48 % Allowed : 11.99 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: 0.43 (0.28), residues: 898 helix: 1.35 (0.26), residues: 398 sheet: -0.39 (0.60), residues: 79 loop : -0.56 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1048 TYR 0.023 0.002 TYR A 698 PHE 0.030 0.002 PHE A 76 TRP 0.010 0.001 TRP A 145 HIS 0.005 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00415 (10176) covalent geometry : angle 0.62034 (14366) SS BOND : bond 0.00276 ( 5) SS BOND : angle 1.78586 ( 10) hydrogen bonds : bond 0.06022 ( 432) hydrogen bonds : angle 3.93709 ( 1150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8253 (mt0) cc_final: 0.7807 (mt0) REVERT: A 217 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: A 230 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.5898 (mpt90) REVERT: A 802 GLN cc_start: 0.6949 (tp40) cc_final: 0.6444 (tt0) REVERT: A 804 LYS cc_start: 0.8131 (tttp) cc_final: 0.7911 (tppt) REVERT: A 805 GLU cc_start: 0.7238 (tp30) cc_final: 0.6601 (tp30) REVERT: A 882 LEU cc_start: 0.8256 (tp) cc_final: 0.7959 (tp) REVERT: A 894 ASP cc_start: 0.6740 (t0) cc_final: 0.6378 (t0) REVERT: A 895 GLU cc_start: 0.6566 (mp0) cc_final: 0.6002 (pm20) outliers start: 11 outliers final: 5 residues processed: 61 average time/residue: 0.8831 time to fit residues: 56.7707 Evaluate side-chains 60 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 741 SER Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 905 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 41 optimal weight: 0.0970 chunk 37 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 69 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 75 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS A 946 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.206258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.159031 restraints weight = 9677.583| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.91 r_work: 0.3383 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10181 Z= 0.123 Angle : 0.545 6.673 14376 Z= 0.287 Chirality : 0.037 0.270 1653 Planarity : 0.004 0.042 1420 Dihedral : 21.830 164.590 2766 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.54 % Allowed : 13.34 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: 0.67 (0.28), residues: 898 helix: 1.58 (0.27), residues: 397 sheet: -0.26 (0.61), residues: 79 loop : -0.48 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1048 TYR 0.018 0.001 TYR A 698 PHE 0.025 0.001 PHE A 76 TRP 0.009 0.001 TRP A 161 HIS 0.005 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00259 (10176) covalent geometry : angle 0.54335 (14366) SS BOND : bond 0.00215 ( 5) SS BOND : angle 1.79489 ( 10) hydrogen bonds : bond 0.05162 ( 432) hydrogen bonds : angle 3.77300 ( 1150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8117 (mt0) cc_final: 0.7702 (mt0) REVERT: A 230 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.5867 (mpt90) REVERT: A 802 GLN cc_start: 0.6986 (tp40) cc_final: 0.6455 (tt0) REVERT: A 805 GLU cc_start: 0.7181 (tp30) cc_final: 0.6564 (tp30) REVERT: A 894 ASP cc_start: 0.6772 (t0) cc_final: 0.6447 (t0) REVERT: A 895 GLU cc_start: 0.6421 (mp0) cc_final: 0.5847 (pm20) outliers start: 4 outliers final: 1 residues processed: 61 average time/residue: 0.8659 time to fit residues: 55.7032 Evaluate side-chains 56 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 575 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 97 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS A 946 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.204251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.158046 restraints weight = 9469.871| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.91 r_work: 0.3333 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10181 Z= 0.153 Angle : 0.575 7.250 14376 Z= 0.299 Chirality : 0.038 0.279 1653 Planarity : 0.004 0.051 1420 Dihedral : 21.790 164.342 2766 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.54 % Allowed : 13.21 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: 0.67 (0.28), residues: 898 helix: 1.56 (0.27), residues: 398 sheet: -0.25 (0.61), residues: 79 loop : -0.46 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1048 TYR 0.020 0.002 TYR A 698 PHE 0.027 0.002 PHE A 76 TRP 0.008 0.001 TRP A 184 HIS 0.005 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00325 (10176) covalent geometry : angle 0.57308 (14366) SS BOND : bond 0.00235 ( 5) SS BOND : angle 1.81628 ( 10) hydrogen bonds : bond 0.05492 ( 432) hydrogen bonds : angle 3.79919 ( 1150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8213 (mt0) cc_final: 0.7794 (mt0) REVERT: A 217 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: A 230 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.5911 (mpt90) REVERT: A 805 GLU cc_start: 0.7228 (tp30) cc_final: 0.6601 (tp30) REVERT: A 894 ASP cc_start: 0.6777 (t0) cc_final: 0.6433 (t0) REVERT: A 895 GLU cc_start: 0.6534 (mp0) cc_final: 0.5847 (pm20) outliers start: 4 outliers final: 2 residues processed: 57 average time/residue: 0.8977 time to fit residues: 53.9693 Evaluate side-chains 57 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 905 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 30 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 25 optimal weight: 0.0770 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 56 optimal weight: 0.0050 chunk 63 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 HIS A 802 GLN A 946 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.206933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.161693 restraints weight = 9710.446| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.89 r_work: 0.3368 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10181 Z= 0.119 Angle : 0.536 7.098 14376 Z= 0.281 Chirality : 0.037 0.264 1653 Planarity : 0.004 0.046 1420 Dihedral : 21.701 165.630 2766 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.40 % Allowed : 13.75 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.35 % 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: 0.77 (0.28), residues: 898 helix: 1.68 (0.27), residues: 397 sheet: -0.14 (0.61), residues: 79 loop : -0.45 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1048 TYR 0.017 0.001 TYR A 698 PHE 0.023 0.001 PHE A 76 TRP 0.009 0.001 TRP A 161 HIS 0.006 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00251 (10176) covalent geometry : angle 0.53423 (14366) SS BOND : bond 0.00190 ( 5) SS BOND : angle 1.78569 ( 10) hydrogen bonds : bond 0.04955 ( 432) hydrogen bonds : angle 3.70218 ( 1150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3319.96 seconds wall clock time: 57 minutes 12.87 seconds (3432.87 seconds total)