Starting phenix.real_space_refine on Wed Sep 17 04:08:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3v_38900/09_2025/8y3v_38900.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3v_38900/09_2025/8y3v_38900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y3v_38900/09_2025/8y3v_38900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3v_38900/09_2025/8y3v_38900.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y3v_38900/09_2025/8y3v_38900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3v_38900/09_2025/8y3v_38900.map" } resolution = 3.46 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= 0.013 sd= 0.166 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 12 5.16 5 C 2387 2.51 5 N 639 2.21 5 O 747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3785 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 951 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 939 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 121} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 939 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 121} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 956 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 1.33, per 1000 atoms: 0.35 Number of scatterers: 3785 At special positions: 0 Unit cell: (63.05, 94.09, 87.3, 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 12 16.00 O 747 8.00 N 639 7.00 C 2387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 173.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 954 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 5 sheets defined 19.5% alpha, 50.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 116 through 124 Processing helix chain 'B' and resid 97 through 112 removed outlier: 4.190A pdb=" N LEU B 112 " --> pdb=" O MET B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 125 Processing helix chain 'C' and resid 97 through 111 removed outlier: 3.524A pdb=" N CYS C 101 " --> pdb=" O THR C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 125 removed outlier: 3.532A pdb=" N ASN C 125 " --> pdb=" O ALA C 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 112 removed outlier: 3.603A pdb=" N CYS D 101 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 112 " --> pdb=" O MET D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10 removed outlier: 6.619A pdb=" N VAL A 18 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE A 33 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 26 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG A 56 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR A 91 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR A 58 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU A 89 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 60 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASN A 87 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 62 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR A 85 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A 64 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ARG A 83 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LYS A 66 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ARG A 83 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 89 " --> pdb=" O ASN B 87 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A 91 " --> pdb=" O TYR B 85 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N ARG B 83 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 70 " --> pdb=" O PRO B 78 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ALA B 80 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA B 68 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TRP B 82 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 92 " --> pdb=" O ARG B 56 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE B 33 " --> pdb=" O PRO B 22 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 18 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 7 through 10 removed outlier: 6.676A pdb=" N VAL C 18 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU C 31 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE C 25 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL C 64 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ARG C 83 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LYS C 66 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 7 through 10 removed outlier: 6.676A pdb=" N VAL C 18 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU C 31 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE C 25 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 7 through 10 removed outlier: 6.556A pdb=" N VAL D 18 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE D 33 " --> pdb=" O PRO D 22 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA D 26 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL D 64 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ARG D 83 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS D 66 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 7 through 10 removed outlier: 6.556A pdb=" N VAL D 18 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE D 33 " --> pdb=" O PRO D 22 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA D 26 " --> pdb=" O VAL D 29 " (cutoff:3.500A) 207 hydrogen bonds defined for protein. 558 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: 0.53 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1245 1.34 - 1.46: 546 1.46 - 1.57: 2040 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 3851 Sorted by residual: bond pdb=" CA THR A 69 " pdb=" C THR A 69 " ideal model delta sigma weight residual 1.523 1.541 -0.019 1.61e-02 3.86e+03 1.34e+00 bond pdb=" CG LEU B 111 " pdb=" CD1 LEU B 111 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CB THR C 59 " pdb=" CG2 THR C 59 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.02e+00 bond pdb=" CB VAL C 29 " pdb=" CG1 VAL C 29 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.33e-01 bond pdb=" CA THR C 69 " pdb=" CB THR C 69 " ideal model delta sigma weight residual 1.528 1.545 -0.018 1.82e-02 3.02e+03 9.29e-01 ... (remaining 3846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 4773 1.14 - 2.29: 390 2.29 - 3.43: 68 3.43 - 4.58: 19 4.58 - 5.72: 9 Bond angle restraints: 5259 Sorted by residual: angle pdb=" CA GLN C 40 " pdb=" CB GLN C 40 " pdb=" CG GLN C 40 " ideal model delta sigma weight residual 114.10 119.74 -5.64 2.00e+00 2.50e-01 7.96e+00 angle pdb=" OG1 THR C 69 " pdb=" CB THR C 69 " pdb=" CG2 THR C 69 " ideal model delta sigma weight residual 109.30 103.80 5.50 2.00e+00 2.50e-01 7.57e+00 angle pdb=" C CYS D 101 " pdb=" N GLU D 102 " pdb=" CA GLU D 102 " ideal model delta sigma weight residual 120.28 116.38 3.90 1.44e+00 4.82e-01 7.33e+00 angle pdb=" CA TRP A 32 " pdb=" CB TRP A 32 " pdb=" CG TRP A 32 " ideal model delta sigma weight residual 113.60 118.59 -4.99 1.90e+00 2.77e-01 6.91e+00 angle pdb=" N GLU D 102 " pdb=" CA GLU D 102 " pdb=" CB GLU D 102 " ideal model delta sigma weight residual 110.22 114.09 -3.87 1.54e+00 4.22e-01 6.31e+00 ... (remaining 5254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 2090 16.17 - 32.34: 176 32.34 - 48.51: 31 48.51 - 64.68: 6 64.68 - 80.85: 2 Dihedral angle restraints: 2305 sinusoidal: 828 harmonic: 1477 Sorted by residual: dihedral pdb=" CA SER C 51 " pdb=" C SER C 51 " pdb=" N SER C 52 " pdb=" CA SER C 52 " ideal model delta harmonic sigma weight residual 180.00 -155.21 -24.79 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA LEU A 77 " pdb=" C LEU A 77 " pdb=" N PRO A 78 " pdb=" CA PRO A 78 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA SER C 52 " pdb=" C SER C 52 " pdb=" N ALA C 53 " pdb=" CA ALA C 53 " ideal model delta harmonic sigma weight residual -180.00 -163.07 -16.93 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 2302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 302 0.028 - 0.057: 184 0.057 - 0.085: 81 0.085 - 0.114: 43 0.114 - 0.142: 23 Chirality restraints: 633 Sorted by residual: chirality pdb=" CB THR C 69 " pdb=" CA THR C 69 " pdb=" OG1 THR C 69 " pdb=" CG2 THR C 69 " both_signs ideal model delta sigma weight residual False 2.55 2.69 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA PHE B 95 " pdb=" N PHE B 95 " pdb=" C PHE B 95 " pdb=" CB PHE B 95 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE D 60 " pdb=" N ILE D 60 " pdb=" C ILE D 60 " pdb=" CB ILE D 60 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 630 not shown) Planarity restraints: 679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 69 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C THR C 69 " -0.042 2.00e-02 2.50e+03 pdb=" O THR C 69 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL C 70 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 77 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A 78 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 78 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 78 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 116 " -0.031 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO A 117 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " -0.026 5.00e-02 4.00e+02 ... (remaining 676 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1326 2.85 - 3.37: 3255 3.37 - 3.88: 5729 3.88 - 4.39: 6020 4.39 - 4.90: 11505 Nonbonded interactions: 27835 Sorted by model distance: nonbonded pdb=" OD1 ASP C 114 " pdb=" N GLY C 115 " model vdw 2.342 3.120 nonbonded pdb=" OD1 ASN C 24 " pdb=" N PHE C 25 " model vdw 2.362 3.120 nonbonded pdb=" OG SER B 52 " pdb=" N ALA B 53 " model vdw 2.379 3.120 nonbonded pdb=" O GLY D 110 " pdb=" ND2 ASN D 116 " model vdw 2.390 3.120 nonbonded pdb=" ND2 ASN A 12 " pdb=" O GLY A 16 " model vdw 2.422 3.120 ... (remaining 27830 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )) or resid 55 through 128)) selection = (chain 'B' and resid 2 through 128) selection = (chain 'C' and resid 2 through 128) selection = (chain 'D' and (resid 2 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )) or resid 55 through 128)) } 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: 1.090 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.820 Find NCS groups from input model: 0.080 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 0.036 3851 Z= 0.246 Angle : 0.731 5.723 5259 Z= 0.409 Chirality : 0.050 0.142 633 Planarity : 0.006 0.049 679 Dihedral : 12.738 80.852 1351 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.06 (0.37), residues: 505 helix: 0.31 (0.51), residues: 96 sheet: -1.27 (0.36), residues: 208 loop : -2.20 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.010 0.002 TYR D 58 PHE 0.028 0.003 PHE D 25 TRP 0.024 0.003 TRP A 32 Details of bonding type rmsd covalent geometry : bond 0.00593 ( 3851) covalent geometry : angle 0.73095 ( 5259) hydrogen bonds : bond 0.16192 ( 171) hydrogen bonds : angle 6.69336 ( 558) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.150 Fit side-chains REVERT: B 103 LEU cc_start: 0.8451 (tp) cc_final: 0.8224 (tp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0554 time to fit residues: 4.1101 Evaluate side-chains 52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 125 ASN C 109 GLN D 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.118458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.091535 restraints weight = 4859.444| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.74 r_work: 0.2926 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3851 Z= 0.159 Angle : 0.601 5.812 5259 Z= 0.323 Chirality : 0.048 0.135 633 Planarity : 0.005 0.042 679 Dihedral : 5.184 22.750 537 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.49 % Allowed : 9.47 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.53 (0.38), residues: 505 helix: 0.90 (0.50), residues: 100 sheet: -0.95 (0.37), residues: 200 loop : -1.98 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 49 TYR 0.010 0.001 TYR D 58 PHE 0.021 0.002 PHE D 25 TRP 0.020 0.002 TRP A 32 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 3851) covalent geometry : angle 0.60125 ( 5259) hydrogen bonds : bond 0.04173 ( 171) hydrogen bonds : angle 4.61498 ( 558) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.145 Fit side-chains REVERT: B 103 LEU cc_start: 0.8367 (tp) cc_final: 0.8140 (tp) outliers start: 2 outliers final: 0 residues processed: 51 average time/residue: 0.0503 time to fit residues: 3.5464 Evaluate side-chains 48 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN D 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.116320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.089861 restraints weight = 4822.717| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.66 r_work: 0.2846 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3851 Z= 0.240 Angle : 0.655 5.844 5259 Z= 0.349 Chirality : 0.049 0.136 633 Planarity : 0.005 0.040 679 Dihedral : 5.338 23.128 537 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 0.97 % Allowed : 14.56 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.38), residues: 505 helix: 1.09 (0.52), residues: 100 sheet: -0.88 (0.37), residues: 200 loop : -2.14 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 49 TYR 0.008 0.001 TYR D 42 PHE 0.022 0.002 PHE D 25 TRP 0.022 0.003 TRP A 32 Details of bonding type rmsd covalent geometry : bond 0.00600 ( 3851) covalent geometry : angle 0.65492 ( 5259) hydrogen bonds : bond 0.04671 ( 171) hydrogen bonds : angle 4.43283 ( 558) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.151 Fit side-chains REVERT: B 103 LEU cc_start: 0.8405 (tp) cc_final: 0.8166 (tp) REVERT: D 102 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7542 (mp0) outliers start: 4 outliers final: 2 residues processed: 55 average time/residue: 0.0483 time to fit residues: 3.6881 Evaluate side-chains 54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 125 ASN C 109 GLN D 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.118190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.091577 restraints weight = 4810.644| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.67 r_work: 0.2866 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3851 Z= 0.153 Angle : 0.588 5.718 5259 Z= 0.313 Chirality : 0.047 0.133 633 Planarity : 0.005 0.037 679 Dihedral : 5.092 21.969 537 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 1.70 % Allowed : 16.50 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.26 (0.38), residues: 505 helix: 1.42 (0.52), residues: 100 sheet: -0.69 (0.38), residues: 200 loop : -2.10 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 83 TYR 0.009 0.001 TYR A 58 PHE 0.014 0.002 PHE D 25 TRP 0.019 0.002 TRP A 32 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 3851) covalent geometry : angle 0.58831 ( 5259) hydrogen bonds : bond 0.03904 ( 171) hydrogen bonds : angle 4.18707 ( 558) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.154 Fit side-chains REVERT: B 103 LEU cc_start: 0.8312 (tp) cc_final: 0.8093 (tp) REVERT: D 102 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7508 (mp0) outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 0.0469 time to fit residues: 3.9210 Evaluate side-chains 56 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.090174 restraints weight = 4831.018| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.72 r_work: 0.2860 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3851 Z= 0.182 Angle : 0.603 5.744 5259 Z= 0.321 Chirality : 0.047 0.133 633 Planarity : 0.005 0.036 679 Dihedral : 5.084 22.014 537 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 2.18 % Allowed : 16.99 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.38), residues: 505 helix: 1.56 (0.52), residues: 100 sheet: -0.63 (0.38), residues: 200 loop : -2.10 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 83 TYR 0.008 0.001 TYR D 58 PHE 0.013 0.002 PHE D 25 TRP 0.020 0.002 TRP A 32 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 3851) covalent geometry : angle 0.60314 ( 5259) hydrogen bonds : bond 0.04041 ( 171) hydrogen bonds : angle 4.14280 ( 558) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: B 94 ILE cc_start: 0.8483 (mt) cc_final: 0.8208 (mt) REVERT: B 103 LEU cc_start: 0.8364 (tp) cc_final: 0.8122 (tp) outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 0.0438 time to fit residues: 3.6282 Evaluate side-chains 57 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 17 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.117584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.090462 restraints weight = 4873.443| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.74 r_work: 0.2922 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3851 Z= 0.156 Angle : 0.588 5.697 5259 Z= 0.311 Chirality : 0.047 0.132 633 Planarity : 0.004 0.034 679 Dihedral : 4.959 22.368 537 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.43 % Allowed : 17.48 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.05 (0.38), residues: 505 helix: 1.66 (0.51), residues: 100 sheet: -0.54 (0.37), residues: 207 loop : -2.09 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 83 TYR 0.009 0.001 TYR D 58 PHE 0.011 0.002 PHE D 25 TRP 0.019 0.002 TRP A 32 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 3851) covalent geometry : angle 0.58809 ( 5259) hydrogen bonds : bond 0.03797 ( 171) hydrogen bonds : angle 4.01111 ( 558) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: B 94 ILE cc_start: 0.8505 (mt) cc_final: 0.8233 (mt) REVERT: B 103 LEU cc_start: 0.8324 (tp) cc_final: 0.8104 (tp) outliers start: 10 outliers final: 7 residues processed: 62 average time/residue: 0.0460 time to fit residues: 4.0066 Evaluate side-chains 59 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 109 GLN D 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.115772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.088958 restraints weight = 4973.512| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.70 r_work: 0.2842 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3851 Z= 0.257 Angle : 0.668 5.821 5259 Z= 0.356 Chirality : 0.049 0.135 633 Planarity : 0.005 0.037 679 Dihedral : 5.352 26.698 537 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 2.18 % Allowed : 18.69 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.17 (0.38), residues: 505 helix: 1.55 (0.52), residues: 100 sheet: -0.63 (0.37), residues: 207 loop : -2.13 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 49 TYR 0.009 0.002 TYR B 58 PHE 0.011 0.002 PHE B 95 TRP 0.020 0.003 TRP A 32 Details of bonding type rmsd covalent geometry : bond 0.00641 ( 3851) covalent geometry : angle 0.66820 ( 5259) hydrogen bonds : bond 0.04603 ( 171) hydrogen bonds : angle 4.23478 ( 558) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: B 40 GLN cc_start: 0.9169 (tp-100) cc_final: 0.8800 (tp-100) REVERT: B 94 ILE cc_start: 0.8653 (mt) cc_final: 0.8402 (mt) REVERT: B 103 LEU cc_start: 0.8371 (tp) cc_final: 0.8155 (tp) outliers start: 9 outliers final: 8 residues processed: 61 average time/residue: 0.0466 time to fit residues: 4.0159 Evaluate side-chains 61 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.119075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.091879 restraints weight = 4816.105| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.74 r_work: 0.2929 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3851 Z= 0.114 Angle : 0.563 5.653 5259 Z= 0.298 Chirality : 0.047 0.131 633 Planarity : 0.004 0.034 679 Dihedral : 4.826 23.041 537 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.94 % Allowed : 18.93 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.87 (0.38), residues: 505 helix: 1.88 (0.51), residues: 100 sheet: -0.43 (0.37), residues: 206 loop : -2.03 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 83 TYR 0.010 0.001 TYR D 58 PHE 0.007 0.001 PHE A 4 TRP 0.020 0.002 TRP A 32 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3851) covalent geometry : angle 0.56350 ( 5259) hydrogen bonds : bond 0.03350 ( 171) hydrogen bonds : angle 3.89444 ( 558) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: B 40 GLN cc_start: 0.9038 (tp-100) cc_final: 0.8745 (tp-100) REVERT: B 94 ILE cc_start: 0.8680 (mt) cc_final: 0.8443 (mt) REVERT: B 103 LEU cc_start: 0.8318 (tp) cc_final: 0.8102 (tp) REVERT: B 113 LYS cc_start: 0.8629 (ttmt) cc_final: 0.7971 (tttm) outliers start: 8 outliers final: 7 residues processed: 68 average time/residue: 0.0497 time to fit residues: 4.6482 Evaluate side-chains 64 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN C 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.090121 restraints weight = 4824.883| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.72 r_work: 0.2880 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3851 Z= 0.176 Angle : 0.614 5.727 5259 Z= 0.325 Chirality : 0.048 0.170 633 Planarity : 0.004 0.034 679 Dihedral : 4.954 24.059 537 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 1.94 % Allowed : 19.90 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.38), residues: 505 helix: 1.97 (0.51), residues: 100 sheet: -0.40 (0.37), residues: 207 loop : -2.10 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 83 TYR 0.014 0.001 TYR A 58 PHE 0.008 0.002 PHE A 4 TRP 0.019 0.002 TRP A 32 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 3851) covalent geometry : angle 0.61393 ( 5259) hydrogen bonds : bond 0.03888 ( 171) hydrogen bonds : angle 3.93759 ( 558) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: B 40 GLN cc_start: 0.9067 (tp-100) cc_final: 0.8720 (tp-100) REVERT: B 94 ILE cc_start: 0.8684 (mt) cc_final: 0.8452 (mt) REVERT: B 103 LEU cc_start: 0.8396 (tp) cc_final: 0.8170 (tp) REVERT: B 113 LYS cc_start: 0.8669 (ttmt) cc_final: 0.8036 (tttm) outliers start: 8 outliers final: 8 residues processed: 60 average time/residue: 0.0441 time to fit residues: 3.7053 Evaluate side-chains 60 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 0.0870 chunk 33 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 8.9990 chunk 21 optimal weight: 0.0060 chunk 10 optimal weight: 0.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN C 109 GLN D 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.121974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.094632 restraints weight = 4828.813| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.77 r_work: 0.2931 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3851 Z= 0.095 Angle : 0.541 5.621 5259 Z= 0.284 Chirality : 0.047 0.146 633 Planarity : 0.004 0.034 679 Dihedral : 4.499 19.572 537 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.18 % Allowed : 19.66 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.38), residues: 505 helix: 2.19 (0.50), residues: 100 sheet: -0.13 (0.37), residues: 212 loop : -2.09 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 56 TYR 0.013 0.001 TYR A 58 PHE 0.006 0.001 PHE A 4 TRP 0.019 0.002 TRP D 32 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 3851) covalent geometry : angle 0.54131 ( 5259) hydrogen bonds : bond 0.02928 ( 171) hydrogen bonds : angle 3.70019 ( 558) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: B 40 GLN cc_start: 0.8990 (tp-100) cc_final: 0.8720 (tp-100) REVERT: B 94 ILE cc_start: 0.8617 (mt) cc_final: 0.8379 (mt) REVERT: B 113 LYS cc_start: 0.8553 (ttmt) cc_final: 0.7897 (tttm) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.0422 time to fit residues: 4.1284 Evaluate side-chains 63 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN C 109 GLN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.088845 restraints weight = 4870.781| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.72 r_work: 0.2882 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 3851 Z= 0.261 Angle : 0.680 5.768 5259 Z= 0.360 Chirality : 0.050 0.137 633 Planarity : 0.005 0.036 679 Dihedral : 5.159 25.601 537 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 1.46 % Allowed : 21.12 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.80 (0.38), residues: 505 helix: 2.04 (0.51), residues: 99 sheet: -0.37 (0.37), residues: 207 loop : -2.05 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 49 TYR 0.014 0.002 TYR A 58 PHE 0.011 0.002 PHE C 95 TRP 0.017 0.003 TRP A 32 Details of bonding type rmsd covalent geometry : bond 0.00656 ( 3851) covalent geometry : angle 0.68026 ( 5259) hydrogen bonds : bond 0.04518 ( 171) hydrogen bonds : angle 4.08898 ( 558) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 989.69 seconds wall clock time: 17 minutes 42.10 seconds (1062.10 seconds total)