Starting phenix.real_space_refine on Sat Apr 26 23:23:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3v_38900/04_2025/8y3v_38900.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3v_38900/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8y3v_38900/04_2025/8y3v_38900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3v_38900/04_2025/8y3v_38900.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3v_38900/04_2025/8y3v_38900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3v_38900/04_2025/8y3v_38900.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 1, 'ARG:plan': 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: {'GLN:plan1': 1, 'ARG:plan': 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: 3.22, per 1000 atoms: 0.85 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: 0.89 Conformation dependent library (CDL) restraints added in 470.5 milliseconds 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: 0.55 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: 0.97 Time building geometry restraints manager: 1.07 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: 1.290 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.380 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.960 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.024 0.003 TRP A 32 PHE 0.028 0.003 PHE D 25 TYR 0.010 0.002 TYR D 58 ARG 0.002 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.16192 ( 171) hydrogen bonds : angle 6.69336 ( 558) covalent geometry : bond 0.00593 ( 3851) covalent geometry : angle 0.73095 ( 5259) *********************** 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 : 0.388 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: 0.1239 time to fit residues: 9.0990 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 : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.0170 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.119713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.092880 restraints weight = 4769.147| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.72 r_work: 0.2937 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3851 Z= 0.127 Angle : 0.573 5.697 5259 Z= 0.307 Chirality : 0.047 0.134 633 Planarity : 0.005 0.042 679 Dihedral : 5.037 22.324 537 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.49 % Allowed : 8.74 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.38), residues: 505 helix: 0.95 (0.50), residues: 100 sheet: -0.93 (0.37), residues: 199 loop : -1.93 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 32 PHE 0.019 0.002 PHE D 25 TYR 0.010 0.001 TYR D 58 ARG 0.002 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 171) hydrogen bonds : angle 4.57461 ( 558) covalent geometry : bond 0.00305 ( 3851) covalent geometry : angle 0.57333 ( 5259) *********************** 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 56 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.388 Fit side-chains REVERT: B 103 LEU cc_start: 0.8336 (tp) cc_final: 0.8120 (tp) outliers start: 2 outliers final: 0 residues processed: 55 average time/residue: 0.1218 time to fit residues: 8.9390 Evaluate side-chains 49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3372 r_free = 0.3372 target = 0.117799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.090830 restraints weight = 4788.742| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.72 r_work: 0.2920 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3851 Z= 0.175 Angle : 0.595 5.736 5259 Z= 0.316 Chirality : 0.048 0.132 633 Planarity : 0.005 0.040 679 Dihedral : 5.027 22.400 537 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.97 % Allowed : 14.08 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.38), residues: 505 helix: 1.35 (0.51), residues: 100 sheet: -0.73 (0.38), residues: 200 loop : -2.02 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 32 PHE 0.018 0.002 PHE D 25 TYR 0.008 0.001 TYR A 58 ARG 0.001 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 171) hydrogen bonds : angle 4.24517 ( 558) covalent geometry : bond 0.00435 ( 3851) covalent geometry : angle 0.59487 ( 5259) *********************** 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 : 0.381 Fit side-chains REVERT: B 103 LEU cc_start: 0.8326 (tp) cc_final: 0.8085 (tp) REVERT: D 102 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7508 (mp0) outliers start: 4 outliers final: 1 residues processed: 55 average time/residue: 0.1116 time to fit residues: 8.4197 Evaluate side-chains 53 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 ASN 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 25 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 13 optimal weight: 0.0980 chunk 33 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 overall best weight: 2.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 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 = 0.3378 r_free = 0.3378 target = 0.118197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.091295 restraints weight = 4786.686| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.72 r_work: 0.2935 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1215 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= 0.151 Angle : 0.572 5.701 5259 Z= 0.304 Chirality : 0.047 0.131 633 Planarity : 0.005 0.036 679 Dihedral : 4.934 21.704 537 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.97 % Allowed : 16.02 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.38), residues: 505 helix: 1.57 (0.52), residues: 100 sheet: -0.58 (0.38), residues: 200 loop : -2.03 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 32 PHE 0.013 0.002 PHE D 25 TYR 0.009 0.001 TYR A 58 ARG 0.001 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 171) hydrogen bonds : angle 4.10096 ( 558) covalent geometry : bond 0.00376 ( 3851) covalent geometry : angle 0.57181 ( 5259) *********************** 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 58 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: B 103 LEU cc_start: 0.8345 (tp) cc_final: 0.8115 (tp) outliers start: 4 outliers final: 2 residues processed: 58 average time/residue: 0.1149 time to fit residues: 9.1344 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 : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.117590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.090452 restraints weight = 4914.877| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.75 r_work: 0.2900 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1276 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= 0.173 Angle : 0.592 5.721 5259 Z= 0.314 Chirality : 0.047 0.132 633 Planarity : 0.005 0.039 679 Dihedral : 4.952 21.634 537 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 1.70 % Allowed : 17.96 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.38), residues: 505 helix: 1.63 (0.51), residues: 100 sheet: -0.50 (0.38), residues: 200 loop : -2.06 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 32 PHE 0.014 0.002 PHE D 25 TYR 0.009 0.001 TYR D 58 ARG 0.001 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 171) hydrogen bonds : angle 4.04121 ( 558) covalent geometry : bond 0.00432 ( 3851) covalent geometry : angle 0.59174 ( 5259) *********************** 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: 7 poor density : 53 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: B 103 LEU cc_start: 0.8344 (tp) cc_final: 0.8105 (tp) outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 0.1097 time to fit residues: 9.1529 Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 47 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.117564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.090415 restraints weight = 4817.367| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.73 r_work: 0.2921 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3851 Z= 0.179 Angle : 0.601 5.731 5259 Z= 0.318 Chirality : 0.047 0.132 633 Planarity : 0.004 0.034 679 Dihedral : 4.959 21.184 537 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 1.94 % Allowed : 18.69 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.38), residues: 505 helix: 1.63 (0.51), residues: 100 sheet: -0.45 (0.37), residues: 207 loop : -2.05 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 32 PHE 0.012 0.002 PHE D 25 TYR 0.008 0.001 TYR D 58 ARG 0.001 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 171) hydrogen bonds : angle 4.01550 ( 558) covalent geometry : bond 0.00447 ( 3851) covalent geometry : angle 0.60121 ( 5259) *********************** 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 61 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: B 103 LEU cc_start: 0.8334 (tp) cc_final: 0.8111 (tp) outliers start: 8 outliers final: 6 residues processed: 61 average time/residue: 0.1000 time to fit residues: 8.3920 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 : 0.383 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.0470 chunk 32 optimal weight: 3.9990 overall best weight: 1.9484 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.118642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.091563 restraints weight = 4800.188| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.72 r_work: 0.2909 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3851 Z= 0.140 Angle : 0.569 5.676 5259 Z= 0.301 Chirality : 0.047 0.132 633 Planarity : 0.004 0.034 679 Dihedral : 4.789 20.551 537 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 1.46 % Allowed : 19.17 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.38), residues: 505 helix: 1.84 (0.51), residues: 100 sheet: -0.34 (0.37), residues: 207 loop : -2.00 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 32 PHE 0.009 0.001 PHE D 25 TYR 0.009 0.001 TYR D 58 ARG 0.001 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 171) hydrogen bonds : angle 3.88403 ( 558) covalent geometry : bond 0.00348 ( 3851) covalent geometry : angle 0.56939 ( 5259) *********************** 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 59 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: B 103 LEU cc_start: 0.8398 (tp) cc_final: 0.8173 (tp) REVERT: B 113 LYS cc_start: 0.8665 (ttmt) cc_final: 0.8031 (tttm) REVERT: D 108 MET cc_start: 0.8411 (mtm) cc_final: 0.8206 (mtm) outliers start: 6 outliers final: 6 residues processed: 59 average time/residue: 0.1026 time to fit residues: 8.3591 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 : 0.374 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.117466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.090415 restraints weight = 4835.314| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.72 r_work: 0.2859 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1482 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= 0.171 Angle : 0.597 5.736 5259 Z= 0.316 Chirality : 0.048 0.154 633 Planarity : 0.004 0.034 679 Dihedral : 4.910 21.935 537 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 1.46 % Allowed : 20.15 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.38), residues: 505 helix: 1.87 (0.51), residues: 100 sheet: -0.34 (0.37), residues: 207 loop : -2.07 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 32 PHE 0.010 0.002 PHE D 25 TYR 0.009 0.001 TYR D 58 ARG 0.001 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 171) hydrogen bonds : angle 3.92082 ( 558) covalent geometry : bond 0.00427 ( 3851) covalent geometry : angle 0.59715 ( 5259) *********************** 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 58 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: B 94 ILE cc_start: 0.8478 (mt) cc_final: 0.8188 (mt) REVERT: B 103 LEU cc_start: 0.8328 (tp) cc_final: 0.8104 (tp) REVERT: B 113 LYS cc_start: 0.8626 (ttmt) cc_final: 0.7974 (tttm) outliers start: 6 outliers final: 6 residues processed: 58 average time/residue: 0.1079 time to fit residues: 8.6498 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 : 0.423 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.118771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.091773 restraints weight = 4793.287| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.72 r_work: 0.2927 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3851 Z= 0.135 Angle : 0.570 5.674 5259 Z= 0.301 Chirality : 0.047 0.141 633 Planarity : 0.004 0.033 679 Dihedral : 4.749 20.774 537 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 1.70 % Allowed : 19.90 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.38), residues: 505 helix: 2.02 (0.50), residues: 100 sheet: -0.28 (0.37), residues: 207 loop : -2.03 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 32 PHE 0.008 0.001 PHE D 25 TYR 0.009 0.001 TYR D 58 ARG 0.001 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 171) hydrogen bonds : angle 3.81829 ( 558) covalent geometry : bond 0.00335 ( 3851) covalent geometry : angle 0.57011 ( 5259) *********************** 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 62 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: B 94 ILE cc_start: 0.8457 (mt) cc_final: 0.8155 (mt) REVERT: B 103 LEU cc_start: 0.8336 (tp) cc_final: 0.8116 (tp) REVERT: B 113 LYS cc_start: 0.8627 (ttmt) cc_final: 0.7988 (tttm) REVERT: D 108 MET cc_start: 0.8356 (mtm) cc_final: 0.8136 (mtm) outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 0.1092 time to fit residues: 9.2245 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 : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 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 47 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.121759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.094721 restraints weight = 4824.312| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.74 r_work: 0.2971 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3851 Z= 0.098 Angle : 0.546 5.777 5259 Z= 0.283 Chirality : 0.046 0.137 633 Planarity : 0.004 0.033 679 Dihedral : 4.444 19.072 537 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.46 % Allowed : 20.15 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.38), residues: 505 helix: 2.24 (0.50), residues: 100 sheet: -0.13 (0.37), residues: 213 loop : -2.10 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 32 PHE 0.006 0.001 PHE C 4 TYR 0.010 0.001 TYR D 58 ARG 0.001 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.03025 ( 171) hydrogen bonds : angle 3.66582 ( 558) covalent geometry : bond 0.00237 ( 3851) covalent geometry : angle 0.54564 ( 5259) ********************** 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 67 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: B 40 GLN cc_start: 0.9057 (tp-100) cc_final: 0.8854 (tp-100) REVERT: B 103 LEU cc_start: 0.8375 (tp) cc_final: 0.8170 (tp) REVERT: B 113 LYS cc_start: 0.8607 (ttmt) cc_final: 0.7948 (tttm) outliers start: 6 outliers final: 5 residues processed: 67 average time/residue: 0.1134 time to fit residues: 10.3905 Evaluate side-chains 61 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 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 36 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.118271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.091256 restraints weight = 4731.004| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.69 r_work: 0.2929 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1660 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= 0.173 Angle : 0.611 5.708 5259 Z= 0.320 Chirality : 0.048 0.131 633 Planarity : 0.005 0.034 679 Dihedral : 4.765 20.394 537 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 1.46 % Allowed : 20.87 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.38), residues: 505 helix: 2.21 (0.50), residues: 100 sheet: -0.20 (0.37), residues: 207 loop : -1.96 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 32 PHE 0.008 0.002 PHE D 25 TYR 0.015 0.001 TYR A 58 ARG 0.001 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 171) hydrogen bonds : angle 3.80944 ( 558) covalent geometry : bond 0.00433 ( 3851) covalent geometry : angle 0.61051 ( 5259) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2088.59 seconds wall clock time: 36 minutes 38.55 seconds (2198.55 seconds total)